From f46acbbc0b323be03a6e8d79b9fbe4e5c8b5378d Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 5 Dec 2022 10:36:15 -0300 Subject: [PATCH 01/36] update changelog --- jobbergate-api/CHANGELOG.rst | 1 + jobbergate-cli/CHANGELOG.rst | 1 + 2 files changed, 2 insertions(+) diff --git a/jobbergate-api/CHANGELOG.rst b/jobbergate-api/CHANGELOG.rst index e444c6768..c0aa733ce 100644 --- a/jobbergate-api/CHANGELOG.rst +++ b/jobbergate-api/CHANGELOG.rst @@ -6,6 +6,7 @@ This file keeps track of all notable changes to jobbergate-api Unreleased ---------- +* Move SBATCH params to Job Script submission 3.3.4 -- 2022-12-05 ------------------- diff --git a/jobbergate-cli/CHANGELOG.rst b/jobbergate-cli/CHANGELOG.rst index 9bcd2e8c3..64f44fa50 100644 --- a/jobbergate-cli/CHANGELOG.rst +++ b/jobbergate-cli/CHANGELOG.rst @@ -6,6 +6,7 @@ This file keeps track of all notable changes to jobbergate-cli Unreleased ---------- +* Move SBATCH params to Job Script submission 3.3.4 -- 2022-12-05 ------------------- From 86b91102e954b9e86c1f517345c650d00a813746 Mon Sep 17 00:00:00 2001 From: fschuch Date: Wed, 19 Oct 2022 18:10:35 -0300 Subject: [PATCH 02/36] ARMADA-692 add column execution_parameters to job submissions --- ...execution_parameters_to_job_submissions.py | 32 +++++++++++++++++++ .../apps/job_submissions/models.py | 2 ++ 2 files changed, 34 insertions(+) create mode 100644 jobbergate-api/alembic/versions/20221019_174015--81bf4eecc575_add_execution_parameters_to_job_submissions.py diff --git a/jobbergate-api/alembic/versions/20221019_174015--81bf4eecc575_add_execution_parameters_to_job_submissions.py b/jobbergate-api/alembic/versions/20221019_174015--81bf4eecc575_add_execution_parameters_to_job_submissions.py new file mode 100644 index 000000000..8bc0a5608 --- /dev/null +++ b/jobbergate-api/alembic/versions/20221019_174015--81bf4eecc575_add_execution_parameters_to_job_submissions.py @@ -0,0 +1,32 @@ +"""Add "execution parameters" to Job Submissions + +Revision ID: 81bf4eecc575 +Revises: d22da0741b7f +Create Date: 2022-10-19 17:40:15.929532 + +""" +import sqlalchemy as sa +from sqlalchemy.dialects import postgresql + +from alembic import op + +# revision identifiers, used by Alembic. +revision = "81bf4eecc575" +down_revision = "d22da0741b7f" +branch_labels = None +depends_on = None + + +def upgrade(): + # ### commands auto generated by Alembic - please adjust! ### + op.add_column( + "job_submissions", + sa.Column("execution_parameters", postgresql.JSONB(astext_type=sa.Text()), nullable=True), + ) + # ### end Alembic commands ### + + +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column("job_submissions", "execution_parameters") + # ### end Alembic commands ### diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/models.py b/jobbergate-api/jobbergate_api/apps/job_submissions/models.py index 82b871002..272961692 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/models.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/models.py @@ -2,6 +2,7 @@ Database model for the JobSubmission resource. """ from sqlalchemy import DateTime, Enum, ForeignKey, Integer, String, Table +from sqlalchemy.dialects.postgresql import JSONB from sqlalchemy.sql import func from sqlalchemy.sql.schema import Column @@ -23,6 +24,7 @@ Column("report_message", String, nullable=True), Column("created_at", DateTime, nullable=False, default=func.now()), Column("updated_at", DateTime, nullable=False, default=func.now(), onupdate=func.now()), + Column("execution_parameters", JSONB, nullable=True), ) searchable_fields = [ From f0bcfcddd3e64db175014ee16db9342956a8d719 Mon Sep 17 00:00:00 2001 From: fschuch Date: Wed, 19 Oct 2022 18:18:04 -0300 Subject: [PATCH 03/36] ARMADA-692 add schema for job properties --- .../apps/job_submissions/schemas.py | 83 ++++++++++++++++++- 1 file changed, 82 insertions(+), 1 deletion(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index 3e6cde8b8..7fb5d9a0c 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -3,7 +3,7 @@ """ from datetime import datetime from pathlib import Path -from typing import Optional +from typing import Any, Dict, List, Optional from pydantic import BaseModel, Extra, Field @@ -63,6 +63,86 @@ ) +class JobProperties(BaseModel, extra=Extra.ignore): + """ + Specialized model for job properties. + + See more details at: https://slurm.schedmd.com/rest_api.html#v0.0.38_job_properties + """ + + account: Optional[str] + account_gather_frequency: Optional[str] + argv: Optional[List[str]] + array: Optional[str] + batch_features: Optional[str] + begin_time: Optional[int] + burst_buffer: Optional[str] + cluster_constraints: Optional[str] + comment: Optional[str] + constrains: Optional[str] + containers: Optional[str] + core_specification: Optional[int] + cores_per_socket: Optional[int] + cpu_binding: Optional[str] + cpu_binding_hint: Optional[str] + cpu_frequency: Optional[str] + cpus_per_gpu: Optional[str] + cpus_per_task: Optional[int] + current_working_directory: Optional[str] + deadline: Optional[str] + delay_boot: Optional[int] + dependency: Optional[str] + distribution: Optional[str] + environment: Optional[Dict[Any, Any]] + exclusive: Optional[str] + get_user_environment: Optional[bool] + gress: Optional[str] + gress_flags: Optional[str] + gpu_binding: Optional[str] + gpu_frequency: Optional[str] + gpus: Optional[str] + gpus_per_node: Optional[str] + gpus_per_socket: Optional[str] + gpus_per_task: Optional[str] + hold: Optional[bool] + kill_on_invalid_dependency: Optional[bool] + licenses = Optional[str] + mail_type: Optional[str] + mail_user: Optional[str] + mcs_label: Optional[str] + memory_binding: Optional[int] + memory_per_gpu: Optional[int] + memory_per_node: Optional[int] + minimum_cpus_per_note: Optional[int] + minimum_nodes: Optional[bool] + name: Optional[str] + nice: Optional[str] + no_kill: Optional[bool] + nodes: Optional[List[int]] + open_mode: Optional[str] + partition: Optional[str] + priority: Optional[str] + qos: Optional[str] + requeue: Optional[bool] + reservation: Optional[str] + signal: Optional[str] + sockets_per_node: Optional[int] + spread_job: Optional[bool] + standard_error: Optional[str] + standard_input: Optional[str] + standard_output: Optional[str] + tasks: Optional[int] + tasks_per_core: Optional[int] + tasks_per_node: Optional[int] + tasks_per_socket: Optional[int] + thread_specification: Optional[int] + threads_per_core: Optional[int] + time_limit: Optional[int] + time_minimum: Optional[int] + wait_all_nodes: Optional[bool] + wckey: Optional[str] + + class JobSubmissionCreateRequest(BaseModel): """ Request model for creating JobSubmission instances. @@ -73,6 +153,7 @@ class JobSubmissionCreateRequest(BaseModel): job_script_id: int execution_directory: Optional[Path] client_id: Optional[str] + execution_parameters: Optional[JobProperties] class Config: schema_extra = job_submission_meta_mapper From 552739e6809e12c21b2e3bb83e2db701fb950bde Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 25 Nov 2022 18:29:12 -0300 Subject: [PATCH 04/36] update schema for JobProperties --- .../apps/job_submissions/schemas.py | 261 +++++++++++++----- 1 file changed, 187 insertions(+), 74 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index 7fb5d9a0c..3ff5cd6b3 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -3,7 +3,7 @@ """ from datetime import datetime from pathlib import Path -from typing import Any, Dict, List, Optional +from typing import Dict, List, Literal, Optional from pydantic import BaseModel, Extra, Field @@ -63,84 +63,197 @@ ) -class JobProperties(BaseModel, extra=Extra.ignore): +class JobProperties(BaseModel, extra=Extra.forbid): """ Specialized model for job properties. - See more details at: https://slurm.schedmd.com/rest_api.html#v0.0.38_job_properties + See more details at: https://slurm.schedmd.com/rest_api.html#v0.0.36_job_properties """ - account: Optional[str] - account_gather_frequency: Optional[str] - argv: Optional[List[str]] - array: Optional[str] - batch_features: Optional[str] - begin_time: Optional[int] - burst_buffer: Optional[str] - cluster_constraints: Optional[str] - comment: Optional[str] - constrains: Optional[str] - containers: Optional[str] - core_specification: Optional[int] - cores_per_socket: Optional[int] - cpu_binding: Optional[str] - cpu_binding_hint: Optional[str] - cpu_frequency: Optional[str] - cpus_per_gpu: Optional[str] - cpus_per_task: Optional[int] - current_working_directory: Optional[str] - deadline: Optional[str] - delay_boot: Optional[int] - dependency: Optional[str] - distribution: Optional[str] - environment: Optional[Dict[Any, Any]] - exclusive: Optional[str] - get_user_environment: Optional[bool] - gress: Optional[str] - gress_flags: Optional[str] - gpu_binding: Optional[str] - gpu_frequency: Optional[str] - gpus: Optional[str] - gpus_per_node: Optional[str] - gpus_per_socket: Optional[str] - gpus_per_task: Optional[str] - hold: Optional[bool] - kill_on_invalid_dependency: Optional[bool] - licenses = Optional[str] - mail_type: Optional[str] - mail_user: Optional[str] - mcs_label: Optional[str] - memory_binding: Optional[int] - memory_per_gpu: Optional[int] - memory_per_node: Optional[int] - minimum_cpus_per_note: Optional[int] - minimum_nodes: Optional[bool] - name: Optional[str] - nice: Optional[str] - no_kill: Optional[bool] - nodes: Optional[List[int]] - open_mode: Optional[str] - partition: Optional[str] - priority: Optional[str] - qos: Optional[str] - requeue: Optional[bool] - reservation: Optional[str] - signal: Optional[str] - sockets_per_node: Optional[int] - spread_job: Optional[bool] - standard_error: Optional[str] - standard_input: Optional[str] - standard_output: Optional[str] - tasks: Optional[int] - tasks_per_core: Optional[int] - tasks_per_node: Optional[int] - tasks_per_socket: Optional[int] - thread_specification: Optional[int] - threads_per_core: Optional[int] - time_limit: Optional[int] - time_minimum: Optional[int] - wait_all_nodes: Optional[bool] - wckey: Optional[str] + account: Optional[str] = Field( + description="Charge resources used by this job to specified account.", + ) + account_gather_freqency: Optional[str] = Field( + description="Define the job accounting and profiling sampling intervals.", + ) + argv: Optional[List[str]] = Field(description="Arguments to the script.") + array: Optional[str] = Field( + description=( + "Submit a job array, multiple jobs to be executed with identical parameters. " + "The indexes specification identifies what array index values should be used." + ) + ) + batch_features: Optional[str] = Field(description="features required for batch script's node") + begin_time: Optional[str] = Field( + description=( + "Submit the batch script to the Slurm controller immediately, like normal, " + "but tell the controller to defer the allocation of the job until the specified time." + ) + ) + burst_buffer: Optional[str] = Field(description="Burst buffer specification.") + cluster_constraints: Optional[str] = Field( + description="Specifies features that a federated cluster must have to have a sibling job submitted to it.", + ) + comment: Optional[str] = Field(description="An arbitrary comment.") + constraints: Optional[str] = Field(description="node features required by job.") + core_specification: Optional[int] = Field( + description=( + "Count of specialized threads per node reserved by the job for system " + "operations and not used by the application." + ) + ) + cores_per_socket: Optional[int] = Field( + description="Restrict node selection to nodes with at least the specified number of cores per socket.", + ) + cpu_binding: Optional[str] = Field(description="Cpu binding") + cpu_binding_hint: Optional[str] = Field(description="Cpu binding hint") + cpu_frequency: Optional[str] = Field( + description=( + "Request that job steps initiated by srun commands inside this sbatch " + "script be run at some requested frequency if possible, on the CPUs " + "selected for the step on the compute node(s)." + ), + ) + cpus_per_gpu: Optional[str] = Field(description="Number of CPUs requested per allocated GPU.") + cpus_per_task: Optional[int] = Field( + description=( + "Advise the Slurm controller that ensuing job steps will require ncpus number of processors per task." + ), + ) + current_working_directory: Optional[str] = Field( + description="Instruct Slurm to connect the batch script's standard output directly to the file name." + ) + deadline: Optional[str] = Field( + description="Remove the job if no ending is possible before this deadline (start > (deadline - time[-min]))." + ) + delay_boot: Optional[int] = Field( + description=( + "Do not reboot nodes in order to satisfied this job's feature specification if " + "the job has been eligible to run for less than this time period." + ) + ) + dependency: Optional[str] = Field( + description="Defer the start of this job until the specified dependencies have been satisfied completed." + ) + distribution: Optional[str] = Field( + description="Specify alternate distribution methods for remote processes." + ) + environment: Optional[Dict[str, str]] = Field(description="Dictionary of environment entries.") + exclusive: Optional[Literal["user", "mcs", "exclusive", "oversubscribe"]] = Field( + description=( + "The job allocation can share nodes just other users with the 'user' option or with the 'mcs' option)." + ) + ) + get_user_environment: Optional[bool] = Field( + description="Load new login environment for user on job node." + ) + gres: Optional[str] = Field( + description="Specifies a comma delimited list of generic consumable resources." + ) + gres_flags: Optional[Literal["disable-binding", "enforce-binding"]] = Field( + description="Specify generic resource task binding options." + ) + gpu_binding: Optional[str] = Field(description="Requested binding of tasks to GPU.") + gpu_frequency: Optional[str] = Field(description="Requested GPU frequency.") + gpus: Optional[str] = Field(description="GPUs per job.") + gpus_per_node: Optional[str] = Field(description="GPUs per node.") + gpus_per_socket: Optional[str] = Field(description="GPUs per socket.") + gpus_per_task: Optional[str] = Field(description="GPUs per task.") + hold: Optional[bool] = Field( + description="Specify the job is to be submitted in a held state (priority of zero)." + ) + kill_on_invalid_dependency: Optional[bool] = Field( + description="If a job has an invalid dependency, then Slurm is to terminate it." + ) + licenses: Optional[str] = Field( + description=( + "Specification of licenses (or other resources available on all nodes of the cluster) " + "which must be allocated to this job." + ) + ) + mail_type: Optional[str] = Field(description="Notify user by email when certain event types occur.") + mail_user: Optional[str] = Field( + description="User to receive email notification of state changes as defined by mail_type." + ) + mcs_label: Optional[str] = Field(description="This parameter is a group among the groups of the user.") + memory_binding: Optional[str] = Field(description="Bind tasks to memory.") + memory_per_cpu: Optional[int] = Field(description="Minimum real memory per cpu (MB).") + memory_per_gpu: Optional[int] = Field(description="Minimum memory required per allocated GPU.") + memory_per_node: Optional[int] = Field(description="Minimum real memory per node (MB).") + minimum_cpus_per_node: Optional[int] = Field(description="Minimum number of CPUs per node.") + minimum_nodes: Optional[bool] = Field( + description="If a range of node counts is given, prefer the smaller count." + ) + name: Optional[str] = Field(description="Specify a name for the job allocation.") + nice: Optional[str] = Field(description="Run the job with an adjusted scheduling priority within Slurm.") + no_kill: Optional[bool] = Field( + description="Do not automatically terminate a job if one of the nodes it has been allocated fails." + ) + nodes: Optional[List[int]] = Field( + description="Request that a minimum of nodes nodes and a maximum node count.", + min_items=1, + max_items=2, + ) + open_mode: Optional[Literal["append", "truncate"]] = Field( + description="Open the output and error files using append or truncate mode as specified." + ) + partition: Optional[str] = Field(description="Request a specific partition for the resource allocation.") + priority: Optional[str] = Field(description="Request a specific job priority.") + qos: Optional[str] = Field(description="Request a quality of service for the job.") + requeue: Optional[bool] = Field( + description="Specifies that the batch job should eligible to being requeue." + ) + reservation: Optional[str] = Field( + description="Allocate resources for the job from the named reservation." + ) + signal: Optional[str] = Field( + description="When a job is within sig_time seconds of its end time, send it the signal sig_num.", + # regex=r"[B:][@]", + ) + sockets_per_node: Optional[int] = Field( + description="Restrict node selection to nodes with at least the specified number of sockets." + ) + spread_job: Optional[bool] = Field( + description=( + "Spread the job allocation over as many nodes as possible and attempt " + "to evenly distribute tasks across the allocated nodes." + ) + ) + standard_error: Optional[str] = Field( + description="Instruct Slurm to connect the batch script's standard error directly to the file name." + ) + standard_in: Optional[str] = Field( + description="Instruct Slurm to connect the batch script's standard input directly to the file name specified." + ) + standard_out: Optional[str] = Field( + description="Instruct Slurm to connect the batch script's standard output directly to the file name." + ) + tasks: Optional[int] = Field( + description=( + "Advises the Slurm controller that job steps run within the allocation " + "will launch a maximum of number tasks and to provide for sufficient resources." + ) + ) + tasks_per_core: Optional[int] = Field(description="Request the maximum ntasks be invoked on each core.") + tasks_per_node: Optional[int] = Field(description="Request the maximum ntasks be invoked on each node.") + tasks_per_socket: Optional[int] = Field( + description="Request the maximum ntasks be invoked on each socket." + ) + thread_specification: Optional[int] = Field( + description=( + "Count of specialized threads per node reserved by the job for system " + "operations and not used by the application." + ) + ) + threads_per_core: Optional[int] = Field( + description="Restrict node selection to nodes with at least the specified number of threads per core." + ) + time_limit: Optional[int] = Field(description="Step time limit.") + time_minimum: Optional[int] = Field(description="Minimum run time in minutes.") + wait_all_nodes: Optional[bool] = Field( + description="Do not begin execution until all nodes are ready for use." + ) + wckey: Optional[str] = Field(description="Specify wckey to be used with job.") class JobSubmissionCreateRequest(BaseModel): From f5d2ba20f0b4ff2205206dfe85cc205ae0684a50 Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 28 Nov 2022 16:08:55 -0300 Subject: [PATCH 05/36] add execution_parameters to job submission schemas --- jobbergate-api/jobbergate_api/apps/job_submissions/routers.py | 2 ++ jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py | 2 ++ 2 files changed, 4 insertions(+) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py index a95a3c4db..b03b79176 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py @@ -300,6 +300,8 @@ async def job_submissions_agent_pending( job_submissions_table.c.id, job_submissions_table.c.job_submission_name, job_submissions_table.c.job_submission_owner_email, + job_submissions_table.c.execution_directory, + job_submissions_table.c.execution_parameters, job_submissions_table.c.job_script_id, job_scripts_table.c.job_script_name, applications_table.c.application_name, diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index 3ff5cd6b3..9f0e40dd8 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -303,6 +303,7 @@ class JobSubmissionResponse(BaseModel): client_id: Optional[str] status: JobSubmissionStatus report_message: Optional[str] + execution_parameters: Optional[JobProperties] class Config: orm_mode = True @@ -320,6 +321,7 @@ class PendingJobSubmission(BaseModel, extra=Extra.ignore): job_submission_name: str job_submission_owner_email: str execution_directory: Optional[Path] + execution_parameters: Optional[JobProperties] job_script_name: str application_name: str job_script_files: JobScriptFiles From 61f1bd38331a5dc295265557b74a544f888c135b Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 28 Nov 2022 16:34:20 -0300 Subject: [PATCH 06/36] fix code quality, limit line length --- .../apps/job_submissions/schemas.py | 26 ++++++++++++++----- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index 9f0e40dd8..f18b7774e 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -92,7 +92,9 @@ class JobProperties(BaseModel, extra=Extra.forbid): ) burst_buffer: Optional[str] = Field(description="Burst buffer specification.") cluster_constraints: Optional[str] = Field( - description="Specifies features that a federated cluster must have to have a sibling job submitted to it.", + description=( + "Specifies features that a federated cluster must have to have a sibling job submitted to it." + ) ) comment: Optional[str] = Field(description="An arbitrary comment.") constraints: Optional[str] = Field(description="node features required by job.") @@ -103,7 +105,9 @@ class JobProperties(BaseModel, extra=Extra.forbid): ) ) cores_per_socket: Optional[int] = Field( - description="Restrict node selection to nodes with at least the specified number of cores per socket.", + description=( + "Restrict node selection to nodes with at least the specified number of cores per socket." + ) ) cpu_binding: Optional[str] = Field(description="Cpu binding") cpu_binding_hint: Optional[str] = Field(description="Cpu binding hint") @@ -117,14 +121,17 @@ class JobProperties(BaseModel, extra=Extra.forbid): cpus_per_gpu: Optional[str] = Field(description="Number of CPUs requested per allocated GPU.") cpus_per_task: Optional[int] = Field( description=( - "Advise the Slurm controller that ensuing job steps will require ncpus number of processors per task." + "Advise the Slurm controller that ensuing job steps will require " + "ncpus number of processors per task." ), ) current_working_directory: Optional[str] = Field( description="Instruct Slurm to connect the batch script's standard output directly to the file name." ) deadline: Optional[str] = Field( - description="Remove the job if no ending is possible before this deadline (start > (deadline - time[-min]))." + description=( + "Remove the job if no ending is possible before this deadline (start > (deadline - time[-min]))." + ) ) delay_boot: Optional[int] = Field( description=( @@ -133,7 +140,9 @@ class JobProperties(BaseModel, extra=Extra.forbid): ) ) dependency: Optional[str] = Field( - description="Defer the start of this job until the specified dependencies have been satisfied completed." + description=( + "Defer the start of this job until the specified dependencies have been satisfied completed." + ) ) distribution: Optional[str] = Field( description="Specify alternate distribution methods for remote processes." @@ -141,7 +150,8 @@ class JobProperties(BaseModel, extra=Extra.forbid): environment: Optional[Dict[str, str]] = Field(description="Dictionary of environment entries.") exclusive: Optional[Literal["user", "mcs", "exclusive", "oversubscribe"]] = Field( description=( - "The job allocation can share nodes just other users with the 'user' option or with the 'mcs' option)." + "The job allocation can share nodes just other users with the " + "'user' option or with the 'mcs' option)." ) ) get_user_environment: Optional[bool] = Field( @@ -223,7 +233,9 @@ class JobProperties(BaseModel, extra=Extra.forbid): description="Instruct Slurm to connect the batch script's standard error directly to the file name." ) standard_in: Optional[str] = Field( - description="Instruct Slurm to connect the batch script's standard input directly to the file name specified." + description=( + "Instruct Slurm to connect the batch script's standard input directly to the file name specified." + ) ) standard_out: Optional[str] = Field( description="Instruct Slurm to connect the batch script's standard output directly to the file name." From 8afaa0f441f318ad62226511f719d4b040320c24 Mon Sep 17 00:00:00 2001 From: fschuch Date: Tue, 29 Nov 2022 11:48:21 -0300 Subject: [PATCH 07/36] add execution_parameters to tests --- .../apps/job_submissions/routers.py | 2 +- .../tests/apps/job_submissions/test_routers.py | 18 ++++++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py index b03b79176..83df5e6c6 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py @@ -104,7 +104,7 @@ async def job_submission_create( logger.debug(f"Job-submission created: {job_submission_data=}") - return job_submission_data + return JobSubmissionResponse(**job_submission_data) @router.get( diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py index f4a550993..689236a4f 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py @@ -51,6 +51,7 @@ async def test_create_job_submission__with_client_id_in_token( job_script_id=inserted_job_script_id, job_submission_name="sub1", job_submission_owner_email="owner1@org.com", + execution_parameters={"name": "job-submission-name", "comment": "I am a comment"}, ) # Removed defaults to make sure these are correctly set by other mechanisms @@ -80,6 +81,10 @@ async def test_create_job_submission__with_client_id_in_token( assert job_submission.created_at in window assert job_submission.updated_at in window + assert job_submission.execution_parameters is not None + assert job_submission.execution_parameters.name == "job-submission-name" + assert job_submission.execution_parameters.comment == "I am a comment" + @pytest.mark.asyncio async def test_create_job_submission__with_client_id_in_request_body( @@ -120,6 +125,10 @@ async def test_create_job_submission__with_client_id_in_request_body( job_submission_name="sub1", job_submission_owner_email="owner1@org.com", client_id="silly-cluster-client", + execution_parameters={ + "name": "job-submission-name", + "comment": "I am a comment", + }, ), ) @@ -142,6 +151,10 @@ async def test_create_job_submission__with_client_id_in_request_body( assert job_submission.created_at in window assert job_submission.updated_at in window + assert job_submission.execution_parameters is not None + assert job_submission.execution_parameters.name == "job-submission-name" + assert job_submission.execution_parameters.comment == "I am a comment" + @pytest.mark.asyncio async def test_create_job_submission__with_execution_directory( @@ -179,6 +192,7 @@ async def test_create_job_submission__with_execution_directory( job_submission_name="sub1", job_submission_owner_email="owner1@org.com", execution_directory="/some/fake/path", + execution_parameters={"name": "job-submission-name", "comment": "I am a comment"}, ) # Removed defaults to make sure these are correctly set by other mechanisms @@ -208,6 +222,10 @@ async def test_create_job_submission__with_execution_directory( assert job_submission.created_at in window assert job_submission.updated_at in window + assert job_submission.execution_parameters is not None + assert job_submission.execution_parameters.name == "job-submission-name" + assert job_submission.execution_parameters.comment == "I am a comment" + @pytest.mark.asyncio async def test_create_job_submission_without_job_script( From 70a5f6567e180b2ba1aefecb7e7ae492cb6b1c7c Mon Sep 17 00:00:00 2001 From: fschuch Date: Tue, 29 Nov 2022 11:48:56 -0300 Subject: [PATCH 08/36] add description to execution_parameters --- .../jobbergate_api/apps/job_submissions/schemas.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index f18b7774e..7a6f1978b 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -40,7 +40,7 @@ description="The foreign-key to the job_script from which this instance was created", example=71, ), - execution_duirectory=MetaField( + execution_directory=MetaField( description="The directory on the cluster where the job should be executed", example="/home/someuser/job-data/test-77", ), @@ -60,6 +60,10 @@ description="The report message received from cluster-agent when a job submission is rejected", example="Unrecognized SBATCH arguments", ), + execution_parameters=MetaField( + description="The parameters to be passed to the job submission", + example={"name": "job-submission-name", "comment": "I am a comment"}, + ), ) From 5d7deba598de52768f0d3947b966281d67b211ee Mon Sep 17 00:00:00 2001 From: fschuch Date: Tue, 29 Nov 2022 14:24:52 -0300 Subject: [PATCH 09/36] fix mypy --- jobbergate-api/jobbergate_api/apps/job_submissions/routers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py index 83df5e6c6..ccd76b4c1 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py @@ -104,7 +104,7 @@ async def job_submission_create( logger.debug(f"Job-submission created: {job_submission_data=}") - return JobSubmissionResponse(**job_submission_data) + return JobSubmissionResponse(**job_submission_data) # type: ignore @router.get( From 12b9b7cff1505ae5dd22eda0d5e95f74c2edee95 Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 5 Dec 2022 15:37:44 -0300 Subject: [PATCH 10/36] add doc url for execution_parameters metadata --- .../jobbergate_api/apps/job_submissions/schemas.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index 7a6f1978b..3d4d0d1be 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -61,7 +61,10 @@ example="Unrecognized SBATCH arguments", ), execution_parameters=MetaField( - description="The parameters to be passed to the job submission", + description=( + "The parameters to be passed to the job submission. " + "See more details at: https://slurm.schedmd.com/rest_api.html#v0.0.36_job_properties" + ), example={"name": "job-submission-name", "comment": "I am a comment"}, ), ) From a074b72fe14fc4fcccdebdb1c5712eb1d296c15f Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 5 Dec 2022 15:41:21 -0300 Subject: [PATCH 11/36] code review on class JobProperties --- jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py | 1 - 1 file changed, 1 deletion(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index 3d4d0d1be..32170279a 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -225,7 +225,6 @@ class JobProperties(BaseModel, extra=Extra.forbid): ) signal: Optional[str] = Field( description="When a job is within sig_time seconds of its end time, send it the signal sig_num.", - # regex=r"[B:][@]", ) sockets_per_node: Optional[int] = Field( description="Restrict node selection to nodes with at least the specified number of sockets." From df7c9b044e8c047ed2b7b189f88aa69225a8a8c5 Mon Sep 17 00:00:00 2001 From: fschuch Date: Thu, 1 Dec 2022 20:39:38 -0300 Subject: [PATCH 12/36] add SBATCH parameters parser --- .../apps/job_submissions/properties_parser.py | 305 ++++++++++ .../job_submissions/test_properties_parser.py | 550 ++++++++++++++++++ jobbergate-api/poetry.lock | 201 ++++--- jobbergate-api/pyproject.toml | 3 +- 4 files changed, 977 insertions(+), 82 deletions(-) create mode 100644 jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py create mode 100644 jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py new file mode 100644 index 000000000..e89840dda --- /dev/null +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py @@ -0,0 +1,305 @@ +from argparse import ArgumentParser +from dataclasses import dataclass, field +from itertools import chain +from typing import Any, Dict, Iterator, List, Union + +from bidict import bidict +from loguru import logger + +_IDENTIFICATION_FLAG = "#SBATCH" +_INLINE_COMMENT_MARK = "#" + + +def _flagged_line(line: str) -> bool: + """ + Identify if a provided line starts with the identification flag. + """ + return line.startswith(_IDENTIFICATION_FLAG) + + +def _clean_line(line: str) -> str: + """ + Clean the provided line by removing the + identification flag at the beginning of the line, + then remove the inline comment mark and anything + after it, and finally strip white spaces at both sides. + """ + return line.lstrip(_IDENTIFICATION_FLAG).split(_INLINE_COMMENT_MARK)[0].strip() + + +def _split_line(line: str) -> List[str]: + """ + Split the provided line at the `=` character if it is found at the line, + otherwise split at the white spaces. This procedure is important because + it is the way argparse expects to receive the parameters. + """ + return line.replace("=", " ").split() + + +def _clean_jobscript(jobscript: str) -> Iterator[str]: + """ + Transform a job script string by filtering only the lines that start with + the identification flag and mapping a cleaning procedure to them in order + to remove the identification flag, remove inline comments, and strip extra + white spaces. Finally, split each pair of parameter/value and chain them + in a single iterator. + """ + jobscript_filtered = filter(_flagged_line, jobscript.splitlines()) + jobscript_cleaned = map(_clean_line, jobscript_filtered) + jobscript_splitted = map(_split_line, jobscript_cleaned) + return chain.from_iterable(jobscript_splitted) + + +@dataclass(frozen=True) +class SbatchToSlurm: + """ + Store the information for each parameter, including its name at Slurm API + and SBATCH, besides any extra argument this parameter needs when added to + the parser. This information is used to build the jobscript/SBATCH parser + and the two-way mapping between Slurm API and SBATCH names. + """ + + slurmrestd_var_name: str + sbatch: str + sbatch_short: str = "" + argparser_param: dict = field(default_factory=dict) + + +sbatch_to_slurm = [ + SbatchToSlurm("account", "--account", "-A"), + SbatchToSlurm("account_gather_freqency", "--acctg-freq"), + SbatchToSlurm("array", "--array", "-a"), + SbatchToSlurm("batch_features", "--batch"), + SbatchToSlurm("burst_buffer", "--bb"), + SbatchToSlurm("", "--bbf"), + SbatchToSlurm("begin_time", "--begin", "-b"), + SbatchToSlurm("current_working_directory", "--chdir", "-D"), + SbatchToSlurm("cluster_constraints", "--cluster-constraint"), + SbatchToSlurm("", "--clusters", "-M"), + SbatchToSlurm("comment", "--comment"), + SbatchToSlurm("constraints", "--constraint", "-C"), + SbatchToSlurm("", "--container"), + SbatchToSlurm("", "--contiguous", "", dict(action="store_const", const=True)), + SbatchToSlurm("core_specification", "--core-spec", "-S", dict(type=int)), + SbatchToSlurm("cores_per_socket", "--cores-per-socket", "", dict(type=int)), + SbatchToSlurm("cpu_binding", "--cpu-bind"), + SbatchToSlurm("cpu_frequency", "--cpu-freq"), + SbatchToSlurm("cpus_per_gpu", "--cpus-per-gpu"), + SbatchToSlurm("cpus_per_task", "--cpus-per-task", "-c", dict(type=int)), + SbatchToSlurm("deadline", "--deadline"), + SbatchToSlurm("delay_boot", "--delay-boot", "", dict(type=int)), + SbatchToSlurm("dependency", "--dependency", "-d"), + SbatchToSlurm("distribution", "--distribution", "-m"), + SbatchToSlurm("standard_error", "--error", "-e"), + SbatchToSlurm("", "--exclude", "-x"), + SbatchToSlurm( + "exclusive", + "--exclusive", + "", + dict( + type=str, + choices={"user", "mcs", "exclusive", "oversubscribe"}, + nargs="?", + const="exclusive", + ), + ), + SbatchToSlurm("", "--export"), + SbatchToSlurm("", "--export-file"), + SbatchToSlurm("", "--extra-node-info", "-B"), + SbatchToSlurm("get_user_environment", "--get-user-env", "", dict(type=int)), + SbatchToSlurm("", "--gid"), + SbatchToSlurm("gpu_binding", "--gpu-bind"), + SbatchToSlurm("gpu_frequency", "--gpu-freq"), + SbatchToSlurm("gpus", "--gpus", "-G"), + SbatchToSlurm("gpus_per_node", "--gpus-per-node"), + SbatchToSlurm("gpus_per_socket", "--gpus-per-socket"), + SbatchToSlurm("gpus_per_task", "--gpus-per-task"), + SbatchToSlurm("gres", "--gres"), + SbatchToSlurm("gres_flags", "--gres-flags"), + SbatchToSlurm("", "--hint"), + SbatchToSlurm("hold", "--hold", "-H", dict(action="store_const", const=True)), + SbatchToSlurm("", "--ignore-pbs", "", dict(action="store_const", const=True)), + SbatchToSlurm("standard_input", "--input", "-i"), + SbatchToSlurm("name", "--job-name", "-J"), + # kill_on_invalid_dependency is an invalid key for Slurm API according to our tests + # SbatchToSlurm( + # "kill_on_invalid_dependency", "--kill-on-invalid-dep", "", dict(type=int) + # ), + SbatchToSlurm("licenses", "--licenses", "-L"), + SbatchToSlurm("mail_type", "--mail-type"), + SbatchToSlurm("mail_user", "--mail-user"), + SbatchToSlurm("mcs_label", "--mcs-label"), + SbatchToSlurm("memory_per_node", "--mem"), + SbatchToSlurm("memory_binding", "--mem-bind"), + SbatchToSlurm("memory_per_cpu", "--mem-per-cpu"), + SbatchToSlurm("memory_per_gpu", "--mem-per-gpu"), + SbatchToSlurm("minimum_cpus_per_node", "--mincpus", "", dict(type=int)), + SbatchToSlurm("", "--network"), + SbatchToSlurm("nice", "--nice"), + SbatchToSlurm("no_kill", "--no-kill", "-k", dict(action="store_const", const=True)), + SbatchToSlurm("", "--no-requeue", "", dict(action="store_false", dest="requeue")), + SbatchToSlurm("", "--nodefile", "-F"), + SbatchToSlurm("", "--nodelist", "-w"), + SbatchToSlurm("nodes", "--nodes", "-N"), + SbatchToSlurm("tasks", "--ntasks", "-n", dict(type=int)), + SbatchToSlurm("tasks_per_core", "--ntasks-per-core", "", dict(type=int)), + SbatchToSlurm("", "--ntasks-per-gpu"), + SbatchToSlurm("tasks_per_node", "--ntasks-per-node", "", dict(type=int)), + SbatchToSlurm("tasks_per_socket", "--ntasks-per-socket", "", dict(type=int)), + SbatchToSlurm("open_mode", "--open-mode"), + SbatchToSlurm("standard_output", "--output", "-o"), + SbatchToSlurm("", "--overcommit", "-O", dict(action="store_const", const=True)), + SbatchToSlurm( + "", + "--oversubscribe", + "-s", + dict(action="store_const", const="oversubscribe", dest="exclusive"), + ), + SbatchToSlurm("", "--parsable", "", dict(action="store_const", const=True)), + SbatchToSlurm("partition", "--partition", "-p"), + SbatchToSlurm("", "--power"), + SbatchToSlurm("priority", "--priority"), + SbatchToSlurm("", "--profile"), + SbatchToSlurm("", "--propagate"), + SbatchToSlurm("qos", "--qos", "-q"), + SbatchToSlurm("", "--quiet", "-Q", dict(action="store_const", const=True)), + SbatchToSlurm("", "--reboot", "", dict(action="store_const", const=True)), + SbatchToSlurm("requeue", "--requeue", "", dict(action="store_const", const=True)), + SbatchToSlurm("reservation", "--reservation"), + SbatchToSlurm("signal", "--signal"), + SbatchToSlurm("sockets_per_node", "--sockets-per-node", "", dict(type=int)), + SbatchToSlurm("spread_job", "--spread-job", "", dict(action="store_const", const=True)), + SbatchToSlurm("", "--switches"), + SbatchToSlurm("", "--test-only", "", dict(action="store_const", const=True)), + SbatchToSlurm("thread_specification", "--thread-spec", "", dict(type=int)), + SbatchToSlurm("threads_per_core", "--threads-per-core", "", dict(type=int)), + SbatchToSlurm("time_limit", "--time", "-t"), + SbatchToSlurm("time_minimum", "--time-min"), + SbatchToSlurm("", "--tmp"), + SbatchToSlurm("", "--uid"), + SbatchToSlurm("", "--usage", "", dict(action="store_const", const=True)), + SbatchToSlurm("minimum_nodes", "--use-min-nodes", "", dict(action="store_const", const=True)), + SbatchToSlurm("", "--verbose", "-v", dict(action="store_const", const=True)), + SbatchToSlurm("", "--version", "-V", dict(action="store_const", const=True)), + SbatchToSlurm("", "--wait", "-W", dict(action="store_const", const=True)), + SbatchToSlurm("wait_all_nodes", "--wait-all-nodes", "", dict(type=int)), + SbatchToSlurm("wckey", "--wckey"), + SbatchToSlurm("", "--wrap"), +] + + +class ArgumentParserCustomExit(ArgumentParser): + """ + Custom implementation of the built-in class for argument parsing. + The sys.exit triggered by the original code is replaced by a ValueError, + besides some friendly logging messages. + """ + + def exit(self, status=0, message=None): + """ + Raise ValueError when parsing invalid parameters or if the type of their + values is not correct. + """ + log_message = f"Argparse exit status {status}: {message}" + if status: + logger.error(log_message) + else: + logger.info(log_message) + raise ValueError(message) + + +def build_parser() -> ArgumentParser: + """ + Build an ArgumentParser to handle all SBATCH + parameters declared at sbatch_to_slurm. + """ + parser = ArgumentParserCustomExit() + for item in sbatch_to_slurm: + args = (i for i in (item.sbatch_short, item.sbatch) if i) + parser.add_argument(*args, **item.argparser_param) + # make --requeue and --no-requeue work together, with default to None + parser.set_defaults(requeue=None) + return parser + + +def build_mapping_sbatch_to_slurm() -> bidict: + """ + Create a mapper that can translate both ways between the parameter + names expected by Slurm REST API and SBATCH. + """ + mapping = bidict() + + for item in sbatch_to_slurm: + if item.slurmrestd_var_name: + sbatch_name = item.sbatch.lstrip("-").replace("-", "_") + mapping[sbatch_name] = item.slurmrestd_var_name + + return mapping + + +def jobscript_to_dict(jobscript: str) -> Dict[str, Union[str, bool]]: + """ + Extract the SBATCH params from a given job script and return them in a + dictionary for mapping the parameter names to their values. + + Raise ValueError if any of the parameters are unknown to the parser. + """ + parsed_args, unknown_arg = parser.parse_known_args(_clean_jobscript(jobscript)) + + if unknown_arg: + raise ValueError("Unrecognized SBATCH arguments: {}".format(" ".join(unknown_arg))) + + sbatch_params = {key: value for key, value in vars(parsed_args).items() if value is not None} + + logger.debug(f"SBATCH params parsed from job script: {sbatch_params}") + + return sbatch_params + + +def convert_sbatch_to_slurm_api(input: Dict[str, Any]) -> Dict[str, Any]: + """ + Take a dictionary containing key-value pairing of SBATCH parameter name + to value and change the keys to Slurm API parameter name while keeping + the values intact. + + Raise KeyError if any of the keys are unknown to the mapper. + """ + + mapped = {} + unknown_keys = [] + + for sbatch_name, value in input.items(): + try: + slurm_name = mapping_sbatch_to_slurm[sbatch_name] + except KeyError: + unknown_keys.append(sbatch_name) + else: + mapped[slurm_name] = value + + if unknown_keys: + error_message = "Impossible to convert from SBATCH to Slurm REST API: {}" + raise KeyError(error_message.format(", ".join(unknown_keys))) + + logger.debug(f"Slurm API params mapped from SBATCH: {mapped}") + + return mapped + + +def get_job_parameters(jobscript: str, **kwargs) -> Dict[str, Any]: + """ + Parse all SBATCH parameters from a job script, map their names to Slurm API + parameters, and return them as a key-value pairing dictionary. + + Extra keyword arguments can be used to overwrite any parameter from the + job script, like name or current_working_directory. + """ + + slurm_parameters = convert_sbatch_to_slurm_api(jobscript_to_dict(jobscript)) + + merged_parameters = {**slurm_parameters, **kwargs} + + return merged_parameters + + +parser = build_parser() +mapping_sbatch_to_slurm = build_mapping_sbatch_to_slurm() diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py new file mode 100644 index 000000000..f2c5635e5 --- /dev/null +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py @@ -0,0 +1,550 @@ +import inspect +from argparse import ArgumentParser +from typing import MutableMapping + +import pytest +from bidict import bidict + +from jobbergate_api.apps.job_submissions.properties_parser import ( + _IDENTIFICATION_FLAG, + _INLINE_COMMENT_MARK, + ArgumentParserCustomExit, + _clean_jobscript, + _clean_line, + _flagged_line, + _split_line, + build_mapping_sbatch_to_slurm, + build_parser, + convert_sbatch_to_slurm_api, + get_job_parameters, + jobscript_to_dict, + sbatch_to_slurm, +) + + +def test_identification_flag(): + """ + Check if the value of the identification flag is the same codded in the tests. + """ + assert _IDENTIFICATION_FLAG == "#SBATCH" + + +def test_inline_comment_mark(): + """ + Check if the inline comment mark is the same codded in the tests. + """ + assert _INLINE_COMMENT_MARK == "#" + + +@pytest.mark.parametrize( + "line, desired_value", + ( + ("#SBATCH -abc", True), + ("##SBATCH -abc", False), + ("run python application", False), + ("# A comment", False), + ), +) +def test_flagged_line(line, desired_value): + """ + Check if the flagged lines are identified properly. + """ + actual_value = _flagged_line(line) + assert actual_value == desired_value + + +@pytest.mark.parametrize( + "line, desired_value", + ( + ("#SBATCH", ""), + ("#SBATCH#SBATCH", ""), + ("#SBATCH -abc # A comment", "-abc"), + ("#SBATCH --abc=0 # A comment", "--abc=0"), + ("#SBATCH --abc 0 # A comment", "--abc 0"), + ("#SBATCH -a 0 # A comment", "-a 0"), + ("#SBATCH -a=0 # A comment", "-a=0"), + ("#SBATCH -a = 0 # A comment", "-a = 0"), + ("#SBATCH -a=C&Aaccount # A comment", "-a=C&Aaccount"), + ), +) +def test_clean_line(line, desired_value): + """ + Check if the provided lines are cleaned properly, i.e., + identification flag, inline comments, and comment mark are all removed. + """ + actual_value = _clean_line(line) + assert actual_value == desired_value + + +@pytest.mark.parametrize( + "line, desired_value", + ( + ("--help", ["--help"]), + ("--abc=0", ["--abc", "0"]), + ("--abc = 0", ["--abc", "0"]), + ("-J job_name", ["-J", "job_name"]), + ("-v -J job_name", ["-v", "-J", "job_name"]), + ("-J job_name -v", ["-J", "job_name", "-v"]), + ("-a=0", ["-a", "0"]), + ("-a = 0", ["-a", "0"]), + ("-a 0", ["-a", "0"]), + ), +) +def test_split_line(line, desired_value): + """ + Check if the provided lines are splitted properly at white spaces and equal + character. This procedure is important because it is the way argparse + expects to receive the parameters. + """ + actual_value = _split_line(line) + assert actual_value == desired_value + + +@pytest.fixture +def dummy_slurm_script(): + """ + Provide a dummy job script for testing. + """ + # TODO: DRY, integrate this one with conftest/dummy_template_source + return inspect.cleandoc( + """ + #!/bin/bash + #SBATCH # Empty line + #SBATCH --no-kill --no-requeue # Flagged params + #SBATCH -n 4 -A # Multiple args per line + #SBATCH --job-name=serial_job_test # Job name + #SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL) + #SBATCH --mail-user=email@somewhere.com # Where to send mail + #SBATCH --mem=1gb # Job memory request + #SBATCH --time=00:05:00 # Time limit hrs:min:sec + #SBATCH --output = serial_test_%j.log # Standard output and error log + #SBATCH --wait-all-nodes=0 # + pwd; hostname; date + + module load python + + echo "Running plot script on a single CPU core" + + python /data/training/SLURM/plot_template.py + + date + """ + ) + + +def test_clean_jobscript(dummy_slurm_script): + """ + Check if all sbatch parameters are correctly extracted from a job script. + This operation combines many of the functions tested above (filter, + clean, and slit the parameters on each line). + """ + desired_list = [ + "--no-kill", + "--no-requeue", + "-n", + "4", + "-A", + "", + "--job-name", + "serial_job_test", + "--mail-type", + "END,FAIL", + "--mail-user", + "email@somewhere.com", + "--mem", + "1gb", + "--time", + "00:05:00", + "--output", + "serial_test_%j.log", + "--wait-all-nodes", + "0", + ] + actual_list = list(_clean_jobscript(dummy_slurm_script)) + assert actual_list == desired_list + + +@pytest.mark.parametrize("item", sbatch_to_slurm) +class TestSbatchToSlurmList: + """ + Test all the fields of the objects SbatchToSlurm that are + stored in the list sbatch_to_slurm. + """ + + def test_slurmrestd_var_name__is_string(self, item): + """ + Check if the field slurmrestd_var_name is a string. + """ + assert isinstance(item.slurmrestd_var_name, str) + + def test_slurmrestd_var_name__only_contains_letters(self, item): + """ + Check if the field slurmrestd_var_name contains only underscores and letters. + """ + if item.slurmrestd_var_name: + assert item.slurmrestd_var_name.replace("_", "").isalpha() + + def test_sbatch__is_string(self, item): + """ + Check if the field sbatch is a string. + """ + assert isinstance(item.sbatch, str) + + def test_sbatch__starts_with_double_hyphen(self, item): + """ + Check if the field sbatch starts with a double hyphen. + """ + assert item.sbatch.startswith("--") + + def test_sbatch__is_not_empty(self, item): + """ + Check if the field sbatch is not empty by asserting that it has more + than three characters, since it starts with a double hyphen. + """ + assert len(item.sbatch) >= 3 + + def test_sbatch__only_contains_letters(self, item): + """ + Check if the field sbatch contains only hyphens and letters. + """ + assert item.sbatch.replace("-", "").isalpha() + + def test_sbatch_short__is_string(self, item): + """ + Check if the optional field sbatch_short is a string. + """ + assert isinstance(item.sbatch_short, str) + + def test_sbatch_short__starts_with_hyphen(self, item): + """ + Check if the optional field sbatch_short starts with a hyphen. + """ + if item.sbatch_short: + assert item.sbatch_short.startswith("-") + + def test_sbatch_short__is_not_empty(self, item): + """ + Check if of the optional field sbatch_short is equal to two, since it + should be a hyphen and a letter. + """ + if item.sbatch_short: + assert len(item.sbatch_short) == 2 + + def test_sbatch_short__only_contains_letters(self, item): + """ + Check if the optional field sbatch_short contains only hyphens and letters. + """ + if item.sbatch_short: + assert item.sbatch_short.replace("-", "").isalpha() + + def test_argparser_param__is_mutable_mapping(self, item): + """ + Check if the field argparser_param is a MutableMapping. + """ + assert isinstance(item.argparser_param, MutableMapping) + + def test_argparser_param__is_valid_for_parser(self, item): + """ + Check if the field argparser_param can be added in a parser. + """ + if item.argparser_param: + args = (i for i in (item.sbatch_short, item.sbatch) if i) + parser = ArgumentParserCustomExit() + parser.add_argument(*args, **item.argparser_param) + + +@pytest.mark.parametrize("field", ["slurmrestd_var_name", "sbatch", "sbatch_short"]) +def test_sbatch_to_slurm_list__contains_only_unique_values(field): + """ + Test that any given field has no duplicated values for all parameters stored + at sbatch_to_slurm. This aims to avoid ambiguity at the SBATCH argparser and + the two-way mapping between SBATCH and Slurm Rest API namespaces. + """ + list_of_values = [getattr(i, field) for i in sbatch_to_slurm if bool(getattr(i, field))] + + assert len(list_of_values) == len(set(list_of_values)) + + +class TestArgumentParserCustomExit: + """ + Test the custom error handling implemented over the built-in argument parser. + """ + + @pytest.fixture(scope="module") + def parser(self): + """ + An instance of parser, used to support the tests in this class. + """ + parser = ArgumentParserCustomExit() + parser.add_argument("--foo", type=int) + parser.add_argument("--bar", action="store_true") + return parser + + def test_argument_parser_success(self, parser): + """ + Test the base case, where the arguments are successfully parsed and + converted to the expected type. + """ + args = parser.parse_args("--foo=10 --bar".split()) + assert {"foo": 10, "bar": True} == vars(args) + + def test_argument_parser_raise_value_error_when_value_is_missing(self, parser): + """ + Test that ValueError is raised when the value for one parameter is missing. + """ + with pytest.raises(ValueError, match="error: argument --foo: expected one argument"): + parser.parse_args("--foo".split()) + + def test_argument_parser_raise_value_error_in_case_of_wrong_type(self, parser): + """ + Test that ValueError is raised when the value for some parameter is + incompatible with its type. + """ + with pytest.raises(ValueError, match="error: argument --foo: invalid int value:"): + parser.parse_args("--foo some_text".split()) + + +def test_build_parser(): + """ + Test if build_parser runs with no problem and returns the correct type. + """ + parser = build_parser() + assert isinstance(parser, ArgumentParser) + + +def test_build_mapping_sbatch_to_slurm(): + """ + Test if build_mapping_sbatch_to_slurm runs with no problem and + returns the correct type. + """ + mapping = build_mapping_sbatch_to_slurm() + assert isinstance(mapping, bidict) + + +def test_jobscript_to_dict__success(dummy_slurm_script): + """ + Test if the SBATCH parameters are properly extracted from a job script + and returned in a dictionary mapping parameters to their value. + """ + + desired_dict = { + "no_kill": True, + "requeue": False, + "account": "", + "job_name": "serial_job_test", + "mail_type": "END,FAIL", + "mail_user": "email@somewhere.com", + "mem": "1gb", + "ntasks": 4, + "output": "serial_test_%j.log", + "time": "00:05:00", + "wait_all_nodes": 0, + } + + actual_dict = jobscript_to_dict(dummy_slurm_script) + + assert actual_dict == desired_dict + + +def test_jobscript_to_dict__raises_exception_for_unknown_parameter(): + """ + Test if jobscript_to_dict raises a ValueError when facing unknown parameters. + """ + with pytest.raises(ValueError, match="Unrecognized SBATCH arguments:"): + jobscript_to_dict("#SBATCH --foo\n#SBATCH --bar=0") + + +@pytest.mark.parametrize("item", filter(lambda i: i.slurmrestd_var_name, sbatch_to_slurm)) +def test_convert_sbatch_to_slurm_api__success(item): + """ + Test if the keys in a dictionary are properly renamed from SBATCH to Slurm + Rest API namespace. Notice the values should not be affected. + """ + desired_dict = {item.slurmrestd_var_name: None} + + sbatch_name = item.sbatch.lstrip("-").replace("-", "_") + actual_dict = convert_sbatch_to_slurm_api({sbatch_name: None}) + + assert actual_dict == desired_dict + + +def test_convert_sbatch_to_slurm_api__raises_exception_for_unknown_parameter(): + """ + Test if the conversion of dictionary keys from SBATCH to Slurm Rest API + namespace raises KeyError when facing unknown names. + """ + with pytest.raises(KeyError, match="Impossible to convert from SBATCH to Slurm REST API:"): + convert_sbatch_to_slurm_api(dict(foo=0, bar=1)) + + +def test_get_job_parameters(dummy_slurm_script): + """ + Test if all SBATCH parameters are properly extracted from a given job script, + the name of each of them is mapped to Slurm Rest API namespace and returned + in a dictionary. Notice get_job_parameters accepts extra keywords that can be + used to overwrite the values from the job script. + """ + extra_options = {"name": "name", "current_working_directory": "cwd"} + + desired_dict = { + "no_kill": True, + "requeue": False, + "account": "", + "name": "serial_job_test", + "mail_type": "END,FAIL", + "mail_user": "email@somewhere.com", + "memory_per_node": "1gb", + "tasks": 4, + "standard_output": "serial_test_%j.log", + "time_limit": "00:05:00", + "wait_all_nodes": 0, + } + + desired_dict.update(extra_options) + + actual_dict = get_job_parameters(dummy_slurm_script, **extra_options) + + assert desired_dict == actual_dict + + +class TestBidictMapping: + """ + Integration test with the requirement bidict (used for two-way mapping). + """ + + @pytest.fixture + def dummy_mapping(self): + """ + A dummy dictionary used for testing. + """ + return {f"key_{i}": f"value_{i}" for i in range(5)} + + def test_bidict__is_mutable_mapping(self): + """ + Check if bidict implements all the necessary protocols to be a MutableMapping. + """ + assert issubclass(bidict, MutableMapping) + + def test_bidict__can_be_compared_to_a_dictionary(self, dummy_mapping): + """ + Check if bidict can be really comparable to a dictionary. + """ + assert dummy_mapping == bidict(dummy_mapping) + + def test_bidict__can_be_compared_to_a_dictionary_inverse(self, dummy_mapping): + """ + Check if bidict can be comparable to a dictionary, this time checking + its inverse capability (i.e., swapping keys and values). + """ + desired_value = {value: key for key, value in dummy_mapping.items()} + + assert desired_value == bidict(dummy_mapping).inverse + + +class TestExclusiveParameter: + """ + --exclusive is a special SBATCH parameter that can be used in some different ways: + + 1. --exclusive as a flag, meaning the value 'exclusive' should be recovered for slurmd. + 2. --exclusive=, meaning the value should be recovered for slurmd. + According to the Slurm documentation, the value can be 'user' or 'mcs'. + 3. On top of that, 'exclusive' is expected to be set to 'oversubscribe' when the + flag --oversubscribe is used. + + Note: When both are used, the last of them takes precedence. + """ + + def test_empty_jobscript(self): + """ + Base case: no --exclusive parameter at all. + """ + jobscript = "" + + desired_dict = {} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict + + def test_exclusive_as_a_flag(self): + """ + Test the first scenario: --exclusive as a flag. + """ + jobscript = "#SBATCH --exclusive" + + desired_dict = {"exclusive": "exclusive"} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict + + @pytest.mark.parametrize("exclusive_value", ["user", "mcs", "exclusive", "oversubscribe"]) + def test_exclusive_with_string_value(self, exclusive_value): + """ + Test the second scenario: --exclusive=. + """ + jobscript = f"#SBATCH --exclusive={exclusive_value}" + + desired_dict = {"exclusive": exclusive_value} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict + + def test_exclusive_with_incorrect_value(self): + """ + Test the second scenario with an incorrect value, ValueError should be raised. + """ + jobscript = "#SBATCH --exclusive=test-test" + + with pytest.raises(ValueError, match="invalid choice: 'test-test'"): + jobscript_to_dict(jobscript) + + def test_oversubscribe(self): + """ + Test the third scenario: --oversubscribe as a flag. + """ + jobscript = "#SBATCH --oversubscribe" + + desired_dict = {"exclusive": "oversubscribe"} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict + + def test_oversubscribe_with_incorrect_value(self): + """ + Test the second scenario with an incorrect value, ValueError should be raised. + """ + jobscript = "#SBATCH --oversubscribe=test-test" + + with pytest.raises(ValueError, match="Unrecognized SBATCH arguments: test-test"): + jobscript_to_dict(jobscript) + + def test_both_exclusive_and_oversubscribe_1(self): + """ + Test that when both are used, the last of them takes precedence. + + In this case, --exclusive is the last one. + """ + jobscript = "#SBATCH --oversubscribe\n#SBATCH --exclusive" + + desired_dict = {"exclusive": "exclusive"} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict + + def test_both_exclusive_and_oversubscribe_2(self): + """ + Test that when both are used, the last of them takes precedence. + + In this case, --oversubscribe is the last one. + """ + jobscript = "#SBATCH --exclusive\n#SBATCH --oversubscribe" + + desired_dict = {"exclusive": "oversubscribe"} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict diff --git a/jobbergate-api/poetry.lock b/jobbergate-api/poetry.lock index f8253678f..fe978b760 100644 --- a/jobbergate-api/poetry.lock +++ b/jobbergate-api/poetry.lock @@ -28,8 +28,8 @@ idna = ">=2.8" sniffio = ">=1.1" [package.extras] -doc = ["packaging", "sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"] -test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=6.0)", "pytest-mock (>=3.6.1)", "trustme", "contextlib2", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"] +doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=6.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] trio = ["trio (>=0.16)"] [[package]] @@ -78,7 +78,7 @@ optional = false python-versions = ">=3.7" [package.extras] -tests = ["pytest", "pytest-asyncio", "mypy (>=0.800)"] +tests = ["mypy (>=0.800)", "pytest", "pytest-asyncio"] [[package]] name = "asyncpg" @@ -89,9 +89,9 @@ optional = false python-versions = ">=3.5.0" [package.extras] -dev = ["Cython (>=0.29.20,<0.30.0)", "pytest (>=3.6.0)", "Sphinx (>=1.7.3,<1.8.0)", "sphinxcontrib-asyncio (>=0.2.0,<0.3.0)", "sphinx-rtd-theme (>=0.2.4,<0.3.0)", "pycodestyle (>=2.5.0,<2.6.0)", "flake8 (>=3.7.9,<3.8.0)", "uvloop (>=0.14.0,<0.15.0)"] -docs = ["Sphinx (>=1.7.3,<1.8.0)", "sphinxcontrib-asyncio (>=0.2.0,<0.3.0)", "sphinx-rtd-theme (>=0.2.4,<0.3.0)"] -test = ["pycodestyle (>=2.5.0,<2.6.0)", "flake8 (>=3.7.9,<3.8.0)", "uvloop (>=0.14.0,<0.15.0)"] +dev = ["Cython (>=0.29.20,<0.30.0)", "Sphinx (>=1.7.3,<1.8.0)", "flake8 (>=3.7.9,<3.8.0)", "pycodestyle (>=2.5.0,<2.6.0)", "pytest (>=3.6.0)", "sphinx-rtd-theme (>=0.2.4,<0.3.0)", "sphinxcontrib-asyncio (>=0.2.0,<0.3.0)", "uvloop (>=0.14.0,<0.15.0)"] +docs = ["Sphinx (>=1.7.3,<1.8.0)", "sphinx-rtd-theme (>=0.2.4,<0.3.0)", "sphinxcontrib-asyncio (>=0.2.0,<0.3.0)"] +test = ["flake8 (>=3.7.9,<3.8.0)", "pycodestyle (>=2.5.0,<2.6.0)", "uvloop (>=0.14.0,<0.15.0)"] [[package]] name = "atomicwrites" @@ -110,10 +110,10 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope.interface"] +docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] +tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope.interface"] +tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"] [[package]] name = "auto-name-enum" @@ -131,6 +131,14 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "bidict" +version = "0.22.0" +description = "The bidirectional mapping library for Python." +category = "main" +optional = false +python-versions = ">=3.7" + [[package]] name = "black" version = "22.3.0" @@ -221,7 +229,7 @@ optional = false python-versions = ">=3.5.0" [package.extras] -unicode_backport = ["unicodedata2"] +unicode-backport = ["unicodedata2"] [[package]] name = "cli-helpers" @@ -292,12 +300,12 @@ python-versions = ">=3.6" cffi = ">=1.12" [package.extras] -docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"] -docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"] +docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx_rtd_theme"] +docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"] pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"] sdist = ["setuptools_rust (>=0.11.4)"] ssh = ["bcrypt (>=3.1.5)"] -test = ["pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"] +test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"] [[package]] name = "databases" @@ -313,9 +321,9 @@ sqlalchemy = ">=1.4,<1.5" [package.extras] mysql = ["aiomysql"] -mysql_asyncmy = ["asyncmy"] +mysql-asyncmy = ["asyncmy"] postgresql = ["asyncpg"] -postgresql_aiopg = ["aiopg"] +postgresql-aiopg = ["aiopg"] sqlite = ["aiosqlite"] [[package]] @@ -343,8 +351,8 @@ optional = false python-versions = ">=3.6,<4.0" [package.extras] -dnssec = ["cryptography (>=2.6,<37.0)"] curio = ["curio (>=1.2,<2.0)", "sniffio (>=1.1,<2.0)"] +dnssec = ["cryptography (>=2.6,<37.0)"] doh = ["h2 (>=4.1.0)", "httpx (>=0.21.1)", "requests (>=2.23.0,<3.0.0)", "requests-toolbelt (>=0.9.1,<0.10.0)"] idna = ["idna (>=2.1,<4.0)"] trio = ["trio (>=0.14,<0.20)"] @@ -365,7 +373,7 @@ websocket-client = ">=0.32.0" [package.extras] ssh = ["paramiko (>=2.4.2)"] -tls = ["pyOpenSSL (>=17.5.0)", "cryptography (>=3.4.7)", "idna (>=2.0.0)"] +tls = ["cryptography (>=3.4.7)", "idna (>=2.0.0)", "pyOpenSSL (>=17.5.0)"] [[package]] name = "ecdsa" @@ -407,10 +415,10 @@ pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1. starlette = "0.14.2" [package.extras] -all = ["requests (>=2.24.0,<3.0.0)", "aiofiles (>=0.5.0,<0.8.0)", "jinja2 (>=2.11.2,<3.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "itsdangerous (>=1.1.0,<2.0.0)", "pyyaml (>=5.3.1,<6.0.0)", "graphene (>=2.1.8,<3.0.0)", "ujson (>=4.0.1,<5.0.0)", "orjson (>=3.2.1,<4.0.0)", "email_validator (>=1.1.1,<2.0.0)", "uvicorn[standard] (>=0.12.0,<0.16.0)", "async_exit_stack (>=1.0.1,<2.0.0)", "async_generator (>=1.10,<2.0.0)"] -dev = ["python-jose[cryptography] (>=3.3.0,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.16.0)", "graphene (>=2.1.8,<3.0.0)"] -doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=7.1.9,<8.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "typer-cli (>=0.0.12,<0.0.13)", "pyyaml (>=5.3.1,<6.0.0)"] -test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "pytest-asyncio (>=0.14.0,<0.16.0)", "mypy (==0.910)", "flake8 (>=3.8.3,<4.0.0)", "black (==21.9b0)", "isort (>=5.0.6,<6.0.0)", "requests (>=2.24.0,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "email_validator (>=1.1.1,<2.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "peewee (>=3.13.3,<4.0.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "orjson (>=3.2.1,<4.0.0)", "ujson (>=4.0.1,<5.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "aiofiles (>=0.5.0,<0.8.0)", "flask (>=1.1.2,<2.0.0)", "async_exit_stack (>=1.0.1,<2.0.0)", "async_generator (>=1.10,<2.0.0)", "types-ujson (==0.1.1)", "types-orjson (==3.6.0)", "types-dataclasses (==0.1.7)"] +all = ["aiofiles (>=0.5.0,<0.8.0)", "async_exit_stack (>=1.0.1,<2.0.0)", "async_generator (>=1.10,<2.0.0)", "email_validator (>=1.1.1,<2.0.0)", "graphene (>=2.1.8,<3.0.0)", "itsdangerous (>=1.1.0,<2.0.0)", "jinja2 (>=2.11.2,<3.0.0)", "orjson (>=3.2.1,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<6.0.0)", "requests (>=2.24.0,<3.0.0)", "ujson (>=4.0.1,<5.0.0)", "uvicorn[standard] (>=0.12.0,<0.16.0)"] +dev = ["autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "graphene (>=2.1.8,<3.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.16.0)"] +doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=7.1.9,<8.0.0)", "pyyaml (>=5.3.1,<6.0.0)", "typer-cli (>=0.0.12,<0.0.13)"] +test = ["aiofiles (>=0.5.0,<0.8.0)", "async_exit_stack (>=1.0.1,<2.0.0)", "async_generator (>=1.10,<2.0.0)", "black (==21.9b0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "email_validator (>=1.1.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "flask (>=1.1.2,<2.0.0)", "httpx (>=0.14.0,<0.19.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "orjson (>=3.2.1,<4.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=6.2.4,<7.0.0)", "pytest-asyncio (>=0.14.0,<0.16.0)", "pytest-cov (>=2.12.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "requests (>=2.24.0,<3.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "types-dataclasses (==0.1.7)", "types-orjson (==3.6.0)", "types-ujson (==0.1.1)", "ujson (>=4.0.1,<5.0.0)"] [[package]] name = "file-storehouse" @@ -480,7 +488,7 @@ optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" [package.extras] -docs = ["sphinx"] +docs = ["Sphinx"] [[package]] name = "h11" @@ -555,9 +563,9 @@ python-versions = ">=3.7" zipp = ">=0.5" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] +docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] +testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] [[package]] name = "importlib-resources" @@ -571,8 +579,8 @@ python-versions = ">=3.7" zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] +docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] +testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [[package]] name = "iniconfig" @@ -601,6 +609,7 @@ pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} pickleshare = "*" prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0" pygments = "*" +setuptools = ">=18.5" traitlets = ">=4.2" [package.extras] @@ -609,10 +618,10 @@ doc = ["Sphinx (>=1.3)"] kernel = ["ipykernel"] nbconvert = ["nbconvert"] nbformat = ["nbformat"] -notebook = ["notebook", "ipywidgets"] +notebook = ["ipywidgets", "notebook"] parallel = ["ipyparallel"] qtconsole = ["qtconsole"] -test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.17)"] +test = ["ipykernel", "nbformat", "nose (>=0.10.1)", "numpy (>=1.17)", "pygments", "requests", "testpath"] [[package]] name = "isort" @@ -623,10 +632,10 @@ optional = false python-versions = ">=3.6.1,<4.0" [package.extras] -pipfile_deprecated_finder = ["pipreqs", "requirementslib"] -requirements_deprecated_finder = ["pipreqs", "pip-api"] colors = ["colorama (>=0.4.3,<0.5.0)"] +pipfile-deprecated-finder = ["pipreqs", "requirementslib"] plugins = ["setuptools"] +requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] name = "jedi" @@ -678,7 +687,7 @@ colorama = {version = ">=0.3.4", markers = "sys_platform == \"win32\""} win32-setctime = {version = ">=1.0.0", markers = "sys_platform == \"win32\""} [package.extras] -dev = ["colorama (>=0.3.4)", "docutils (==0.16)", "flake8 (>=3.7.7)", "tox (>=3.9.0)", "pytest (>=4.6.2)", "pytest-cov (>=2.7.1)", "black (>=19.10b0)", "isort (>=5.1.1)", "Sphinx (>=4.1.1)", "sphinx-autobuild (>=0.7.1)", "sphinx-rtd-theme (>=0.4.3)"] +dev = ["Sphinx (>=4.1.1)", "black (>=19.10b0)", "colorama (>=0.3.4)", "docutils (==0.16)", "flake8 (>=3.7.7)", "isort (>=5.1.1)", "pytest (>=4.6.2)", "pytest-cov (>=2.7.1)", "sphinx-autobuild (>=0.7.1)", "sphinx-rtd-theme (>=0.4.3)", "tox (>=3.9.0)"] [[package]] name = "mako" @@ -692,7 +701,7 @@ python-versions = ">=3.7" MarkupSafe = ">=0.9.2" [package.extras] -babel = ["babel"] +babel = ["Babel"] lingua = ["lingua"] testing = ["pytest"] @@ -806,7 +815,7 @@ python-versions = "*" [package.extras] argon2 = ["argon2-cffi (>=18.2.0)"] bcrypt = ["bcrypt (>=3.1.0)"] -build_docs = ["sphinx (>=1.6)", "sphinxcontrib-fulltoc (>=1.2.0)", "cloud-sptheme (>=1.10.1)"] +build-docs = ["cloud-sptheme (>=1.10.1)", "sphinx (>=1.6)", "sphinxcontrib-fulltoc (>=1.2.0)"] totp = ["cryptography"] [[package]] @@ -1130,7 +1139,7 @@ pytest = ">=4.6" toml = "*" [package.extras] -testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"] +testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"] [[package]] name = "pytest-env" @@ -1212,8 +1221,8 @@ rsa = "*" [package.extras] cryptography = ["cryptography (>=3.4.0)"] -pycrypto = ["pycrypto (>=2.6.0,<2.7.0)", "pyasn1"] -pycryptodome = ["pycryptodome (>=3.3.1,<4.0.0)", "pyasn1"] +pycrypto = ["pyasn1", "pycrypto (>=2.6.0,<2.7.0)"] +pycryptodome = ["pyasn1", "pycryptodome (>=3.3.1,<4.0.0)"] [[package]] name = "python-multipart" @@ -1274,7 +1283,7 @@ urllib3 = ">=1.21.1,<1.27" [package.extras] socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] -use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"] +use-chardet-on-py3 = ["chardet (>=3.0.2,<5)"] [[package]] name = "respx" @@ -1358,11 +1367,11 @@ celery = ["celery (>=3)"] chalice = ["chalice (>=1.16.0)"] django = ["django (>=1.8)"] falcon = ["falcon (>=1.4)"] -flask = ["flask (>=0.11)", "blinker (>=1.1)"] +flask = ["blinker (>=1.1)", "flask (>=0.11)"] httpx = ["httpx (>=0.16.0)"] -pure_eval = ["pure-eval", "executing", "asttokens"] +pure-eval = ["asttokens", "executing", "pure-eval"] pyspark = ["pyspark (>=2.4.4)"] -quart = ["quart (>=0.16.1)", "blinker (>=1.1)"] +quart = ["blinker (>=1.1)", "quart (>=0.16.1)"] rq = ["rq (>=0.6)"] sanic = ["sanic (>=0.8)"] sqlalchemy = ["sqlalchemy (>=1.2)"] @@ -1379,6 +1388,19 @@ python-versions = ">=3.6" [package.extras] test = ["pytest (>=6.1,<6.2)"] +[[package]] +name = "setuptools" +version = "65.6.3" +description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"] +testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] + [[package]] name = "six" version = "1.16.0" @@ -1426,25 +1448,25 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} [package.extras] -aiomysql = ["greenlet (!=0.4.17)", "aiomysql"] -aiosqlite = ["typing_extensions (!=3.10.0.1)", "greenlet (!=0.4.17)", "aiosqlite"] +aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] +aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"] asyncio = ["greenlet (!=0.4.17)"] -asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4)"] -mariadb_connector = ["mariadb (>=1.0.1)"] +asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"] +mariadb-connector = ["mariadb (>=1.0.1)"] mssql = ["pyodbc"] -mssql_pymssql = ["pymssql"] -mssql_pyodbc = ["pyodbc"] -mypy = ["sqlalchemy2-stubs", "mypy (>=0.910)"] -mysql = ["mysqlclient (>=1.4.0,<2)", "mysqlclient (>=1.4.0)"] -mysql_connector = ["mysql-connector-python"] -oracle = ["cx_oracle (>=7,<8)", "cx_oracle (>=7)"] +mssql-pymssql = ["pymssql"] +mssql-pyodbc = ["pyodbc"] +mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"] +mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"] +mysql-connector = ["mysql-connector-python"] +oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"] postgresql = ["psycopg2 (>=2.7)"] -postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"] -postgresql_pg8000 = ["pg8000 (>=1.16.6)"] -postgresql_psycopg2binary = ["psycopg2-binary"] -postgresql_psycopg2cffi = ["psycopg2cffi"] -pymysql = ["pymysql (<1)", "pymysql"] -sqlcipher = ["sqlcipher3-binary"] +postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"] +postgresql-pg8000 = ["pg8000 (>=1.16.6)"] +postgresql-psycopg2binary = ["psycopg2-binary"] +postgresql-psycopg2cffi = ["psycopg2cffi"] +pymysql = ["pymysql", "pymysql (<1)"] +sqlcipher = ["sqlcipher3_binary"] [[package]] name = "sqlalchemy-stubs" @@ -1540,8 +1562,8 @@ click = ">=7.1.1,<9.0.0" [package.extras] all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"] dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)"] -doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)"] -test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", 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setproctitle = [ {file = "setproctitle-1.2.2-cp39-cp39-win_amd64.whl", hash = "sha256:4fc5bebd34f451dc87d2772ae6093adea1ea1dc29afc24641b250140decd23bb"}, {file = "setproctitle-1.2.2.tar.gz", hash = "sha256:7dfb472c8852403d34007e01d6e3c68c57eb66433fb8a5c77b13b89a160d97df"}, ] +setuptools = [ + {file = "setuptools-65.6.3-py3-none-any.whl", hash = "sha256:57f6f22bde4e042978bcd50176fdb381d7c21a9efa4041202288d3737a0c6a54"}, + {file = "setuptools-65.6.3.tar.gz", hash = "sha256:a7620757bf984b58deaf32fc8a4577a9bbc0850cf92c20e1ce41c38c19e5fb75"}, +] six = [ {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"}, {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, diff --git a/jobbergate-api/pyproject.toml b/jobbergate-api/pyproject.toml index 4e2f09119..a9a77da9e 100644 --- a/jobbergate-api/pyproject.toml +++ b/jobbergate-api/pyproject.toml @@ -42,6 +42,7 @@ sendgrid = "^6.9.7" file-storehouse = "0.5.0" py-buzz = "^3.2.1" toml = "^0.10.2" +bidict = "^0.22.0" [tool.poetry.dev-dependencies] black = "^22" @@ -49,7 +50,7 @@ pre-commit = "^2.9.2" pytest = "^6.2" pytest-asyncio = "^0.12" pytest-cov = "^2.8" -python-status = "i^1.0" +python-status = "^1.0" requests = "^2.23.0" nest_asyncio = "^1.3.3" coverage = "^5.1" From f7bbba35201d1aa42eb3fd08b1e03f6eee89be7b Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 2 Dec 2022 13:25:44 -0300 Subject: [PATCH 13/36] Add the logic for SBATCH param mapping to the `job_submissions` POST endpoint --- .../apps/job_submissions/properties_parser.py | 20 ++- .../apps/job_submissions/routers.py | 11 ++ .../apps/job_submissions/schemas.py | 2 +- .../job_submissions/test_properties_parser.py | 117 +++++++++++++++++- .../apps/job_submissions/test_routers.py | 54 +++++--- 5 files changed, 173 insertions(+), 31 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py index e89840dda..7243e2a6e 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py @@ -5,6 +5,9 @@ from bidict import bidict from loguru import logger +from jobbergate_api.apps.job_scripts.job_script_files import JobScriptFiles + +from jobbergate_api.apps.job_submissions.schemas import JobProperties _IDENTIFICATION_FLAG = "#SBATCH" _INLINE_COMMENT_MARK = "#" @@ -285,20 +288,25 @@ def convert_sbatch_to_slurm_api(input: Dict[str, Any]) -> Dict[str, Any]: return mapped -def get_job_parameters(jobscript: str, **kwargs) -> Dict[str, Any]: +def get_job_parameters(jobscript: str) -> Dict[str, Any]: """ Parse all SBATCH parameters from a job script, map their names to Slurm API parameters, and return them as a key-value pairing dictionary. + """ + return convert_sbatch_to_slurm_api(jobscript_to_dict(jobscript)) + + +def get_job_properties_from_job_script(job_script_id: int, **kwargs) -> JobProperties: + """ + Get the job properties for Slurm REST API from a job script file, given its id. Extra keyword arguments can be used to overwrite any parameter from the job script, like name or current_working_directory. """ - - slurm_parameters = convert_sbatch_to_slurm_api(jobscript_to_dict(jobscript)) - + job_script_files = JobScriptFiles.get_from_s3(job_script_id) + slurm_parameters = get_job_parameters(job_script_files.main_file) merged_parameters = {**slurm_parameters, **kwargs} - - return merged_parameters + return JobProperties.parse_obj(merged_parameters) parser = build_parser() diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py index ccd76b4c1..63c7b927a 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py @@ -17,6 +17,7 @@ searchable_fields, sortable_fields, ) +from jobbergate_api.apps.job_submissions.properties_parser import get_job_properties_from_job_script from jobbergate_api.apps.job_submissions.schemas import ( ActiveJobSubmission, JobSubmissionCreateRequest, @@ -90,6 +91,16 @@ async def job_submission_create( detail=message, ) + try: + job_properties = get_job_properties_from_job_script( + job_submission.job_script_id, **job_submission.execution_parameters.dict(exclude_unset=True) + ) + create_dict["execution_parameters"] = job_properties.dict(exclude_unset=True) + except Exception as e: + message = f"Error extracting execution parameters from job script: {str(e)}" + logger.error(message) + raise HTTPException(status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=message) + logger.debug("Inserting job-submission") async with database.transaction(): diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index 32170279a..70e3dc395 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -284,7 +284,7 @@ class JobSubmissionCreateRequest(BaseModel): job_script_id: int execution_directory: Optional[Path] client_id: Optional[str] - execution_parameters: Optional[JobProperties] + execution_parameters: JobProperties = Field(default_factory=dict) class Config: schema_extra = job_submission_meta_mapper diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py index f2c5635e5..263706d17 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py @@ -1,10 +1,15 @@ +import contextlib import inspect from argparse import ArgumentParser +from pathlib import Path from typing import MutableMapping +from unittest import mock +from pydantic import ValidationError import pytest from bidict import bidict +from jobbergate_api.apps.job_scripts.job_script_files import JobScriptFiles from jobbergate_api.apps.job_submissions.properties_parser import ( _IDENTIFICATION_FLAG, _INLINE_COMMENT_MARK, @@ -17,9 +22,11 @@ build_parser, convert_sbatch_to_slurm_api, get_job_parameters, + get_job_properties_from_job_script, jobscript_to_dict, sbatch_to_slurm, ) +from jobbergate_api.apps.job_submissions.schemas import JobProperties def test_identification_flag(): @@ -384,8 +391,6 @@ def test_get_job_parameters(dummy_slurm_script): in a dictionary. Notice get_job_parameters accepts extra keywords that can be used to overwrite the values from the job script. """ - extra_options = {"name": "name", "current_working_directory": "cwd"} - desired_dict = { "no_kill": True, "requeue": False, @@ -400,13 +405,115 @@ def test_get_job_parameters(dummy_slurm_script): "wait_all_nodes": 0, } - desired_dict.update(extra_options) - - actual_dict = get_job_parameters(dummy_slurm_script, **extra_options) + actual_dict = get_job_parameters(dummy_slurm_script) assert desired_dict == actual_dict +@pytest.fixture +def mock_job_script_files(): + """ + Create a dummy job script file with the given content and mock JobScriptFiles.get_from_s3. + """ + + @contextlib.contextmanager + def _helper(main_file_content): + main_file_name = Path("jobbergate.sh") + job_script_files = JobScriptFiles( + main_file_path=main_file_name, + files={main_file_name: main_file_content}, + ) + with mock.patch( + "jobbergate_api.apps.job_submissions.properties_parser.JobScriptFiles.get_from_s3" + ) as mocked: + mocked.return_value = job_script_files + yield mocked + + return _helper + + +class TestGetJobPropertiesFromJobScript: + """ + Test the get_job_properties_from_job_script function.It covers job properties obtained + from the job script and from the users when creating a job submission. + """ + + def test_base_case(self, mock_job_script_files): + """ + Base case, not SBATCH parameters on the job script and no extra parameters. + """ + job_script_id = 1 + desired_job_properties = JobProperties() + + with mock_job_script_files("almost-empty-file") as mocked: + actual_job_properties = get_job_properties_from_job_script(job_script_id) + mocked.assert_called_once_with(job_script_id) + + assert actual_job_properties == desired_job_properties + + def test_properties_only_from_file(self, mock_job_script_files): + """ + Job properties are obtained only from the job script. + """ + job_script_id = 1 + desired_job_properties = JobProperties(exclusive="exclusive", name="test-test") + + with mock_job_script_files("#SBATCH --exclusive\n#SBATCH -J test-test") as mocked: + actual_job_properties = get_job_properties_from_job_script(job_script_id) + mocked.assert_called_once_with(job_script_id) + + assert actual_job_properties == desired_job_properties + + def test_properties_only_from_arguments(self, mock_job_script_files): + """ + Job properties are obtained only from the extra arguments. + """ + job_script_id = 1 + + job_properties = dict(exclusive="exclusive", name="test-test") + desired_job_properties = JobProperties.parse_obj(job_properties) + + with mock_job_script_files("almost-empty-file") as mocked: + actual_job_properties = get_job_properties_from_job_script( + job_script_id, + **job_properties, + ) + mocked.assert_called_once_with(job_script_id) + + assert actual_job_properties == desired_job_properties + + def test_properties_priority_when_both_are_provided(self, mock_job_script_files): + """ + Job properties are obtained from the job script and from the extra arguments. + + The ones from the extra arguments have priority over the ones from the job script. + """ + job_script_id = 1 + + job_properties = dict(exclusive="exclusive", name="high-priority-test") + desired_job_properties = JobProperties.parse_obj(job_properties) + + with mock_job_script_files("#SBATCH --exclusive\n#SBATCH -J test-test") as mocked: + actual_job_properties = get_job_properties_from_job_script( + job_script_id, + **job_properties, + ) + mocked.assert_called_once_with(job_script_id) + + assert actual_job_properties == desired_job_properties + + def test_properties_fails_with_unknown_field(self, mock_job_script_files): + """ + The function fails when the extra arguments contain unknown fields. + """ + job_script_id = 1 + + with mock_job_script_files("almost-empty-file") as mocked: + with pytest.raises(ValidationError, match="1 validation error for JobProperties"): + get_job_properties_from_job_script(job_script_id, foo="bar") + mocked.assert_called_once_with(job_script_id) + + class TestBidictMapping: """ Integration test with the requirement bidict (used for two-way mapping). diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py index 689236a4f..3f89b58c0 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py @@ -2,6 +2,7 @@ Tests for the /job-submissions/ endpoint. """ import pathlib +from unittest import mock import pytest from fastapi import status @@ -11,7 +12,7 @@ from jobbergate_api.apps.job_scripts.models import job_scripts_table from jobbergate_api.apps.job_submissions.constants import JobSubmissionStatus from jobbergate_api.apps.job_submissions.models import job_submissions_table -from jobbergate_api.apps.job_submissions.schemas import JobSubmissionResponse +from jobbergate_api.apps.job_submissions.schemas import JobProperties, JobSubmissionResponse from jobbergate_api.apps.permissions import Permissions from jobbergate_api.storage import database @@ -58,8 +59,12 @@ async def test_create_job_submission__with_client_id_in_token( create_data.pop("status", None) create_data.pop("client_id", None) - with time_frame() as window: - response = await client.post("/jobbergate/job-submissions/", json=create_data) + with mock.patch( + "jobbergate_api.apps.job_submissions.routers.get_job_properties_from_job_script" + ) as mocked: + mocked.return_value = JobProperties.parse_obj(create_data["execution_parameters"]) + with time_frame() as window: + response = await client.post("/jobbergate/job-submissions/", json=create_data) assert response.status_code == status.HTTP_201_CREATED @@ -117,20 +122,27 @@ async def test_create_job_submission__with_client_id_in_request_body( Permissions.JOB_SUBMISSIONS_EDIT, client_id="dummy-cluster-client", ) - with time_frame() as window: - response = await client.post( - "/jobbergate/job-submissions/", - json=fill_job_submission_data( - job_script_id=inserted_job_script_id, - job_submission_name="sub1", - job_submission_owner_email="owner1@org.com", - client_id="silly-cluster-client", - execution_parameters={ - "name": "job-submission-name", - "comment": "I am a comment", - }, - ), - ) + + execution_parameters = { + "name": "job-submission-name", + "comment": "I am a comment", + } + + with mock.patch( + "jobbergate_api.apps.job_submissions.routers.get_job_properties_from_job_script" + ) as mocked: + mocked.return_value = JobProperties.parse_obj(execution_parameters) + with time_frame() as window: + response = await client.post( + "/jobbergate/job-submissions/", + json=fill_job_submission_data( + job_script_id=inserted_job_script_id, + job_submission_name="sub1", + job_submission_owner_email="owner1@org.com", + client_id="silly-cluster-client", + execution_parameters=execution_parameters, + ), + ) assert response.status_code == status.HTTP_201_CREATED @@ -199,8 +211,12 @@ async def test_create_job_submission__with_execution_directory( create_data.pop("status", None) create_data.pop("client_id", None) - with time_frame() as window: - response = await client.post("/jobbergate/job-submissions/", json=create_data) + with mock.patch( + "jobbergate_api.apps.job_submissions.routers.get_job_properties_from_job_script" + ) as mocked: + mocked.return_value = JobProperties.parse_obj(create_data["execution_parameters"]) + with time_frame() as window: + response = await client.post("/jobbergate/job-submissions/", json=create_data) assert response.status_code == status.HTTP_201_CREATED From 7258c6abc3ca8a6db17974cf08c31bfdf0c409ee Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 5 Dec 2022 18:27:56 -0300 Subject: [PATCH 14/36] fix tests for job submission creation assert if mocked method is called --- .../tests/apps/job_submissions/test_routers.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py index 3f89b58c0..8cf0412e9 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py @@ -65,6 +65,10 @@ async def test_create_job_submission__with_client_id_in_token( mocked.return_value = JobProperties.parse_obj(create_data["execution_parameters"]) with time_frame() as window: response = await client.post("/jobbergate/job-submissions/", json=create_data) + mocked.assert_called_once_with( + inserted_job_script_id, + **create_data["execution_parameters"], + ) assert response.status_code == status.HTTP_201_CREATED @@ -217,6 +221,10 @@ async def test_create_job_submission__with_execution_directory( mocked.return_value = JobProperties.parse_obj(create_data["execution_parameters"]) with time_frame() as window: response = await client.post("/jobbergate/job-submissions/", json=create_data) + mocked.assert_called_once_with( + inserted_job_script_id, + **create_data["execution_parameters"], + ) assert response.status_code == status.HTTP_201_CREATED From 0bf47aec585a26ef494b83828c8ca3e85a3382ae Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 5 Dec 2022 18:55:05 -0300 Subject: [PATCH 15/36] remove test data from test_split_line --- .../tests/apps/job_submissions/test_properties_parser.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py index 263706d17..ccd560b8e 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py @@ -88,7 +88,6 @@ def test_clean_line(line, desired_value): ( ("--help", ["--help"]), ("--abc=0", ["--abc", "0"]), - ("--abc = 0", ["--abc", "0"]), ("-J job_name", ["-J", "job_name"]), ("-v -J job_name", ["-v", "-J", "job_name"]), ("-J job_name -v", ["-J", "job_name", "-v"]), @@ -124,7 +123,7 @@ def dummy_slurm_script(): #SBATCH --mail-user=email@somewhere.com # Where to send mail #SBATCH --mem=1gb # Job memory request #SBATCH --time=00:05:00 # Time limit hrs:min:sec - #SBATCH --output = serial_test_%j.log # Standard output and error log + #SBATCH --output=serial_test_%j.log # Standard output and error log #SBATCH --wait-all-nodes=0 # pwd; hostname; date From 06d34f8621fa5041a9b464fa911bc47d8855880f Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 5 Dec 2022 19:02:40 -0300 Subject: [PATCH 16/36] rename local variable at job_submission_create --- .../jobbergate_api/apps/job_submissions/routers.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py index 63c7b927a..a42e631bf 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py @@ -67,17 +67,17 @@ async def job_submission_create( detail=message, ) - create_dict = dict( + new_job_submission_data: Dict[str, Any] = dict( **job_submission.dict(exclude_unset=True), job_submission_owner_email=identity_claims.email, status=JobSubmissionStatus.CREATED, ) if job_submission.client_id is None: - create_dict.update(client_id=client_id) + new_job_submission_data.update(client_id=client_id) - exec_dir = create_dict.pop("execution_directory", None) + exec_dir = new_job_submission_data.pop("execution_directory", None) if exec_dir is not None: - create_dict.update(execution_directory=str(exec_dir)) + new_job_submission_data.update(execution_directory=str(exec_dir)) select_query = job_scripts_table.select().where(job_scripts_table.c.id == job_submission.job_script_id) logger.trace(f"job_scripts select_query = {render_sql(select_query)}") @@ -95,7 +95,7 @@ async def job_submission_create( job_properties = get_job_properties_from_job_script( job_submission.job_script_id, **job_submission.execution_parameters.dict(exclude_unset=True) ) - create_dict["execution_parameters"] = job_properties.dict(exclude_unset=True) + new_job_submission_data["execution_parameters"] = job_properties.dict(exclude_unset=True) except Exception as e: message = f"Error extracting execution parameters from job script: {str(e)}" logger.error(message) @@ -107,7 +107,7 @@ async def job_submission_create( try: insert_query = job_submissions_table.insert().returning(job_submissions_table) logger.trace(f"job_submissions insert_query = {render_sql(insert_query)}") - job_submission_data = await database.fetch_one(query=insert_query, values=create_dict) + job_submission_data = await database.fetch_one(query=insert_query, values=new_job_submission_data) except INTEGRITY_CHECK_EXCEPTIONS as e: logger.error(f"Reverting database transaction: {str(e)}") From fa832e2e88e15a7c04d5d976bbedc1f4838c74ff Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 5 Dec 2022 19:55:18 -0300 Subject: [PATCH 17/36] update poetry.lock --- jobbergate-api/poetry.lock | 1448 ++++++++++++++++++++---------------- 1 file changed, 797 insertions(+), 651 deletions(-) diff --git a/jobbergate-api/poetry.lock b/jobbergate-api/poetry.lock index fe978b760..d113f24e9 100644 --- a/jobbergate-api/poetry.lock +++ b/jobbergate-api/poetry.lock @@ -1,10 +1,10 @@ [[package]] name = "alembic" -version = "1.7.7" +version = "1.8.1" description = "A database migration tool for SQLAlchemy." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] importlib-metadata = {version = "*", markers = "python_version < \"3.9\""} @@ -17,7 +17,7 @@ tz = ["python-dateutil"] [[package]] name = "anyio" -version = "3.5.0" +version = "3.6.2" description = "High level compatibility layer for multiple asynchronous event loop implementations" category = "main" optional = false @@ -29,8 +29,8 @@ sniffio = ">=1.1" [package.extras] doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=6.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] -trio = ["trio (>=0.16)"] +test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] +trio = ["trio (>=0.16,<0.22)"] [[package]] name = "appnope" @@ -42,7 +42,7 @@ python-versions = "*" [[package]] name = "armasec" -version = "0.11.0" +version = "0.11.3" description = "Injectable FastAPI auth via OIDC" category = "main" optional = false @@ -50,13 +50,13 @@ python-versions = ">=3.6.2,<4.0.0" [package.dependencies] auto-name-enum = ">=2,<3" -fastapi = ">=0.68.0,<0.69.0" +fastapi = ">=0.68" httpx = ">=0,<1" -py-buzz = ">=3.1.0,<4.0.0" -pytest = ">=6.2.5,<7.0.0" -python-jose = {version = ">=3.2.0,<4.0.0", extras = ["cryptography"]} -respx = ">=0.17.1,<0.18.0" -snick = ">=1.3.0,<2.0.0" +py-buzz = ">=3.1,<4.0" +pytest = ">=6,<7" +python-jose = {version = ">=3.2,<4.0", extras = ["cryptography"]} +respx = ">=0,<1" +snick = ">=1.3,<2.0" [[package]] name = "asgi-lifespan" @@ -71,7 +71,7 @@ sniffio = "*" [[package]] name = "asgiref" -version = "3.5.0" +version = "3.5.2" description = "ASGI specs, helper code, and adapters" category = "main" optional = false @@ -95,7 +95,7 @@ test = ["flake8 (>=3.7.9,<3.8.0)", "pycodestyle (>=2.5.0,<2.6.0)", "uvloop (>=0. [[package]] name = "atomicwrites" -version = "1.4.0" +version = "1.4.1" description = "Atomic file writes." category = "main" optional = false @@ -103,17 +103,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "21.4.0" +version = "22.1.0" description = "Classes Without Boilerplate" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.5" [package.extras] -dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope.interface"] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] -tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope.interface"] -tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"] +tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"] +tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"] [[package]] name = "auto-name-enum" @@ -131,6 +131,17 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "backports-zoneinfo" +version = "0.2.1" +description = "Backport of the standard library zoneinfo module" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.extras] +tzdata = ["tzdata"] + [[package]] name = "bidict" version = "0.22.0" @@ -141,18 +152,18 @@ python-versions = ">=3.7" [[package]] name = "black" -version = "22.3.0" +version = "22.10.0" description = "The uncompromising code formatter." category = "dev" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7" [package.dependencies] click = ">=8.0.0" mypy-extensions = ">=0.4.3" pathspec = ">=0.9.0" platformdirs = ">=2" -tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} +tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""} typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""} [package.extras] @@ -163,14 +174,14 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "boto3" -version = "1.24.38" +version = "1.26.23" description = "The AWS SDK for Python" category = "main" optional = false python-versions = ">= 3.7" [package.dependencies] -botocore = ">=1.27.38,<1.28.0" +botocore = ">=1.29.23,<1.30.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.6.0,<0.7.0" @@ -179,7 +190,7 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.27.38" +version = "1.29.23" description = "Low-level, data-driven core of boto 3." category = "main" optional = false @@ -191,19 +202,19 @@ python-dateutil = ">=2.1,<3.0.0" urllib3 = ">=1.25.4,<1.27" [package.extras] -crt = ["awscrt (==0.13.8)"] +crt = ["awscrt (==0.15.3)"] [[package]] name = "certifi" -version = "2021.10.8" +version = "2022.9.24" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "cffi" -version = "1.15.0" +version = "1.15.1" description = "Foreign Function Interface for Python calling C code." category = "main" optional = false @@ -222,11 +233,11 @@ python-versions = ">=3.6.1" [[package]] name = "charset-normalizer" -version = "2.0.12" +version = "2.1.1" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "dev" optional = false -python-versions = ">=3.5.0" +python-versions = ">=3.6.0" [package.extras] unicode-backport = ["unicodedata2"] @@ -249,7 +260,7 @@ styles = ["Pygments (>=1.6)"] [[package]] name = "click" -version = "8.1.2" +version = "8.1.3" description = "Composable command line interface toolkit" category = "main" optional = false @@ -260,11 +271,11 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "colorama" -version = "0.4.4" +version = "0.4.6" description = "Cross-platform colored terminal text." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" [[package]] name = "configobj" @@ -290,7 +301,7 @@ toml = ["toml"] [[package]] name = "cryptography" -version = "36.0.2" +version = "38.0.4" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." category = "main" optional = false @@ -300,12 +311,12 @@ python-versions = ">=3.6" cffi = ">=1.12" [package.extras] -docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx_rtd_theme"] +docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"] docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"] pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"] -sdist = ["setuptools_rust (>=0.11.4)"] +sdist = ["setuptools-rust (>=0.11.4)"] ssh = ["bcrypt (>=3.1.5)"] -test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"] +test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"] [[package]] name = "databases" @@ -336,7 +347,7 @@ python-versions = ">=3.5" [[package]] name = "distlib" -version = "0.3.4" +version = "0.3.6" description = "Distribution utilities" category = "dev" optional = false @@ -377,7 +388,7 @@ tls = ["cryptography (>=3.4.7)", "idna (>=2.0.0)", "pyOpenSSL (>=17.5.0)"] [[package]] name = "ecdsa" -version = "0.17.0" +version = "0.18.0" description = "ECDSA cryptographic signature library (pure python)" category = "main" optional = false @@ -392,8 +403,8 @@ gmpy2 = ["gmpy2"] [[package]] name = "email-validator" -version = "1.1.3" -description = "A robust email syntax and deliverability validation library for Python 2.x/3.x." +version = "1.3.0" +description = "A robust email address syntax and deliverability validation library." category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" @@ -433,15 +444,15 @@ boto3 = ">=1.24.36,<2.0.0" [[package]] name = "filelock" -version = "3.6.0" +version = "3.8.2" description = "A platform independent file lock." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"] -testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"] +docs = ["furo (>=2022.9.29)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"] +testing = ["covdefaults (>=2.2.2)", "coverage (>=6.5)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"] [[package]] name = "flake8" @@ -470,7 +481,7 @@ pydocstyle = ">=2.1" [[package]] name = "freezegun" -version = "1.2.1" +version = "1.2.2" description = "Let your Python tests travel through time" category = "dev" optional = false @@ -481,60 +492,65 @@ python-dateutil = ">=2.7" [[package]] name = "greenlet" -version = "1.1.2" +version = "2.0.1" description = "Lightweight in-process concurrent programming" category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" [package.extras] -docs = ["Sphinx"] +docs = ["Sphinx", "docutils (<0.18)"] +test = ["faulthandler", "objgraph", "psutil"] [[package]] name = "h11" -version = "0.12.0" +version = "0.14.0" description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "httpcore" -version = "0.13.7" +version = "0.16.2" description = "A minimal low-level HTTP client." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -anyio = ">=3.0.0,<4.0.0" -h11 = ">=0.11,<0.13" +anyio = ">=3.0,<5.0" +certifi = "*" +h11 = ">=0.13,<0.15" sniffio = ">=1.0.0,<2.0.0" [package.extras] http2 = ["h2 (>=3,<5)"] +socks = ["socksio (>=1.0.0,<2.0.0)"] [[package]] name = "httpx" -version = "0.18.2" +version = "0.23.1" description = "The next generation HTTP client." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] certifi = "*" -httpcore = ">=0.13.3,<0.14.0" +httpcore = ">=0.15.0,<0.17.0" rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]} sniffio = "*" [package.extras] -brotli = ["brotlicffi (>=1.0.0,<2.0.0)"] -http2 = ["h2 (>=3.0.0,<4.0.0)"] +brotli = ["brotli", "brotlicffi"] +cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<13)"] +http2 = ["h2 (>=3,<5)"] +socks = ["socksio (>=1.0.0,<2.0.0)"] [[package]] name = "identify" -version = "2.4.12" +version = "2.5.9" description = "File identification library for Python" category = "dev" optional = false @@ -545,7 +561,7 @@ license = ["ukkonen"] [[package]] name = "idna" -version = "3.3" +version = "3.4" description = "Internationalized Domain Names in Applications (IDNA)" category = "main" optional = false @@ -553,7 +569,7 @@ python-versions = ">=3.5" [[package]] name = "importlib-metadata" -version = "4.11.3" +version = "5.1.0" description = "Read metadata from Python packages" category = "main" optional = false @@ -563,13 +579,13 @@ python-versions = ">=3.7" zipp = ">=0.5" [package.extras] -docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] perf = ["ipython"] -testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] +testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] [[package]] name = "importlib-resources" -version = "5.6.0" +version = "5.10.0" description = "Read resources from Python packages" category = "main" optional = false @@ -579,8 +595,8 @@ python-versions = ">=3.7" zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] -docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] -testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] +testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [[package]] name = "iniconfig" @@ -592,7 +608,7 @@ python-versions = "*" [[package]] name = "ipython" -version = "7.32.0" +version = "7.34.0" description = "IPython: Productive Interactive Computing" category = "dev" optional = false @@ -639,7 +655,7 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] name = "jedi" -version = "0.18.1" +version = "0.18.2" description = "An autocompletion tool for Python that can be used for text editors." category = "dev" optional = false @@ -649,12 +665,13 @@ python-versions = ">=3.6" parso = ">=0.8.0,<0.9.0" [package.extras] +docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"] qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] -testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"] +testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] [[package]] name = "jinja2" -version = "3.1.1" +version = "3.1.2" description = "A very fast and expressive template engine." category = "main" optional = false @@ -668,7 +685,7 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "jmespath" -version = "1.0.0" +version = "1.0.1" description = "JSON Matching Expressions" category = "main" optional = false @@ -691,7 +708,7 @@ dev = ["Sphinx (>=4.1.1)", "black (>=19.10b0)", "colorama (>=0.3.4)", "docutils [[package]] name = "mako" -version = "1.2.0" +version = "1.2.4" description = "A super-fast templating language that borrows the best ideas from the existing templating languages." category = "main" optional = false @@ -715,7 +732,7 @@ python-versions = ">=3.7" [[package]] name = "matplotlib-inline" -version = "0.1.3" +version = "0.1.6" description = "Inline Matplotlib backend for Jupyter" category = "dev" optional = false @@ -734,7 +751,7 @@ python-versions = "*" [[package]] name = "multidict" -version = "6.0.2" +version = "6.0.3" description = "multidict implementation" category = "main" optional = false @@ -767,7 +784,7 @@ python-versions = "*" [[package]] name = "nest-asyncio" -version = "1.5.5" +version = "1.5.6" description = "Patch asyncio to allow nested event loops" category = "dev" optional = false @@ -775,11 +792,14 @@ python-versions = ">=3.5" [[package]] name = "nodeenv" -version = "1.6.0" +version = "1.7.0" description = "Node.js virtual environment builder" category = "dev" optional = false -python-versions = "*" +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*" + +[package.dependencies] +setuptools = "*" [[package]] name = "packaging" @@ -820,11 +840,11 @@ totp = ["cryptography"] [[package]] name = "pathspec" -version = "0.9.0" +version = "0.10.2" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = ">=3.7" [[package]] name = "pendulum" @@ -851,20 +871,20 @@ ptyprocess = ">=0.5" [[package]] name = "pgcli" -version = "3.4.1" +version = "3.5.0" description = "CLI for Postgres Database. With auto-completion and syntax highlighting." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] cli-helpers = {version = ">=2.2.1", extras = ["styles"]} click = ">=4.1" configobj = ">=5.0.6" pendulum = ">=2.1.0" -pgspecial = ">=1.13.1,<2.0.0" +pgspecial = ">=2.0.0" prompt-toolkit = ">=2.0.6,<4.0.0" -psycopg2 = ">=2.8" +psycopg = ">=3.0.14" Pygments = ">=2.0" setproctitle = ">=1.1.9" sqlparse = ">=0.3.0,<0.5" @@ -875,7 +895,7 @@ sshtunnel = ["sshtunnel (>=0.4.0)"] [[package]] name = "pgspecial" -version = "1.13.1" +version = "2.0.1" description = "Meta-commands handler for Postgres Database." category = "dev" optional = false @@ -883,7 +903,7 @@ python-versions = "*" [package.dependencies] click = ">=4.1" -psycopg2 = ">=2.7.4" +psycopg = ">=3.0.10" sqlparse = ">=0.1.19" [[package]] @@ -896,15 +916,15 @@ python-versions = "*" [[package]] name = "platformdirs" -version = "2.5.1" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +version = "2.5.4" +description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] -test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] +docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"] +test = ["appdirs (==1.4.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] [[package]] name = "pluggy" @@ -928,7 +948,7 @@ python-versions = "*" [[package]] name = "pre-commit" -version = "2.18.1" +version = "2.20.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." category = "dev" optional = false @@ -944,7 +964,7 @@ virtualenv = ">=20.0.8" [[package]] name = "prompt-toolkit" -version = "3.0.29" +version = "3.0.33" description = "Library for building powerful interactive command lines in Python" category = "dev" optional = false @@ -954,12 +974,25 @@ python-versions = ">=3.6.2" wcwidth = "*" [[package]] -name = "psycopg2" -version = "2.9.3" -description = "psycopg2 - Python-PostgreSQL Database Adapter" +name = "psycopg" +version = "3.1.4" +description = "PostgreSQL database adapter for Python" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" + +[package.dependencies] +"backports.zoneinfo" = {version = ">=0.2.0", markers = "python_version < \"3.9\""} +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} +tzdata = {version = "*", markers = "sys_platform == \"win32\""} + +[package.extras] +binary = ["psycopg-binary (==3.1.4)"] +c = ["psycopg-c (==3.1.4)"] +dev = ["black (>=22.3.0)", "dnspython (>=2.1)", "flake8 (>=4.0)", "mypy (>=0.981)", "types-setuptools (>=57.4)", "wheel (>=0.37)"] +docs = ["Sphinx (>=5.0)", "furo (==2022.6.21)", "sphinx-autobuild (>=2021.3.14)", "sphinx-autodoc-typehints (>=1.12)"] +pool = ["psycopg-pool"] +test = ["mypy (>=0.981)", "pproxy (>=2.7)", "pytest (>=6.2.5)", "pytest-asyncio (>=0.17)", "pytest-cov (>=3.0)", "pytest-randomly (>=3.10)"] [[package]] name = "ptyprocess" @@ -1024,14 +1057,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pydantic" -version = "1.9.0" -description = "Data validation and settings management using python 3.6 type hinting" +version = "1.10.2" +description = "Data validation and settings management using python type hints" category = "main" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.7" [package.dependencies] -typing-extensions = ">=3.7.4.3" +typing-extensions = ">=4.1.0" [package.extras] dotenv = ["python-dotenv (>=0.10.4)"] @@ -1061,34 +1094,37 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.11.2" +version = "2.13.0" description = "Pygments is a syntax highlighting package written in Python." category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" + +[package.extras] +plugins = ["importlib-metadata"] [[package]] name = "pyparsing" -version = "3.0.7" -description = "Python parsing module" +version = "3.0.9" +description = "pyparsing module - Classes and methods to define and execute parsing grammars" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.6.8" [package.extras] diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pyproject-flake8" -version = "0.0.1a3" +version = "0.0.1a5" description = "pyproject-flake8 (`pflake8`), a monkey patching wrapper to connect flake8 with pyproject.toml configuration" category = "dev" optional = false python-versions = "*" [package.dependencies] -flake8 = "*" -tomli = {version = "*", markers = "python_version < \"3.11.0a7\""} +flake8 = "<5.0.0" +tomli = {version = "*", markers = "python_version < \"3.11\""} [[package]] name = "pytest" @@ -1166,7 +1202,7 @@ pytest = ">=3.0.0" [[package]] name = "pytest-random-order" -version = "1.0.4" +version = "1.1.0" description = "Randomise the order in which pytest tests are run with some control over the randomness" category = "dev" optional = false @@ -1269,21 +1305,21 @@ python-versions = ">=3.6" [[package]] name = "requests" -version = "2.27.1" +version = "2.28.1" description = "Python HTTP for Humans." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.7, <4" [package.dependencies] certifi = ">=2017.4.17" -charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""} -idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""} +charset-normalizer = ">=2,<3" +idna = ">=2.5,<4" urllib3 = ">=1.21.1,<1.27" [package.extras] -socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] -use-chardet-on-py3 = ["chardet (>=3.0.2,<5)"] +socks = ["PySocks (>=1.5.6,!=1.5.7)"] +use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "respx" @@ -1312,7 +1348,7 @@ idna2008 = ["idna"] [[package]] name = "rsa" -version = "4.8" +version = "4.9" description = "Pure-Python RSA implementation" category = "main" optional = false @@ -1349,7 +1385,7 @@ starkbank-ecdsa = ">=2.0.1" [[package]] name = "sentry-sdk" -version = "1.5.8" +version = "1.11.1" description = "Python client for Sentry (https://sentry.io)" category = "main" optional = false @@ -1357,7 +1393,7 @@ python-versions = "*" [package.dependencies] certifi = "*" -urllib3 = ">=1.10.0" +urllib3 = {version = ">=1.26.11", markers = "python_version >= \"3.6\""} [package.extras] aiohttp = ["aiohttp (>=3.5)"] @@ -1367,26 +1403,29 @@ celery = ["celery (>=3)"] chalice = ["chalice (>=1.16.0)"] django = ["django (>=1.8)"] falcon = ["falcon (>=1.4)"] +fastapi = ["fastapi (>=0.79.0)"] flask = ["blinker (>=1.1)", "flask (>=0.11)"] httpx = ["httpx (>=0.16.0)"] pure-eval = ["asttokens", "executing", "pure-eval"] +pymongo = ["pymongo (>=3.1)"] pyspark = ["pyspark (>=2.4.4)"] quart = ["blinker (>=1.1)", "quart (>=0.16.1)"] rq = ["rq (>=0.6)"] sanic = ["sanic (>=0.8)"] sqlalchemy = ["sqlalchemy (>=1.2)"] +starlette = ["starlette (>=0.19.1)"] tornado = ["tornado (>=5)"] [[package]] name = "setproctitle" -version = "1.2.2" +version = "1.3.2" description = "A Python module to customize the process title" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] -test = ["pytest (>=6.1,<6.2)"] +test = ["pytest"] [[package]] name = "setuptools" @@ -1422,11 +1461,11 @@ pprintpp = ">=0.4.0,<0.5.0" [[package]] name = "sniffio" -version = "1.2.0" +version = "1.3.0" description = "Sniff out which async library your code is running under" category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.7" [[package]] name = "snowballstemmer" @@ -1438,7 +1477,7 @@ python-versions = "*" [[package]] name = "sqlalchemy" -version = "1.4.34" +version = "1.4.44" description = "Database Abstraction Library" category = "main" optional = false @@ -1452,7 +1491,7 @@ aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"] asyncio = ["greenlet (!=0.4.17)"] asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"] -mariadb-connector = ["mariadb (>=1.0.1)"] +mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"] mssql = ["pyodbc"] mssql-pymssql = ["pymssql"] mssql-pyodbc = ["pyodbc"] @@ -1462,7 +1501,7 @@ mysql-connector = ["mysql-connector-python"] oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"] postgresql = ["psycopg2 (>=2.7)"] postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"] -postgresql-pg8000 = ["pg8000 (>=1.16.6)"] +postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"] postgresql-psycopg2binary = ["psycopg2-binary"] postgresql-psycopg2cffi = ["psycopg2cffi"] pymysql = ["pymysql", "pymysql (<1)"] @@ -1482,7 +1521,7 @@ typing-extensions = ">=3.7.4" [[package]] name = "sqlparse" -version = "0.4.2" +version = "0.4.3" description = "A non-validating SQL parser." category = "dev" optional = false @@ -1490,7 +1529,7 @@ python-versions = ">=3.5" [[package]] name = "starkbank-ecdsa" -version = "2.0.3" +version = "2.2.0" description = "A lightweight and fast pure python ECDSA library" category = "main" optional = false @@ -1539,18 +1578,19 @@ python-versions = ">=3.7" [[package]] name = "traitlets" -version = "5.1.1" +version = "5.6.0" description = "Traitlets Python configuration system" category = "dev" optional = false python-versions = ">=3.7" [package.extras] -test = ["pytest"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] +test = ["pre-commit", "pytest"] [[package]] name = "typer" -version = "0.4.1" +version = "0.4.2" description = "Typer, build great CLIs. Easy to code. Based on Python type hints." category = "main" optional = false @@ -1561,29 +1601,37 @@ click = ">=7.1.1,<9.0.0" [package.extras] all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"] -dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)"] +dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"] doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"] test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "shellingham (>=1.3.0,<2.0.0)"] [[package]] name = "typing-extensions" -version = "4.1.1" -description = "Backported and Experimental Type Hints for Python 3.6+" +version = "4.4.0" +description = "Backported and Experimental Type Hints for Python 3.7+" category = "main" optional = false -python-versions = 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"httptools (>=0.2.0,<0.3.0)", [[package]] name = "virtualenv" -version = "20.14.0" +version = "20.17.1" description = "Virtual Python Environment builder" category = "dev" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = ">=3.6" [package.dependencies] -distlib = ">=0.3.1,<1" -filelock = ">=3.2,<4" -platformdirs = ">=2,<3" -six = ">=1.9.0,<2" +distlib = ">=0.3.6,<1" +filelock = ">=3.4.1,<4" +platformdirs = ">=2.4,<3" [package.extras] -docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=21.3)"] -testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "packaging (>=20.0)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)"] +docs = ["proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-argparse (>=0.3.2)", "sphinx-rtd-theme (>=1)", "towncrier (>=22.8)"] +testing = 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jobbergate-api/poetry.lock | 1434 ++++++++++++++++-------------------- 1 file changed, 645 insertions(+), 789 deletions(-) diff --git a/jobbergate-api/poetry.lock b/jobbergate-api/poetry.lock index d113f24e9..f61a2cbf7 100644 --- a/jobbergate-api/poetry.lock +++ b/jobbergate-api/poetry.lock @@ -1,10 +1,10 @@ [[package]] name = "alembic" -version = "1.8.1" +version = "1.7.7" description = "A database migration tool for SQLAlchemy." category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.6" [package.dependencies] importlib-metadata = {version = "*", markers = "python_version < \"3.9\""} @@ -17,7 +17,7 @@ tz = ["python-dateutil"] [[package]] name = "anyio" -version = "3.6.2" +version = "3.5.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" category = "main" optional = false @@ -29,8 +29,8 @@ sniffio = ">=1.1" [package.extras] doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] 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package which provides cryptographic recipes and primitives to Python developers." category = "main" optional = false @@ -311,12 +300,12 @@ python-versions = ">=3.6" cffi = ">=1.12" [package.extras] -docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"] +docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx_rtd_theme"] docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"] pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"] -sdist = ["setuptools-rust (>=0.11.4)"] +sdist = ["setuptools_rust (>=0.11.4)"] ssh = ["bcrypt (>=3.1.5)"] -test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"] +test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"] [[package]] name = "databases" @@ -347,7 +336,7 @@ python-versions = ">=3.5" [[package]] name = "distlib" -version = "0.3.6" +version = "0.3.4" description = "Distribution utilities" category = "dev" optional = false @@ -388,7 +377,7 @@ tls = ["cryptography (>=3.4.7)", "idna (>=2.0.0)", "pyOpenSSL (>=17.5.0)"] [[package]] name = "ecdsa" -version = "0.18.0" +version = "0.17.0" description = "ECDSA cryptographic signature library (pure python)" category = "main" optional = false @@ -403,8 +392,8 @@ gmpy2 = ["gmpy2"] [[package]] name = "email-validator" -version = "1.3.0" -description = "A robust email address syntax and deliverability validation library." +version = "1.1.3" +description = "A robust email syntax and deliverability validation library for Python 2.x/3.x." category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" @@ -444,15 +433,15 @@ boto3 = ">=1.24.36,<2.0.0" [[package]] name = "filelock" -version = "3.8.2" +version = "3.6.0" description = "A platform independent file lock." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2022.9.29)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"] -testing = ["covdefaults (>=2.2.2)", "coverage (>=6.5)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"] +testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"] [[package]] name = "flake8" @@ -481,7 +470,7 @@ pydocstyle = ">=2.1" [[package]] name = "freezegun" -version = "1.2.2" +version = "1.2.1" description = "Let your Python tests travel through time" category = "dev" optional = false @@ -492,65 +481,60 @@ python-dateutil = ">=2.7" [[package]] name = "greenlet" -version = "2.0.1" +version = "1.1.2" description = "Lightweight in-process concurrent programming" category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" [package.extras] -docs = ["Sphinx", "docutils (<0.18)"] -test = ["faulthandler", "objgraph", "psutil"] +docs = ["Sphinx"] [[package]] name = "h11" -version = "0.14.0" +version = "0.12.0" description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.6" [[package]] name = "httpcore" -version = "0.16.2" +version = "0.13.7" description = "A minimal low-level HTTP client." category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.6" [package.dependencies] -anyio = ">=3.0,<5.0" -certifi = "*" -h11 = ">=0.13,<0.15" +anyio = ">=3.0.0,<4.0.0" +h11 = ">=0.11,<0.13" sniffio = ">=1.0.0,<2.0.0" [package.extras] http2 = ["h2 (>=3,<5)"] -socks = ["socksio (>=1.0.0,<2.0.0)"] [[package]] name = "httpx" -version = "0.23.1" +version = "0.18.2" description = "The next generation HTTP client." category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.6" [package.dependencies] certifi = "*" -httpcore = ">=0.15.0,<0.17.0" +httpcore = ">=0.13.3,<0.14.0" rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]} sniffio = "*" [package.extras] -brotli = ["brotli", "brotlicffi"] -cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<13)"] -http2 = ["h2 (>=3,<5)"] -socks = ["socksio (>=1.0.0,<2.0.0)"] +brotli = ["brotlicffi (>=1.0.0,<2.0.0)"] +http2 = ["h2 (>=3.0.0,<4.0.0)"] [[package]] name = "identify" -version = "2.5.9" +version = "2.4.12" description = "File identification library for Python" category = "dev" optional = false @@ -561,7 +545,7 @@ license = ["ukkonen"] [[package]] name = "idna" -version = "3.4" +version = "3.3" description = "Internationalized Domain Names in Applications (IDNA)" category = "main" optional = false @@ -569,7 +553,7 @@ python-versions = ">=3.5" [[package]] name = "importlib-metadata" -version = "5.1.0" +version = "4.11.3" description = "Read metadata from Python packages" category = "main" optional = false @@ -579,13 +563,13 @@ python-versions = ">=3.7" zipp = ">=0.5" [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] +docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] perf = ["ipython"] -testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] +testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] [[package]] name = "importlib-resources" -version = "5.10.0" +version = "5.6.0" description = "Read resources from Python packages" category = "main" optional = false @@ -595,8 +579,8 @@ python-versions = ">=3.7" zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] -testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] +testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [[package]] name = "iniconfig" @@ -608,7 +592,7 @@ python-versions = "*" [[package]] name = "ipython" -version = "7.34.0" +version = "7.32.0" description = "IPython: Productive Interactive Computing" category = "dev" optional = false @@ -655,7 +639,7 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] name = "jedi" -version = "0.18.2" +version = "0.18.1" description = "An autocompletion tool for Python that can be used for text editors." category = "dev" optional = false @@ -665,13 +649,12 @@ python-versions = ">=3.6" parso = ">=0.8.0,<0.9.0" [package.extras] -docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"] qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] -testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] +testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"] [[package]] name = "jinja2" -version = "3.1.2" +version = "3.1.1" description = "A very fast and expressive template engine." category = "main" optional = false @@ -685,7 +668,7 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "jmespath" -version = "1.0.1" +version = "1.0.0" description = "JSON Matching Expressions" category = "main" optional = false @@ -708,7 +691,7 @@ dev = ["Sphinx (>=4.1.1)", "black (>=19.10b0)", "colorama (>=0.3.4)", "docutils [[package]] name = "mako" -version = "1.2.4" +version = "1.2.0" description = "A super-fast templating language that borrows the best ideas from the existing templating languages." category = "main" optional = false @@ -732,7 +715,7 @@ python-versions = ">=3.7" [[package]] name = "matplotlib-inline" -version = "0.1.6" +version = "0.1.3" description = "Inline Matplotlib backend for Jupyter" category = "dev" optional = false @@ -751,7 +734,7 @@ python-versions = "*" [[package]] name = "multidict" -version = "6.0.3" +version = "6.0.2" description = "multidict implementation" category = "main" optional = false @@ -784,7 +767,7 @@ python-versions = "*" [[package]] name = "nest-asyncio" -version = "1.5.6" +version = "1.5.5" description = "Patch asyncio to allow nested event loops" category = "dev" optional = false @@ -792,14 +775,11 @@ python-versions = ">=3.5" [[package]] name = "nodeenv" -version = "1.7.0" +version = "1.6.0" description = "Node.js virtual environment builder" category = "dev" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*" - -[package.dependencies] -setuptools = "*" +python-versions = "*" [[package]] name = "packaging" @@ -840,11 +820,11 @@ totp = ["cryptography"] [[package]] name = "pathspec" -version = "0.10.2" +version = "0.9.0" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false -python-versions = ">=3.7" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" [[package]] name = "pendulum" @@ -871,20 +851,20 @@ ptyprocess = ">=0.5" [[package]] name = "pgcli" -version = "3.5.0" +version = "3.4.1" description = "CLI for Postgres Database. With auto-completion and syntax highlighting." category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.6" [package.dependencies] cli-helpers = {version = ">=2.2.1", extras = ["styles"]} click = ">=4.1" configobj = ">=5.0.6" pendulum = ">=2.1.0" -pgspecial = ">=2.0.0" +pgspecial = ">=1.13.1,<2.0.0" prompt-toolkit = ">=2.0.6,<4.0.0" -psycopg = ">=3.0.14" +psycopg2 = ">=2.8" Pygments = ">=2.0" setproctitle = ">=1.1.9" sqlparse = ">=0.3.0,<0.5" @@ -895,7 +875,7 @@ sshtunnel = ["sshtunnel (>=0.4.0)"] [[package]] name = "pgspecial" -version = "2.0.1" +version = "1.13.1" description = "Meta-commands handler for Postgres Database." category = "dev" optional = false @@ -903,7 +883,7 @@ python-versions = "*" [package.dependencies] click = ">=4.1" -psycopg = ">=3.0.10" +psycopg2 = ">=2.7.4" sqlparse = ">=0.1.19" [[package]] @@ -916,15 +896,15 @@ python-versions = "*" [[package]] name = "platformdirs" -version = "2.5.4" -description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +version = "2.5.1" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"] -test = ["appdirs (==1.4.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] +docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] +test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] [[package]] name = "pluggy" @@ -948,7 +928,7 @@ python-versions = "*" [[package]] name = "pre-commit" -version = "2.20.0" +version = "2.18.1" description = "A framework for managing and maintaining multi-language pre-commit hooks." category = "dev" optional = false @@ -964,7 +944,7 @@ virtualenv = ">=20.0.8" [[package]] name = "prompt-toolkit" -version = "3.0.33" +version = "3.0.29" description = "Library for building powerful interactive command lines in Python" category = "dev" optional = false @@ -974,25 +954,12 @@ python-versions = ">=3.6.2" wcwidth = "*" [[package]] -name = "psycopg" -version = "3.1.4" -description = "PostgreSQL database adapter for Python" +name = "psycopg2" +version = "2.9.3" +description = "psycopg2 - Python-PostgreSQL Database Adapter" category = "dev" optional = false -python-versions = ">=3.7" - -[package.dependencies] -"backports.zoneinfo" = {version = ">=0.2.0", markers = "python_version < \"3.9\""} -typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} -tzdata = {version = "*", markers = "sys_platform == \"win32\""} - -[package.extras] -binary = ["psycopg-binary (==3.1.4)"] -c = ["psycopg-c (==3.1.4)"] -dev = ["black (>=22.3.0)", "dnspython (>=2.1)", "flake8 (>=4.0)", "mypy (>=0.981)", "types-setuptools (>=57.4)", "wheel (>=0.37)"] -docs = ["Sphinx (>=5.0)", "furo (==2022.6.21)", "sphinx-autobuild (>=2021.3.14)", "sphinx-autodoc-typehints (>=1.12)"] -pool = ["psycopg-pool"] -test = ["mypy (>=0.981)", "pproxy (>=2.7)", "pytest (>=6.2.5)", "pytest-asyncio (>=0.17)", "pytest-cov (>=3.0)", "pytest-randomly (>=3.10)"] +python-versions = ">=3.6" [[package]] name = "ptyprocess" @@ -1057,14 +1024,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pydantic" -version = "1.10.2" -description = "Data validation and settings management using python type hints" +version = "1.9.0" +description = "Data validation and settings management using python 3.6 type hinting" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.6.1" [package.dependencies] -typing-extensions = ">=4.1.0" +typing-extensions = ">=3.7.4.3" [package.extras] dotenv = ["python-dotenv (>=0.10.4)"] @@ -1094,37 +1061,34 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.13.0" +version = "2.11.2" description = "Pygments is a syntax highlighting package written in Python." category = "dev" optional = false -python-versions = ">=3.6" - -[package.extras] -plugins = ["importlib-metadata"] +python-versions = ">=3.5" [[package]] name = "pyparsing" -version = "3.0.9" -description = "pyparsing module - Classes and methods to define and execute parsing grammars" +version = "3.0.7" +description = "Python parsing module" category = "main" optional = false -python-versions = ">=3.6.8" +python-versions = ">=3.6" [package.extras] diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pyproject-flake8" -version = "0.0.1a5" +version = "0.0.1a3" description = "pyproject-flake8 (`pflake8`), a monkey patching wrapper to connect flake8 with pyproject.toml configuration" category = "dev" optional = false python-versions = "*" [package.dependencies] -flake8 = "<5.0.0" -tomli = {version = "*", markers = "python_version < \"3.11\""} +flake8 = "*" +tomli = {version = "*", markers = "python_version < \"3.11.0a7\""} [[package]] name = "pytest" @@ -1202,7 +1166,7 @@ pytest = ">=3.0.0" [[package]] name = "pytest-random-order" -version = "1.1.0" +version = "1.0.4" description = "Randomise the order in which pytest tests are run with some control over the randomness" category = "dev" optional = false @@ -1305,21 +1269,21 @@ python-versions = ">=3.6" [[package]] name = "requests" -version = "2.28.1" +version = "2.27.1" description = "Python HTTP for Humans." category = "dev" optional = false -python-versions = ">=3.7, <4" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [package.dependencies] certifi = ">=2017.4.17" -charset-normalizer = ">=2,<3" -idna = ">=2.5,<4" +charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""} +idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""} urllib3 = ">=1.21.1,<1.27" [package.extras] -socks = ["PySocks (>=1.5.6,!=1.5.7)"] -use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] +socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] +use-chardet-on-py3 = ["chardet (>=3.0.2,<5)"] [[package]] name = "respx" @@ -1348,7 +1312,7 @@ idna2008 = ["idna"] [[package]] name = "rsa" -version = "4.9" +version = "4.8" description = "Pure-Python RSA implementation" category = "main" optional = false @@ -1385,7 +1349,7 @@ starkbank-ecdsa = ">=2.0.1" [[package]] name = "sentry-sdk" -version = "1.11.1" +version = "1.5.8" description = "Python client for Sentry (https://sentry.io)" category = "main" optional = false @@ -1393,7 +1357,7 @@ python-versions = "*" [package.dependencies] certifi = "*" -urllib3 = {version = ">=1.26.11", markers = "python_version >= \"3.6\""} +urllib3 = ">=1.10.0" [package.extras] aiohttp = ["aiohttp (>=3.5)"] @@ -1403,29 +1367,26 @@ celery = ["celery (>=3)"] chalice = ["chalice (>=1.16.0)"] django = ["django (>=1.8)"] falcon = ["falcon (>=1.4)"] -fastapi = ["fastapi (>=0.79.0)"] flask = ["blinker (>=1.1)", "flask (>=0.11)"] httpx = ["httpx (>=0.16.0)"] pure-eval = ["asttokens", "executing", "pure-eval"] -pymongo = ["pymongo (>=3.1)"] pyspark = ["pyspark (>=2.4.4)"] quart = ["blinker (>=1.1)", "quart (>=0.16.1)"] rq = ["rq (>=0.6)"] sanic = ["sanic (>=0.8)"] sqlalchemy = ["sqlalchemy (>=1.2)"] -starlette = ["starlette (>=0.19.1)"] tornado = ["tornado (>=5)"] [[package]] name = "setproctitle" -version = "1.3.2" +version = "1.2.2" description = "A Python module to customize the process title" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.6" [package.extras] -test = ["pytest"] +test = ["pytest (>=6.1,<6.2)"] [[package]] name = "setuptools" @@ -1461,11 +1422,11 @@ pprintpp = ">=0.4.0,<0.5.0" [[package]] name = "sniffio" -version = "1.3.0" +version = "1.2.0" description = "Sniff out which async library your code is running under" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.5" [[package]] name = "snowballstemmer" @@ -1477,7 +1438,7 @@ python-versions = "*" [[package]] name = "sqlalchemy" -version = "1.4.44" +version = "1.4.34" description = "Database Abstraction Library" category = "main" optional = false @@ -1491,7 +1452,7 @@ aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"] asyncio = ["greenlet (!=0.4.17)"] asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"] -mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"] +mariadb-connector = ["mariadb (>=1.0.1)"] mssql = ["pyodbc"] mssql-pymssql = ["pymssql"] mssql-pyodbc = ["pyodbc"] @@ -1501,7 +1462,7 @@ mysql-connector = ["mysql-connector-python"] oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"] postgresql = ["psycopg2 (>=2.7)"] postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"] -postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"] +postgresql-pg8000 = ["pg8000 (>=1.16.6)"] postgresql-psycopg2binary = ["psycopg2-binary"] postgresql-psycopg2cffi = ["psycopg2cffi"] pymysql = ["pymysql", "pymysql (<1)"] @@ -1521,7 +1482,7 @@ typing-extensions = ">=3.7.4" [[package]] name = "sqlparse" -version = "0.4.3" +version = "0.4.2" description = "A non-validating SQL parser." category = "dev" optional = false @@ -1529,7 +1490,7 @@ python-versions = ">=3.5" [[package]] name = "starkbank-ecdsa" -version = "2.2.0" +version = "2.0.3" description = "A lightweight and fast pure python ECDSA library" category = "main" optional = false @@ -1578,19 +1539,18 @@ python-versions = ">=3.7" [[package]] name = "traitlets" -version = "5.6.0" +version = "5.1.1" description = "Traitlets Python configuration system" category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] -test = ["pre-commit", "pytest"] +test = ["pytest"] [[package]] name = "typer" -version = "0.4.2" +version = "0.4.1" description = "Typer, build great CLIs. Easy to code. Based on Python type hints." category = "main" optional = false @@ -1601,37 +1561,29 @@ click = ">=7.1.1,<9.0.0" [package.extras] all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"] -dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"] +dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)"] doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"] test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "shellingham (>=1.3.0,<2.0.0)"] [[package]] name = "typing-extensions" -version = "4.4.0" -description = "Backported and Experimental Type Hints for Python 3.7+" +version = "4.1.1" +description = "Backported and Experimental Type Hints for Python 3.6+" category = "main" optional = false -python-versions = 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b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py @@ -75,11 +75,16 @@ async def test_create_job_submission__with_client_id_in_token( count = await database.fetch_all("SELECT COUNT(*) FROM job_submissions") assert count[0][0] == 1 - id_rows = await database.fetch_all("SELECT id FROM job_submissions") - assert len(id_rows) == 1 - job_submission = JobSubmissionResponse(**response.json()) - assert job_submission.id == id_rows[0][0] + + # Check that the response correspond to the entry in the database + job_submission_raw_data = await database.fetch_one( + query=job_submissions_table.select().where(job_submissions_table.c.id == 1) + ) + assert job_submission == JobSubmissionResponse(**job_submission_raw_data) # type: ignore + + # Check that each field is correctly set + assert job_submission.id == 1 assert job_submission.job_submission_name == "sub1" assert job_submission.job_submission_owner_email == "owner1@org.com" assert job_submission.job_submission_description is None @@ -153,11 +158,16 @@ async def test_create_job_submission__with_client_id_in_request_body( count = await database.fetch_all("SELECT COUNT(*) FROM job_submissions") assert count[0][0] == 1 - id_rows = await database.fetch_all("SELECT id FROM job_submissions") - assert len(id_rows) == 1 - job_submission = JobSubmissionResponse(**response.json()) - assert job_submission.id == id_rows[0][0] + + # Check that the response correspond to the entry in the database + job_submission_raw_data = await database.fetch_one( + query=job_submissions_table.select().where(job_submissions_table.c.id == 1) + ) + assert job_submission == JobSubmissionResponse(**job_submission_raw_data) # type: ignore + + # Check that each field is correctly set + assert job_submission.id == 1 assert job_submission.job_submission_name == "sub1" assert job_submission.job_submission_owner_email == "owner1@org.com" assert job_submission.job_submission_description is None @@ -231,11 +241,15 @@ async def test_create_job_submission__with_execution_directory( count = await database.fetch_all("SELECT COUNT(*) FROM job_submissions") assert count[0][0] == 1 - id_rows = await database.fetch_all("SELECT id FROM job_submissions") - assert len(id_rows) == 1 - job_submission = JobSubmissionResponse(**response.json()) - assert job_submission.id == id_rows[0][0] + + # Check that the response correspond to the entry in the database + job_submission_raw_data = await database.fetch_one( + query=job_submissions_table.select().where(job_submissions_table.c.id == 1) + ) + assert job_submission == JobSubmissionResponse(**job_submission_raw_data) # type: ignore + + assert job_submission.id == 1 assert job_submission.job_submission_name == "sub1" assert job_submission.job_submission_owner_email == "owner1@org.com" assert job_submission.job_submission_description is None From 614ed6091409ceb714e8ba46aa0eb607b0308dea Mon Sep 17 00:00:00 2001 From: fschuch Date: Tue, 6 Dec 2022 12:19:56 -0300 Subject: [PATCH 20/36] fix lint --- .../apps/job_submissions/properties_parser.py | 55 +++++++------ .../job_submissions/test_properties_parser.py | 80 ++++++++++--------- 2 files changed, 73 insertions(+), 62 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py index 7243e2a6e..8e1851025 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py @@ -1,3 +1,6 @@ +""" +Parser for Slurm REST API parameters from SBATCH parameters at the job script file. +""" from argparse import ArgumentParser from dataclasses import dataclass, field from itertools import chain @@ -5,8 +8,8 @@ from bidict import bidict from loguru import logger -from jobbergate_api.apps.job_scripts.job_script_files import JobScriptFiles +from jobbergate_api.apps.job_scripts.job_script_files import JobScriptFiles from jobbergate_api.apps.job_submissions.schemas import JobProperties _IDENTIFICATION_FLAG = "#SBATCH" @@ -22,26 +25,28 @@ def _flagged_line(line: str) -> bool: def _clean_line(line: str) -> str: """ - Clean the provided line by removing the - identification flag at the beginning of the line, - then remove the inline comment mark and anything - after it, and finally strip white spaces at both sides. + Clean the provided line. + + It includes removing the identification flag at the beginning of the line, + then remove the inline comment mark and anything after it, and finally strip white spaces at both sides. """ return line.lstrip(_IDENTIFICATION_FLAG).split(_INLINE_COMMENT_MARK)[0].strip() def _split_line(line: str) -> List[str]: """ - Split the provided line at the `=` character if it is found at the line, - otherwise split at the white spaces. This procedure is important because - it is the way argparse expects to receive the parameters. + Split the provided line at the equal and with spaces characters. + + This procedure is important because it is the way argparse expects to receive the parameters. """ return line.replace("=", " ").split() def _clean_jobscript(jobscript: str) -> Iterator[str]: """ - Transform a job script string by filtering only the lines that start with + Transform a job script string. + + It is done by filtering only the lines that start with the identification flag and mapping a cleaning procedure to them in order to remove the identification flag, remove inline comments, and strip extra white spaces. Finally, split each pair of parameter/value and chain them @@ -56,8 +61,9 @@ def _clean_jobscript(jobscript: str) -> Iterator[str]: @dataclass(frozen=True) class SbatchToSlurm: """ - Store the information for each parameter, including its name at Slurm API - and SBATCH, besides any extra argument this parameter needs when added to + Store the information for each parameter, including its name at Slurm API and SBATCH. + + Besides that, any extra argument this parameter needs when added to the parser. This information is used to build the jobscript/SBATCH parser and the two-way mapping between Slurm API and SBATCH names. """ @@ -194,14 +200,14 @@ class SbatchToSlurm: class ArgumentParserCustomExit(ArgumentParser): """ Custom implementation of the built-in class for argument parsing. + The sys.exit triggered by the original code is replaced by a ValueError, besides some friendly logging messages. """ def exit(self, status=0, message=None): """ - Raise ValueError when parsing invalid parameters or if the type of their - values is not correct. + Raise ValueError when parsing invalid parameters or if the type of their values is not correct. """ log_message = f"Argparse exit status {status}: {message}" if status: @@ -213,8 +219,7 @@ def exit(self, status=0, message=None): def build_parser() -> ArgumentParser: """ - Build an ArgumentParser to handle all SBATCH - parameters declared at sbatch_to_slurm. + Build an ArgumentParser to handle all SBATCH parameters declared at sbatch_to_slurm. """ parser = ArgumentParserCustomExit() for item in sbatch_to_slurm: @@ -227,8 +232,7 @@ def build_parser() -> ArgumentParser: def build_mapping_sbatch_to_slurm() -> bidict: """ - Create a mapper that can translate both ways between the parameter - names expected by Slurm REST API and SBATCH. + Create a mapper to translate in both ways between the names expected by Slurm REST API and SBATCH. """ mapping = bidict() @@ -242,8 +246,9 @@ def build_mapping_sbatch_to_slurm() -> bidict: def jobscript_to_dict(jobscript: str) -> Dict[str, Union[str, bool]]: """ - Extract the SBATCH params from a given job script and return them in a - dictionary for mapping the parameter names to their values. + Extract the SBATCH params from a given job script. + + It returns them in a dictionary for mapping the parameter names to their values. Raise ValueError if any of the parameters are unknown to the parser. """ @@ -261,13 +266,12 @@ def jobscript_to_dict(jobscript: str) -> Dict[str, Union[str, bool]]: def convert_sbatch_to_slurm_api(input: Dict[str, Any]) -> Dict[str, Any]: """ - Take a dictionary containing key-value pairing of SBATCH parameter name - to value and change the keys to Slurm API parameter name while keeping - the values intact. + Take a dictionary containing key-value pairing of SBATCH parameter name space to Slurm API namespace. + + Notice the values should not be affected. Raise KeyError if any of the keys are unknown to the mapper. """ - mapped = {} unknown_keys = [] @@ -290,8 +294,9 @@ def convert_sbatch_to_slurm_api(input: Dict[str, Any]) -> Dict[str, Any]: def get_job_parameters(jobscript: str) -> Dict[str, Any]: """ - Parse all SBATCH parameters from a job script, map their names to Slurm API - parameters, and return them as a key-value pairing dictionary. + Parse all SBATCH parameters from a job script, map their names to Slurm API parameters. + + They are returned as a key-value pairing dictionary. """ return convert_sbatch_to_slurm_api(jobscript_to_dict(jobscript)) diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py index ccd560b8e..48f0f8fd1 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py @@ -1,13 +1,16 @@ +""" +Test the properties parser module. +""" import contextlib import inspect from argparse import ArgumentParser from pathlib import Path from typing import MutableMapping from unittest import mock -from pydantic import ValidationError import pytest from bidict import bidict +from pydantic import ValidationError from jobbergate_api.apps.job_scripts.job_script_files import JobScriptFiles from jobbergate_api.apps.job_submissions.properties_parser import ( @@ -76,8 +79,9 @@ def test_flagged_line(line, desired_value): ) def test_clean_line(line, desired_value): """ - Check if the provided lines are cleaned properly, i.e., - identification flag, inline comments, and comment mark are all removed. + Check if the provided lines are cleaned properly. + + I.e., identification flag, inline comments, and comment mark are all removed. """ actual_value = _clean_line(line) assert actual_value == desired_value @@ -98,9 +102,9 @@ def test_clean_line(line, desired_value): ) def test_split_line(line, desired_value): """ - Check if the provided lines are splitted properly at white spaces and equal - character. This procedure is important because it is the way argparse - expects to receive the parameters. + Check if the provided lines are splitted properly at white spaces and equal character. + + This procedure is important because it is the way argparse expects to receive the parameters. """ actual_value = _split_line(line) assert actual_value == desired_value @@ -141,6 +145,7 @@ def dummy_slurm_script(): def test_clean_jobscript(dummy_slurm_script): """ Check if all sbatch parameters are correctly extracted from a job script. + This operation combines many of the functions tested above (filter, clean, and slit the parameters on each line). """ @@ -173,8 +178,7 @@ def test_clean_jobscript(dummy_slurm_script): @pytest.mark.parametrize("item", sbatch_to_slurm) class TestSbatchToSlurmList: """ - Test all the fields of the objects SbatchToSlurm that are - stored in the list sbatch_to_slurm. + Test all the fields of the objects SbatchToSlurm that are stored in the list sbatch_to_slurm. """ def test_slurmrestd_var_name__is_string(self, item): @@ -204,8 +208,9 @@ def test_sbatch__starts_with_double_hyphen(self, item): def test_sbatch__is_not_empty(self, item): """ - Check if the field sbatch is not empty by asserting that it has more - than three characters, since it starts with a double hyphen. + Check if the field sbatch is not empty by asserting that it has more than three characters. + + Notice it is supposed to start with a double hyphen. """ assert len(item.sbatch) >= 3 @@ -230,8 +235,7 @@ def test_sbatch_short__starts_with_hyphen(self, item): def test_sbatch_short__is_not_empty(self, item): """ - Check if of the optional field sbatch_short is equal to two, since it - should be a hyphen and a letter. + Check if of the optional field sbatch_short is equal to two, since it should be a hyphen and a letter. """ if item.sbatch_short: assert len(item.sbatch_short) == 2 @@ -262,9 +266,10 @@ def test_argparser_param__is_valid_for_parser(self, item): @pytest.mark.parametrize("field", ["slurmrestd_var_name", "sbatch", "sbatch_short"]) def test_sbatch_to_slurm_list__contains_only_unique_values(field): """ - Test that any given field has no duplicated values for all parameters stored - at sbatch_to_slurm. This aims to avoid ambiguity at the SBATCH argparser and - the two-way mapping between SBATCH and Slurm Rest API namespaces. + Test that any given field has no duplicated values for all parameters stored at sbatch_to_slurm. + + This aims to avoid ambiguity at the SBATCH argparser and the two-way mapping between + SBATCH and Slurm Rest API namespaces. """ list_of_values = [getattr(i, field) for i in sbatch_to_slurm if bool(getattr(i, field))] @@ -279,7 +284,7 @@ class TestArgumentParserCustomExit: @pytest.fixture(scope="module") def parser(self): """ - An instance of parser, used to support the tests in this class. + Support the tests in this class bt providing an instance of the parser. """ parser = ArgumentParserCustomExit() parser.add_argument("--foo", type=int) @@ -288,8 +293,7 @@ def parser(self): def test_argument_parser_success(self, parser): """ - Test the base case, where the arguments are successfully parsed and - converted to the expected type. + Test the base case, where the arguments are successfully parsed and converted to the expected type. """ args = parser.parse_args("--foo=10 --bar".split()) assert {"foo": 10, "bar": True} == vars(args) @@ -303,8 +307,7 @@ def test_argument_parser_raise_value_error_when_value_is_missing(self, parser): def test_argument_parser_raise_value_error_in_case_of_wrong_type(self, parser): """ - Test that ValueError is raised when the value for some parameter is - incompatible with its type. + Test that ValueError is raised when the value for some parameter is incompatible with its type. """ with pytest.raises(ValueError, match="error: argument --foo: invalid int value:"): parser.parse_args("--foo some_text".split()) @@ -320,8 +323,7 @@ def test_build_parser(): def test_build_mapping_sbatch_to_slurm(): """ - Test if build_mapping_sbatch_to_slurm runs with no problem and - returns the correct type. + Test if build_mapping_sbatch_to_slurm runs with no problem and returns the correct type. """ mapping = build_mapping_sbatch_to_slurm() assert isinstance(mapping, bidict) @@ -329,10 +331,10 @@ def test_build_mapping_sbatch_to_slurm(): def test_jobscript_to_dict__success(dummy_slurm_script): """ - Test if the SBATCH parameters are properly extracted from a job script - and returned in a dictionary mapping parameters to their value. - """ + Test if the SBATCH parameters are properly extracted from a job script. + They are expected to be returned a dictionary mapping parameters to their value. + """ desired_dict = { "no_kill": True, "requeue": False, @@ -363,8 +365,9 @@ def test_jobscript_to_dict__raises_exception_for_unknown_parameter(): @pytest.mark.parametrize("item", filter(lambda i: i.slurmrestd_var_name, sbatch_to_slurm)) def test_convert_sbatch_to_slurm_api__success(item): """ - Test if the keys in a dictionary are properly renamed from SBATCH to Slurm - Rest API namespace. Notice the values should not be affected. + Test if the keys in a dictionary are properly renamed from SBATCH to Slurm Rest API namespace. + + Notice the values should not be affected. """ desired_dict = {item.slurmrestd_var_name: None} @@ -376,8 +379,7 @@ def test_convert_sbatch_to_slurm_api__success(item): def test_convert_sbatch_to_slurm_api__raises_exception_for_unknown_parameter(): """ - Test if the conversion of dictionary keys from SBATCH to Slurm Rest API - namespace raises KeyError when facing unknown names. + Test the conversion of dict keys from SBATCH to Slurm Rest API raises KeyError when facing unknown names. """ with pytest.raises(KeyError, match="Impossible to convert from SBATCH to Slurm REST API:"): convert_sbatch_to_slurm_api(dict(foo=0, bar=1)) @@ -385,8 +387,9 @@ def test_convert_sbatch_to_slurm_api__raises_exception_for_unknown_parameter(): def test_get_job_parameters(dummy_slurm_script): """ - Test if all SBATCH parameters are properly extracted from a given job script, - the name of each of them is mapped to Slurm Rest API namespace and returned + Test if all SBATCH parameters are properly extracted from a given job script. + + The name of each of them is mapped to Slurm Rest API namespace and returned in a dictionary. Notice get_job_parameters accepts extra keywords that can be used to overwrite the values from the job script. """ @@ -433,8 +436,9 @@ def _helper(main_file_content): class TestGetJobPropertiesFromJobScript: """ - Test the get_job_properties_from_job_script function.It covers job properties obtained - from the job script and from the users when creating a job submission. + Test the get_job_properties_from_job_script function. + + It covers job properties obtained from the job script and from the users when creating a job submission. """ def test_base_case(self, mock_job_script_files): @@ -521,7 +525,7 @@ class TestBidictMapping: @pytest.fixture def dummy_mapping(self): """ - A dummy dictionary used for testing. + Provide a dummy dictionary used for testing. """ return {f"key_{i}": f"value_{i}" for i in range(5)} @@ -539,8 +543,9 @@ def test_bidict__can_be_compared_to_a_dictionary(self, dummy_mapping): def test_bidict__can_be_compared_to_a_dictionary_inverse(self, dummy_mapping): """ - Check if bidict can be comparable to a dictionary, this time checking - its inverse capability (i.e., swapping keys and values). + Check if bidict can be comparable to a dictionary. + + This time checking its inverse capability (i.e., swapping keys and values). """ desired_value = {value: key for key, value in dummy_mapping.items()} @@ -549,8 +554,9 @@ def test_bidict__can_be_compared_to_a_dictionary_inverse(self, dummy_mapping): class TestExclusiveParameter: """ - --exclusive is a special SBATCH parameter that can be used in some different ways: + --exclusive is a special SBATCH parameter that can be used in some different ways. + See the details: 1. --exclusive as a flag, meaning the value 'exclusive' should be recovered for slurmd. 2. --exclusive=, meaning the value should be recovered for slurmd. According to the Slurm documentation, the value can be 'user' or 'mcs'. From 515b9ae68aa06355b9a8b7fc6782712b1fb68ff2 Mon Sep 17 00:00:00 2001 From: fschuch Date: Tue, 6 Dec 2022 15:15:29 -0300 Subject: [PATCH 21/36] improve tests for job submission creation --- .../apps/job_submissions/test_routers.py | 24 ++++++++++++++----- 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py index 692baa521..bbdd6dd84 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py @@ -75,16 +75,20 @@ async def test_create_job_submission__with_client_id_in_token( count = await database.fetch_all("SELECT COUNT(*) FROM job_submissions") assert count[0][0] == 1 + id_rows = await database.fetch_all("SELECT id FROM job_submissions") + assert len(id_rows) == 1 + job_submission = JobSubmissionResponse(**response.json()) # Check that the response correspond to the entry in the database job_submission_raw_data = await database.fetch_one( - query=job_submissions_table.select().where(job_submissions_table.c.id == 1) + query=job_submissions_table.select().where(job_submissions_table.c.id == id_rows[0][0]) ) + assert job_submission_raw_data is not None assert job_submission == JobSubmissionResponse(**job_submission_raw_data) # type: ignore # Check that each field is correctly set - assert job_submission.id == 1 + assert job_submission.id == job_submission_raw_data.get("id") assert job_submission.job_submission_name == "sub1" assert job_submission.job_submission_owner_email == "owner1@org.com" assert job_submission.job_submission_description is None @@ -158,16 +162,20 @@ async def test_create_job_submission__with_client_id_in_request_body( count = await database.fetch_all("SELECT COUNT(*) FROM job_submissions") assert count[0][0] == 1 + id_rows = await database.fetch_all("SELECT id FROM job_submissions") + assert len(id_rows) == 1 + job_submission = JobSubmissionResponse(**response.json()) # Check that the response correspond to the entry in the database job_submission_raw_data = await database.fetch_one( - query=job_submissions_table.select().where(job_submissions_table.c.id == 1) + query=job_submissions_table.select().where(job_submissions_table.c.id == id_rows[0][0]) ) + assert job_submission_raw_data is not None assert job_submission == JobSubmissionResponse(**job_submission_raw_data) # type: ignore # Check that each field is correctly set - assert job_submission.id == 1 + assert job_submission.id == job_submission_raw_data.get("id") assert job_submission.job_submission_name == "sub1" assert job_submission.job_submission_owner_email == "owner1@org.com" assert job_submission.job_submission_description is None @@ -241,15 +249,19 @@ async def test_create_job_submission__with_execution_directory( count = await database.fetch_all("SELECT COUNT(*) FROM job_submissions") assert count[0][0] == 1 + id_rows = await database.fetch_all("SELECT id FROM job_submissions") + assert len(id_rows) == 1 + job_submission = JobSubmissionResponse(**response.json()) # Check that the response correspond to the entry in the database job_submission_raw_data = await database.fetch_one( - query=job_submissions_table.select().where(job_submissions_table.c.id == 1) + query=job_submissions_table.select().where(job_submissions_table.c.id == id_rows[0][0]) ) + assert job_submission_raw_data is not None assert job_submission == JobSubmissionResponse(**job_submission_raw_data) # type: ignore - assert job_submission.id == 1 + assert job_submission.id == job_submission_raw_data.get("id") assert job_submission.job_submission_name == "sub1" assert job_submission.job_submission_owner_email == "owner1@org.com" assert job_submission.job_submission_description is None From 9892cc51c1627e1f08af92cb851cee66ef7a315a Mon Sep 17 00:00:00 2001 From: fschuch Date: Tue, 6 Dec 2022 15:45:39 -0300 Subject: [PATCH 22/36] fix mypy --- .../apps/job_submissions/properties_parser.py | 8 +++++--- .../tests/apps/job_submissions/test_properties_parser.py | 5 ++++- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py index 8e1851025..fa8dff1fd 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py @@ -4,7 +4,7 @@ from argparse import ArgumentParser from dataclasses import dataclass, field from itertools import chain -from typing import Any, Dict, Iterator, List, Union +from typing import Any, Dict, Iterator, List, Sequence, Union, cast from bidict import bidict from loguru import logger @@ -234,7 +234,7 @@ def build_mapping_sbatch_to_slurm() -> bidict: """ Create a mapper to translate in both ways between the names expected by Slurm REST API and SBATCH. """ - mapping = bidict() + mapping: bidict = bidict() for item in sbatch_to_slurm: if item.slurmrestd_var_name: @@ -252,7 +252,9 @@ def jobscript_to_dict(jobscript: str) -> Dict[str, Union[str, bool]]: Raise ValueError if any of the parameters are unknown to the parser. """ - parsed_args, unknown_arg = parser.parse_known_args(_clean_jobscript(jobscript)) + parsed_args, unknown_arg = parser.parse_known_args( + cast(Sequence[str], _clean_jobscript(jobscript)), + ) if unknown_arg: raise ValueError("Unrecognized SBATCH arguments: {}".format(" ".join(unknown_arg))) diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py index 48f0f8fd1..8bc12380a 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py @@ -362,7 +362,10 @@ def test_jobscript_to_dict__raises_exception_for_unknown_parameter(): jobscript_to_dict("#SBATCH --foo\n#SBATCH --bar=0") -@pytest.mark.parametrize("item", filter(lambda i: i.slurmrestd_var_name, sbatch_to_slurm)) +@pytest.mark.parametrize( + "item", + filter(lambda i: getattr(i, "slurmrestd_var_name", False), sbatch_to_slurm), +) def test_convert_sbatch_to_slurm_api__success(item): """ Test if the keys in a dictionary are properly renamed from SBATCH to Slurm Rest API namespace. From 49844dcd380d6b4b1034ac3e6de5d1a92b38ca1a Mon Sep 17 00:00:00 2001 From: fschuch Date: Wed, 7 Dec 2022 08:06:53 -0300 Subject: [PATCH 23/36] enhance tests for get_job_submission --- jobbergate-api/jobbergate_api/apps/job_submissions/routers.py | 2 +- jobbergate-api/jobbergate_api/tests/apps/conftest.py | 4 ++++ .../jobbergate_api/tests/apps/job_submissions/test_routers.py | 3 +++ 3 files changed, 8 insertions(+), 1 deletion(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py index a42e631bf..7ff0ad4a1 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/routers.py @@ -144,7 +144,7 @@ async def job_submission_get(job_submission_id: int = Query(...)): logger.debug(f"Job-submission data: {job_submission_data=}") - return job_submission_data + return JobSubmissionResponse(**job_submission_data) # type: ignore @router.get( diff --git a/jobbergate-api/jobbergate_api/tests/apps/conftest.py b/jobbergate-api/jobbergate_api/tests/apps/conftest.py index b16b1beb2..722b97a40 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/conftest.py +++ b/jobbergate-api/jobbergate_api/tests/apps/conftest.py @@ -92,6 +92,10 @@ def job_submission_data(): "job_submission_owner_email": "owner1@org.com", "client_id": "dummy-client-id", "status": JobSubmissionStatus.CREATED, + "execution_parameters": { + "name": "job-submission-name", + "comment": "I am a comment", + }, } diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py index bbdd6dd84..a3d77d5c6 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py @@ -426,6 +426,9 @@ async def test_get_job_submission_by_id( assert data["job_submission_owner_email"] == "owner1@org.com" assert data["job_script_id"] == inserted_job_script_id + assert data["execution_parameters"]["name"] == "job-submission-name" + assert data["execution_parameters"]["comment"] == "I am a comment" + @pytest.mark.asyncio async def test_get_job_submission_by_id_bad_permission( From 3427a8734fd840aefd23fb048fd8db938dd3b748 Mon Sep 17 00:00:00 2001 From: fschuch Date: Wed, 7 Dec 2022 08:08:39 -0300 Subject: [PATCH 24/36] add execution parameters for submissions (CLI) --- jobbergate-cli/jobbergate_cli/schemas.py | 2 ++ .../subapps/job_submissions/app.py | 31 ++++++++++++++++--- .../subapps/job_submissions/tools.py | 8 +++++ 3 files changed, 36 insertions(+), 5 deletions(-) diff --git a/jobbergate-cli/jobbergate_cli/schemas.py b/jobbergate-cli/jobbergate_cli/schemas.py index 52f1e964a..a2099e66c 100644 --- a/jobbergate-cli/jobbergate_cli/schemas.py +++ b/jobbergate-cli/jobbergate_cli/schemas.py @@ -145,6 +145,7 @@ class JobSubmissionResponse(pydantic.BaseModel, extra=pydantic.Extra.ignore): created_at: Optional[datetime] updated_at: Optional[datetime] report_message: Optional[str] + execution_parameters: Optional[Dict[str, Any]] class JobScriptCreateRequestData(pydantic.BaseModel): @@ -169,6 +170,7 @@ class JobSubmissionCreateRequestData(pydantic.BaseModel): job_script_id: int client_id: Optional[str] = pydantic.Field(None, alias="cluster_name") execution_directory: Optional[Path] = None + execution_parameters: Optional[Dict[str, Any]] = None class Pagination(pydantic.BaseModel): diff --git a/jobbergate-cli/jobbergate_cli/subapps/job_submissions/app.py b/jobbergate-cli/jobbergate_cli/subapps/job_submissions/app.py index 4fd7316f5..e4282236a 100644 --- a/jobbergate-cli/jobbergate_cli/subapps/job_submissions/app.py +++ b/jobbergate-cli/jobbergate_cli/subapps/job_submissions/app.py @@ -3,6 +3,7 @@ """ from pathlib import Path +from textwrap import dedent from typing import Any, Dict, Optional, cast import typer @@ -19,6 +20,7 @@ HIDDEN_FIELDS = [ "created_at", "updated_at", + "execution_parameters", ] @@ -50,12 +52,26 @@ def create( ), execution_directory: Optional[Path] = typer.Option( None, - help=""" + help=dedent( + """ The path on the cluster where the job script should be executed. If provided as a relative path, it will be converted as an absolute path from your current - working directory. If you use "~" to denote your home directory, the path will be expanded to an absolute - path for your home directory on *this* machine. - """, + working directory. If you use "~" to denote your home directory, the path will be expanded to an + absolute path for your home directory on *this* machine. + """ + ).strip(), + ), + execution_parameters: Optional[Path] = typer.Option( + None, + help=dedent( + """ + The path to a JSON file containing the parameters to be passed to the job submission. + See more details at: https://slurm.schedmd.com/rest_api.html#v0.0.36_job_properties + """ + ).strip(), + exists=True, + readable=True, + resolve_path=True, ), ): """ @@ -73,6 +89,7 @@ def create( description=description, execution_directory=execution_directory, cluster_name=cluster_name, + execution_parameters_file=execution_parameters, ) render_single_result( jg_ctx, @@ -86,7 +103,11 @@ def create( @handle_abort def list_all( ctx: typer.Context, - show_all: bool = typer.Option(False, "--all", help="Show all job submissions, even the ones owned by others"), + show_all: bool = typer.Option( + False, + "--all", + help="Show all job submissions, even the ones owned by others", + ), search: Optional[str] = typer.Option(None, help="Apply a search term to results"), sort_order: SortOrder = typer.Option(SortOrder.UNSORTED, help="Specify sort order"), sort_field: Optional[str] = typer.Option(None, help="The field by which results should be sorted"), diff --git a/jobbergate-cli/jobbergate_cli/subapps/job_submissions/tools.py b/jobbergate-cli/jobbergate_cli/subapps/job_submissions/tools.py index 12a63256c..ccd183f5a 100644 --- a/jobbergate-cli/jobbergate_cli/subapps/job_submissions/tools.py +++ b/jobbergate-cli/jobbergate_cli/subapps/job_submissions/tools.py @@ -9,6 +9,7 @@ from jobbergate_cli.exceptions import Abort from jobbergate_cli.requests import make_request from jobbergate_cli.schemas import JobbergateContext, JobSubmissionCreateRequestData, JobSubmissionResponse +from jobbergate_cli.subapps.job_scripts.tools import validate_parameter_file def create_job_submission( @@ -18,6 +19,7 @@ def create_job_submission( description: Optional[str] = None, cluster_name: Optional[str] = None, execution_directory: Optional[Path] = None, + execution_parameters_file: Optional[Path] = None, ) -> JobSubmissionResponse: """ Create a Job Submission from the given Job Script. @@ -51,11 +53,17 @@ def create_job_submission( ), ) + if execution_parameters_file is None: + execution_parameters = None + else: + execution_parameters = validate_parameter_file(execution_parameters_file) + job_submission_data = JobSubmissionCreateRequestData( job_submission_name=name, job_submission_description=description, job_script_id=job_script_id, cluster_name=cluster_name, + execution_parameters=execution_parameters, ) if execution_directory is not None: From 8391e8ed2b2376afb9161dac09dc9119b141f280 Mon Sep 17 00:00:00 2001 From: fschuch Date: Wed, 7 Dec 2022 10:30:07 -0300 Subject: [PATCH 25/36] enhance tests for get_job_submission --- .../jobbergate_api/tests/apps/conftest.py | 4 -- .../apps/job_submissions/test_routers.py | 44 +++++++++++++++++++ 2 files changed, 44 insertions(+), 4 deletions(-) diff --git a/jobbergate-api/jobbergate_api/tests/apps/conftest.py b/jobbergate-api/jobbergate_api/tests/apps/conftest.py index 722b97a40..b16b1beb2 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/conftest.py +++ b/jobbergate-api/jobbergate_api/tests/apps/conftest.py @@ -92,10 +92,6 @@ def job_submission_data(): "job_submission_owner_email": "owner1@org.com", "client_id": "dummy-client-id", "status": JobSubmissionStatus.CREATED, - "execution_parameters": { - "name": "job-submission-name", - "comment": "I am a comment", - }, } diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py index a3d77d5c6..37ef64618 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_routers.py @@ -410,6 +410,10 @@ async def test_get_job_submission_by_id( job_script_id=inserted_job_script_id, job_submission_name="sub1", job_submission_owner_email="owner1@org.com", + execution_parameters={ + "name": "job-submission-name", + "comment": "I am a comment", + }, ), ) @@ -509,16 +513,28 @@ async def test_get_job_submissions__no_param( job_script_id=inserted_job_script_id, job_submission_name="sub1", job_submission_owner_email="owner1@org.com", + execution_parameters={ + "name": "job-submission-name-1", + "comment": "I am a comment", + }, ), dict( job_script_id=inserted_job_script_id, job_submission_name="sub2", job_submission_owner_email="owner999@org.com", + execution_parameters={ + "name": "job-submission-name-2", + "comment": "I am a comment", + }, ), dict( job_script_id=inserted_job_script_id, job_submission_name="sub3", job_submission_owner_email="owner1@org.com", + execution_parameters={ + "name": "job-submission-name-3", + "comment": "I am a comment", + }, ), ), ) @@ -612,16 +628,28 @@ async def test_get_job_submissions__with_all_param( job_script_id=inserted_job_script_id, job_submission_name="sub1", job_submission_owner_email="owner1@org.com", + execution_parameters={ + "name": "job-submission-name-1", + "comment": "I am a comment", + }, ), dict( job_script_id=inserted_job_script_id, job_submission_name="sub2", job_submission_owner_email="owner999@org.com", + execution_parameters={ + "name": "job-submission-name-2", + "comment": "I am a comment", + }, ), dict( job_script_id=inserted_job_script_id, job_submission_name="sub3", job_submission_owner_email="owner1@org.com", + execution_parameters={ + "name": "job-submission-name-3", + "comment": "I am a comment", + }, ), ), ) @@ -1414,6 +1442,10 @@ async def test_job_submissions_agent_pending__success( job_submission_owner_email="email1@dummy.com", status=JobSubmissionStatus.CREATED, client_id="dummy-client", + execution_parameters={ + "name": "job-submission-name-1", + "comment": "I am a comment", + }, ), dict( job_script_id=inserted_job_script_id, @@ -1421,6 +1453,10 @@ async def test_job_submissions_agent_pending__success( job_submission_owner_email="email2@dummy.com", status=JobSubmissionStatus.COMPLETED, client_id="dummy-client", + execution_parameters={ + "name": "job-submission-name-2", + "comment": "I am a comment", + }, ), dict( job_script_id=inserted_job_script_id, @@ -1428,6 +1464,10 @@ async def test_job_submissions_agent_pending__success( job_submission_owner_email="email3@dummy.com", status=JobSubmissionStatus.CREATED, client_id="silly-client", + execution_parameters={ + "name": "job-submission-name-3", + "comment": "I am a comment", + }, ), dict( job_script_id=inserted_job_script_id, @@ -1435,6 +1475,10 @@ async def test_job_submissions_agent_pending__success( job_submission_owner_email="email4@dummy.com", status=JobSubmissionStatus.CREATED, client_id="dummy-client", + execution_parameters={ + "name": "job-submission-name-4", + "comment": "I am a comment", + }, ), ), ) From bfe22a7c8867cff066c0555ff9c47f9ffee638de Mon Sep 17 00:00:00 2001 From: fschuch Date: Wed, 7 Dec 2022 11:06:26 -0300 Subject: [PATCH 26/36] tests execution parameters for submissions (CLI) --- jobbergate-cli/tests/subapps/conftest.py | 16 ++++++++++++++++ .../tests/subapps/job_submissions/test_app.py | 6 ++++++ 2 files changed, 22 insertions(+) diff --git a/jobbergate-cli/tests/subapps/conftest.py b/jobbergate-cli/tests/subapps/conftest.py index 671adb97b..0036d8432 100644 --- a/jobbergate-cli/tests/subapps/conftest.py +++ b/jobbergate-cli/tests/subapps/conftest.py @@ -165,6 +165,10 @@ def dummy_job_submission_data(dummy_job_script_data): job_script_id=dummy_job_script_data[0]["id"], slurm_job_id=13, status="CREATED", + execution_parameters={ + "name": "job-submission-name-1", + "comment": "I am a comment", + }, ), dict( id=1, @@ -176,6 +180,10 @@ def dummy_job_submission_data(dummy_job_script_data): job_script_id=88, slurm_job_id=8888, status="CREATED", + execution_parameters={ + "name": "job-submission-name-2", + "comment": "I am a comment", + }, ), dict( id=3, @@ -187,6 +195,10 @@ def dummy_job_submission_data(dummy_job_script_data): job_script_id=99, slurm_job_id=9999, status="CREATED", + execution_parameters={ + "name": "job-submission-name-3", + "comment": "I am a comment", + }, ), dict( id=4, @@ -199,6 +211,10 @@ def dummy_job_submission_data(dummy_job_script_data): slurm_job_id=9999, status="REJECTED", report_message="Failed to submit job to slurm", + execution_parameters={ + "name": "job-submission-name-4", + "comment": "I am a comment", + }, ), ] diff --git a/jobbergate-cli/tests/subapps/job_submissions/test_app.py b/jobbergate-cli/tests/subapps/job_submissions/test_app.py index ae19ee9c4..861f82938 100644 --- a/jobbergate-cli/tests/subapps/job_submissions/test_app.py +++ b/jobbergate-cli/tests/subapps/job_submissions/test_app.py @@ -1,3 +1,4 @@ +import json import shlex import httpx @@ -13,12 +14,16 @@ def test_create( dummy_job_submission_data, cli_runner, mocker, + tmp_path, ): job_submission_data = JobSubmissionResponse(**dummy_job_submission_data[0]) job_submission_name = job_submission_data.job_submission_name job_submission_description = job_submission_data.job_submission_description job_script_id = job_submission_data.id + param_file_path = tmp_path / "param_file.json" + param_file_path.write_text(json.dumps(job_submission_data.execution_parameters)) + mocked_render = mocker.patch("jobbergate_cli.subapps.job_submissions.app.render_single_result") patched_create_job_submission = mocker.patch("jobbergate_cli.subapps.job_submissions.app.create_job_submission") patched_create_job_submission.return_value = job_submission_data @@ -32,6 +37,7 @@ def test_create( create --name={job_submission_name} --description='{job_submission_description}' --job-script-id={job_script_id} + --execution-parameters={param_file_path} """ ) ), From 7b5cbedb5f265bda5a231286260e9c7ab423ea97 Mon Sep 17 00:00:00 2001 From: fschuch Date: Wed, 7 Dec 2022 13:30:29 -0300 Subject: [PATCH 27/36] update changelog --- jobbergate-cli/CHANGELOG.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jobbergate-cli/CHANGELOG.rst b/jobbergate-cli/CHANGELOG.rst index 64f44fa50..169bcefaa 100644 --- a/jobbergate-cli/CHANGELOG.rst +++ b/jobbergate-cli/CHANGELOG.rst @@ -6,7 +6,7 @@ This file keeps track of all notable changes to jobbergate-cli Unreleased ---------- -* Move SBATCH params to Job Script submission +* Added support for `execution_parameters` in job submission at the CLI 3.3.4 -- 2022-12-05 ------------------- From 72252385bdd6f7e3583e81bd34a0b496a437fa96 Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 9 Dec 2022 09:43:11 -0300 Subject: [PATCH 28/36] patch a couple fields on JobProperties This is the result of integration tests with slurm restd --- .../jobbergate_api/apps/job_submissions/schemas.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index 70e3dc395..b9a9f6d40 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -80,7 +80,7 @@ class JobProperties(BaseModel, extra=Extra.forbid): account: Optional[str] = Field( description="Charge resources used by this job to specified account.", ) - account_gather_freqency: Optional[str] = Field( + account_gather_frequency: Optional[str] = Field( description="Define the job accounting and profiling sampling intervals.", ) argv: Optional[List[str]] = Field(description="Arguments to the script.") @@ -161,8 +161,11 @@ class JobProperties(BaseModel, extra=Extra.forbid): "'user' option or with the 'mcs' option)." ) ) - get_user_environment: Optional[bool] = Field( - description="Load new login environment for user on job node." + get_user_environment: int = Field( + default=1, + description="Load new login environment for user on job node.", + ge=0, + le=1, ) gres: Optional[str] = Field( description="Specifies a comma delimited list of generic consumable resources." From bd5f3b7c78125550d8965d18fec4b87132e55130 Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 9 Dec 2022 09:48:06 -0300 Subject: [PATCH 29/36] fix python version on test_on_push.yaml --- .github/workflows/test_on_push.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_on_push.yaml b/.github/workflows/test_on_push.yaml index bd0d3e869..b33e4fd17 100644 --- a/.github/workflows/test_on_push.yaml +++ b/.github/workflows/test_on_push.yaml @@ -52,7 +52,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: '3.6' + python-version: '3.6.15' architecture: 'x64' - uses: Gr1N/setup-poetry@v7 with: From 75482b4f45821fff806e5a6adea205ee511c30c3 Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 9 Dec 2022 09:56:49 -0300 Subject: [PATCH 30/36] fix python version on test_on_push.yaml --- .github/workflows/test_on_push.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_on_push.yaml b/.github/workflows/test_on_push.yaml index b33e4fd17..9d1bce55a 100644 --- a/.github/workflows/test_on_push.yaml +++ b/.github/workflows/test_on_push.yaml @@ -52,7 +52,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: '3.6.15' + python-version: 3.6.15 architecture: 'x64' - uses: Gr1N/setup-poetry@v7 with: From 65a288fc031247a87f4c87e44f9ec022eb3aa451 Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 9 Dec 2022 10:03:10 -0300 Subject: [PATCH 31/36] fix ubuntu version on test_on_push.yaml --- .github/workflows/test_on_push.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_on_push.yaml b/.github/workflows/test_on_push.yaml index 9d1bce55a..6d313b0be 100644 --- a/.github/workflows/test_on_push.yaml +++ b/.github/workflows/test_on_push.yaml @@ -47,12 +47,12 @@ jobs: cli-tests: name: "jobbergate-cli tests" - runs-on: "ubuntu-latest" + runs-on: "ubuntu-20.04" steps: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: 3.6.15 + python-version: "3.6" architecture: 'x64' - uses: Gr1N/setup-poetry@v7 with: From 8d49b6b0f4c045df2942165f86e8b578ea9a0463 Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 9 Dec 2022 10:48:43 -0300 Subject: [PATCH 32/36] fix slurm restd link for help --- jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py | 4 ++-- jobbergate-cli/jobbergate_cli/subapps/job_submissions/app.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py index b9a9f6d40..c603365c1 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/schemas.py @@ -63,7 +63,7 @@ execution_parameters=MetaField( description=( "The parameters to be passed to the job submission. " - "See more details at: https://slurm.schedmd.com/rest_api.html#v0.0.36_job_properties" + "See more details at: https://slurm.schedmd.com/rest_api.html" ), example={"name": "job-submission-name", "comment": "I am a comment"}, ), @@ -74,7 +74,7 @@ class JobProperties(BaseModel, extra=Extra.forbid): """ Specialized model for job properties. - See more details at: https://slurm.schedmd.com/rest_api.html#v0.0.36_job_properties + See more details at: https://slurm.schedmd.com/rest_api.html """ account: Optional[str] = Field( diff --git a/jobbergate-cli/jobbergate_cli/subapps/job_submissions/app.py b/jobbergate-cli/jobbergate_cli/subapps/job_submissions/app.py index e4282236a..6964e52a6 100644 --- a/jobbergate-cli/jobbergate_cli/subapps/job_submissions/app.py +++ b/jobbergate-cli/jobbergate_cli/subapps/job_submissions/app.py @@ -66,7 +66,7 @@ def create( help=dedent( """ The path to a JSON file containing the parameters to be passed to the job submission. - See more details at: https://slurm.schedmd.com/rest_api.html#v0.0.36_job_properties + See more details at: https://slurm.schedmd.com/rest_api.html """ ).strip(), exists=True, From 4ac95f991d5dca9640371284ab4e8625d0b92a8a Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 16 Dec 2022 18:03:56 -0300 Subject: [PATCH 33/36] ASP-1915 refactor --requeue param and add tests --- .../apps/job_submissions/properties_parser.py | 7 +- .../job_submissions/test_properties_parser.py | 70 +++++++++++++++++++ 2 files changed, 73 insertions(+), 4 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py index fa8dff1fd..7df8f48c5 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py @@ -146,7 +146,7 @@ class SbatchToSlurm: SbatchToSlurm("", "--network"), SbatchToSlurm("nice", "--nice"), SbatchToSlurm("no_kill", "--no-kill", "-k", dict(action="store_const", const=True)), - SbatchToSlurm("", "--no-requeue", "", dict(action="store_false", dest="requeue")), + SbatchToSlurm("", "--no-requeue", "", dict(action="store_false", dest="requeue", default=None)), SbatchToSlurm("", "--nodefile", "-F"), SbatchToSlurm("", "--nodelist", "-w"), SbatchToSlurm("nodes", "--nodes", "-N"), @@ -173,7 +173,7 @@ class SbatchToSlurm: SbatchToSlurm("qos", "--qos", "-q"), SbatchToSlurm("", "--quiet", "-Q", dict(action="store_const", const=True)), SbatchToSlurm("", "--reboot", "", dict(action="store_const", const=True)), - SbatchToSlurm("requeue", "--requeue", "", dict(action="store_const", const=True)), + SbatchToSlurm("requeue", "--requeue", "", dict(action="store_true", default=None)), SbatchToSlurm("reservation", "--reservation"), SbatchToSlurm("signal", "--signal"), SbatchToSlurm("sockets_per_node", "--sockets-per-node", "", dict(type=int)), @@ -225,8 +225,7 @@ def build_parser() -> ArgumentParser: for item in sbatch_to_slurm: args = (i for i in (item.sbatch_short, item.sbatch) if i) parser.add_argument(*args, **item.argparser_param) - # make --requeue and --no-requeue work together, with default to None - parser.set_defaults(requeue=None) + return parser diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py index 8bc12380a..fe9c34ce9 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py @@ -663,3 +663,73 @@ def test_both_exclusive_and_oversubscribe_2(self): actual_dict = jobscript_to_dict(jobscript) assert actual_dict == desired_dict + + +class TestRequeueParameter: + """ + Requeue is a slurm parameter whose value comes from two sbatch flags: --requeue and --no-requeue. + """ + + def test_empty_jobscript(self): + """ + Base case: no parameters at all. + """ + jobscript = "" + + desired_dict = {} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict + + def test_requeue_flag(self): + """ + Test the first scenario: --requeue. + """ + jobscript = "#SBATCH --requeue" + + desired_dict = {"requeue": True} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict + + def test_no_requeue_flag(self): + """ + Test the first scenario: --no-requeue. + """ + jobscript = "#SBATCH --no-requeue" + + desired_dict = {"requeue": False} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict + + def test_both_exclusive_and_oversubscribe_1(self): + """ + Test that when both are used, the last of them takes precedence. + + In this case, --no-requeue is the last one. + """ + jobscript = "#SBATCH --requeue\n#SBATCH --no-requeue" + + desired_dict = {"requeue": False} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict + + def test_both_exclusive_and_oversubscribe_2(self): + """ + Test that when both are used, the last of them takes precedence. + + In this case, --requeue is the last one. + """ + jobscript = "#SBATCH --no-requeue\n#SBATCH --requeue" + + desired_dict = {"requeue": True} + + actual_dict = jobscript_to_dict(jobscript) + + assert actual_dict == desired_dict From 76d348abc35f274db114252946abd1c969558211 Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 16 Dec 2022 18:38:40 -0300 Subject: [PATCH 34/36] ASP-1915 code review --- .../jobbergate_api/apps/job_submissions/properties_parser.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py index 7df8f48c5..9633f2160 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py @@ -279,10 +279,9 @@ def convert_sbatch_to_slurm_api(input: Dict[str, Any]) -> Dict[str, Any]: for sbatch_name, value in input.items(): try: slurm_name = mapping_sbatch_to_slurm[sbatch_name] + mapped[slurm_name] = value except KeyError: unknown_keys.append(sbatch_name) - else: - mapped[slurm_name] = value if unknown_keys: error_message = "Impossible to convert from SBATCH to Slurm REST API: {}" From aed3bc691d17b3031410250e9b207d6d13e62679 Mon Sep 17 00:00:00 2001 From: fschuch Date: Fri, 16 Dec 2022 19:01:46 -0300 Subject: [PATCH 35/36] ASP-1915 change return type on _clean_jobscript --- .../apps/job_submissions/properties_parser.py | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py index 9633f2160..b579080ba 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py @@ -4,7 +4,7 @@ from argparse import ArgumentParser from dataclasses import dataclass, field from itertools import chain -from typing import Any, Dict, Iterator, List, Sequence, Union, cast +from typing import Any, Dict, List, Union from bidict import bidict from loguru import logger @@ -42,7 +42,7 @@ def _split_line(line: str) -> List[str]: return line.replace("=", " ").split() -def _clean_jobscript(jobscript: str) -> Iterator[str]: +def _clean_jobscript(jobscript: str) -> List[str]: """ Transform a job script string. @@ -50,12 +50,12 @@ def _clean_jobscript(jobscript: str) -> Iterator[str]: the identification flag and mapping a cleaning procedure to them in order to remove the identification flag, remove inline comments, and strip extra white spaces. Finally, split each pair of parameter/value and chain them - in a single iterator. + in a single list. """ jobscript_filtered = filter(_flagged_line, jobscript.splitlines()) jobscript_cleaned = map(_clean_line, jobscript_filtered) jobscript_splitted = map(_split_line, jobscript_cleaned) - return chain.from_iterable(jobscript_splitted) + return list(chain.from_iterable(jobscript_splitted)) @dataclass(frozen=True) @@ -251,9 +251,7 @@ def jobscript_to_dict(jobscript: str) -> Dict[str, Union[str, bool]]: Raise ValueError if any of the parameters are unknown to the parser. """ - parsed_args, unknown_arg = parser.parse_known_args( - cast(Sequence[str], _clean_jobscript(jobscript)), - ) + parsed_args, unknown_arg = parser.parse_known_args(args=_clean_jobscript(jobscript)) if unknown_arg: raise ValueError("Unrecognized SBATCH arguments: {}".format(" ".join(unknown_arg))) From 0cb7dd84488c3495751c08a6922ae0a922ea8f91 Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 19 Dec 2022 10:11:56 -0300 Subject: [PATCH 36/36] ASP-1951 rename a variable on code review from sbatch_to_slurm to sbatch_to_slurm_mapping --- .../apps/job_submissions/properties_parser.py | 6 +++--- .../tests/apps/job_submissions/test_properties_parser.py | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py index b579080ba..c202392de 100644 --- a/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py +++ b/jobbergate-api/jobbergate_api/apps/job_submissions/properties_parser.py @@ -74,7 +74,7 @@ class SbatchToSlurm: argparser_param: dict = field(default_factory=dict) -sbatch_to_slurm = [ +sbatch_to_slurm_mapping = [ SbatchToSlurm("account", "--account", "-A"), SbatchToSlurm("account_gather_freqency", "--acctg-freq"), SbatchToSlurm("array", "--array", "-a"), @@ -222,7 +222,7 @@ def build_parser() -> ArgumentParser: Build an ArgumentParser to handle all SBATCH parameters declared at sbatch_to_slurm. """ parser = ArgumentParserCustomExit() - for item in sbatch_to_slurm: + for item in sbatch_to_slurm_mapping: args = (i for i in (item.sbatch_short, item.sbatch) if i) parser.add_argument(*args, **item.argparser_param) @@ -235,7 +235,7 @@ def build_mapping_sbatch_to_slurm() -> bidict: """ mapping: bidict = bidict() - for item in sbatch_to_slurm: + for item in sbatch_to_slurm_mapping: if item.slurmrestd_var_name: sbatch_name = item.sbatch.lstrip("-").replace("-", "_") mapping[sbatch_name] = item.slurmrestd_var_name diff --git a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py index fe9c34ce9..71ab7c5b2 100644 --- a/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py +++ b/jobbergate-api/jobbergate_api/tests/apps/job_submissions/test_properties_parser.py @@ -27,7 +27,7 @@ get_job_parameters, get_job_properties_from_job_script, jobscript_to_dict, - sbatch_to_slurm, + sbatch_to_slurm_mapping, ) from jobbergate_api.apps.job_submissions.schemas import JobProperties @@ -175,7 +175,7 @@ def test_clean_jobscript(dummy_slurm_script): assert actual_list == desired_list -@pytest.mark.parametrize("item", sbatch_to_slurm) +@pytest.mark.parametrize("item", sbatch_to_slurm_mapping) class TestSbatchToSlurmList: """ Test all the fields of the objects SbatchToSlurm that are stored in the list sbatch_to_slurm. @@ -271,7 +271,7 @@ def test_sbatch_to_slurm_list__contains_only_unique_values(field): This aims to avoid ambiguity at the SBATCH argparser and the two-way mapping between SBATCH and Slurm Rest API namespaces. """ - list_of_values = [getattr(i, field) for i in sbatch_to_slurm if bool(getattr(i, field))] + list_of_values = [getattr(i, field) for i in sbatch_to_slurm_mapping if bool(getattr(i, field))] assert len(list_of_values) == len(set(list_of_values)) @@ -364,7 +364,7 @@ def test_jobscript_to_dict__raises_exception_for_unknown_parameter(): @pytest.mark.parametrize( "item", - filter(lambda i: getattr(i, "slurmrestd_var_name", False), sbatch_to_slurm), + filter(lambda i: getattr(i, "slurmrestd_var_name", False), sbatch_to_slurm_mapping), ) def test_convert_sbatch_to_slurm_api__success(item): """