Skip to content

Commit

Permalink
Changed functions names according to what agreed on PR #20
Browse files Browse the repository at this point in the history
  • Loading branch information
@nitrosx
nitrosx committed Jun 16, 2022
1 parent 479d41d commit 08d524a
Showing 1 changed file with 109 additions and 40 deletions.
149 changes: 109 additions & 40 deletions pyscicat/client.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -152,12 +152,13 @@ def _send_to_scicat(self, url, dataDict=None, cmd="post"):
# err = resp.json()["error"]
# raise ScicatCommError(f"Error creating Sample {err}")

def replace_dataset(self, dataset: Dataset) -> str:
def datasets_replace(self, dataset: Dataset) -> str:
"""
Create a new dataset or update an existing one
This function was renamed.
It is still accessible with the original name for backward compatibility
The original name was upload_dataset
The original names were upload_dataset replace_datasets
This function is obsolete and it will be remove in next relesases
Parameters
Expand Down Expand Up @@ -191,15 +192,17 @@ def replace_dataset(self, dataset: Dataset) -> str:
Upload or create a new dataset
Original name, kept for for backward compatibility
"""
upload_dataset = replace_dataset
upload_dataset = datasets_replace
replace_dataset = datasets_replace

def create_dataset(self, dataset: Dataset) -> str:

def datasets_create(self, dataset: Dataset) -> str:
"""
Upload a new dataset. Uses the generic dataset endpoint.
Relies on the endpoint to sense the dataset type
This function was renamed.
It is still accessible with the original name for backward compatibility
The original name was upload_new_dataset
The original name were create_dataset and upload_new_dataset
Parameters
----------
Expand Down Expand Up @@ -232,14 +235,17 @@ def create_dataset(self, dataset: Dataset) -> str:
Upload a new dataset
Original name, kept for for backward compatibility
"""
upload_new_dataset = create_dataset
upload_new_dataset = datasets_create
create_dataset = datasets_create


def replace_raw_dataset(self, dataset: Dataset) -> str:
def datasets_raw_replace(self, dataset: Dataset) -> str:
"""
Create a new raw dataset or update an existing one
This function was renamed.
It is still accessible with the original name for backward compatibility
The original name was upload_raw_dataset
The original names were repalce_raw_dataset and upload_raw_dataset
THis function is obsolete and it will be removed in future releases
Parameters
----------
Expand Down Expand Up @@ -269,14 +275,17 @@ def replace_raw_dataset(self, dataset: Dataset) -> str:
Upload a raw dataset
Original name, kept for for backward compatibility
"""
upload_raw_dataset = replace_raw_dataset
upload_raw_dataset = datasets_raw_replace
replace_raw_dataset = datasets_raw_replace

def replace_derived_dataset(self, dataset: Dataset) -> str:

def datasets_derived_replace(self, dataset: Dataset) -> str:
"""
Create a new derived dataset or update an existing one
This function was renamed.
It is still accessible with the original name for backward compatibility
The original name was upload_derived_dataset
The original names were replace_derived_dataset and upload_derived_dataset
Parameters
----------
Expand Down Expand Up @@ -308,11 +317,14 @@ def replace_derived_dataset(self, dataset: Dataset) -> str:
Upload a derived dataset
Original name, kept for for backward compatibility
"""
upload_derived_dataset = replace_derived_dataset
upload_derived_dataset = datasets_derived_replace
replace_derived_dataset = datasets_derived_replace

def upsert_raw_dataset(self, dataset: Dataset, filter_fields) -> str:

def datasets_raw_upsert(self, dataset: Dataset, filter_fields) -> str:
"""
Upsert a raw dataset
Update or insert a raw dataset
This function is obsolete is going to be removed in future releases
Parameters
----------
Expand Down Expand Up @@ -342,9 +354,13 @@ def upsert_raw_dataset(self, dataset: Dataset, filter_fields) -> str:
logger.info(f"dataset upserted {new_pid}")
return new_pid

def upsert_derived_dataset(self, dataset: Dataset, filter_fields) -> str:
upsert_raw_dataset = datasets_raw_upsert


def datasets_derived_upsert(self, dataset: Dataset, filter_fields) -> str:
"""
Upsert a derived dataset
Update or insert a derived dataset
This function is obsolete and is going to be removed in future releases
Parameters
----------
Expand Down Expand Up @@ -375,14 +391,19 @@ def upsert_derived_dataset(self, dataset: Dataset, filter_fields) -> str:
logger.info(f"dataset upserted {new_pid}")
return new_pid

def create_dataset_datablock(
upsert_derived_datasets = datasets_derived_upsert


def datasets_datablock_create(
self, datablock: Datablock, datasetType: str = "RawDatasets"
):
"""
Create a new datablock for a dataset.
The dataset can be both Raw or Derived.
It is still accessible with the original name for backward compatibility
The original name was upload_datablock
The original names were create_dataset_datablock and upload_datablock
This function is obsolete and will be removed in future releases
Function datasets_origdatablock_create should be used.
Parameters
----------
Expand Down Expand Up @@ -414,14 +435,16 @@ def create_dataset_datablock(
Upload a Datablock
Original name, kept for for backward compatibility
"""
upload_datablock = create_dataset_datablock
upload_datablock = datasets_datablock_create
create_dataset_datablock = datasets_datablock_create

def create_dataset_origdatablock(self, origdatablock: OrigDatablock) -> dict:

def datasets_origdatablock_create(self, origdatablock: OrigDatablock) -> dict:
"""
Create a new SciCat Dataset OrigDatablock
This function has been renamed.
It is still accessible with the original name for backward compatibility
The original name was upload_dataset_origdatablock
The original names were create_dataset_origdatablock and upload_dataset_origdatablock
Parameters
----------
Expand Down Expand Up @@ -454,9 +477,11 @@ def create_dataset_origdatablock(self, origdatablock: OrigDatablock) -> dict:
Create a new SciCat Dataset OrigDatablock
Original name, kept for for backward compatibility
"""
upload_dataset_origdatablock = create_dataset_origdatablock
upload_dataset_origdatablock = datasets_origdatablock_create
create_dataset_origdatablock = datasets_origdatablock_create


def create_dataset_attachment(
def datasets_attachment_create(
self, attachment: Attachment, datasetType: str = "RawDatasets"
):
"""
Expand All @@ -465,7 +490,7 @@ def create_dataset_attachment(
that this attachment is attached to. This is required for creating the url that SciCat uses.
This function has been renamed.
It is still accessible with the original name for backward compatibility
The original name was upload_attachment
The original names were create_dataset_attachment and upload_attachment
Parameters
----------
Expand Down Expand Up @@ -500,9 +525,11 @@ def create_dataset_attachment(
Create a new attachement for a dataset
Original name, kept for for backward compatibility
"""
upload_attachment = create_dataset_attachment
upload_attachment = datasets_attachment_create
create_dataset_attachment = datasets_attachment_create

def find_datasets_full_query(self, skip=0, limit=25, query_fields=None):

def datasets_find(self, skip=0, limit=25, query_fields=None):
"""
Gets datasets using the fullQuery mechanism of SciCat. This is
appropriate for cases where might want paging and cases where you want to perform
Expand All @@ -516,7 +543,7 @@ def find_datasets_full_query(self, skip=0, limit=25, query_fields=None):
This function was renamed.
It is still accessible with the original name for backward compatibility
The original name was get_datasets_full_query
The original name was find_datasets_full_query and get_datasets_full_query
Parameters
----------
Expand Down Expand Up @@ -547,13 +574,17 @@ def find_datasets_full_query(self, skip=0, limit=25, query_fields=None):
find a set of datasets according the full query provided
Original name, kept for for backward compatibility
"""
get_datasets_full_query = find_datasets_full_query
get_datasets_full_query = datasets_find
find_datasets_full_query = datasets_find


def find_datasets(self, filter_fields=None) -> List[Dataset]:
def datasets_get_many(self, filter_fields=None) -> List[Dataset]:
"""
Gets datasets using the simple fiter mechanism. This
is appropriate when you do not require paging or text search, but
want to be able to limit results based on items in the Dataset object.
This function has been renamed and the old name has been mantained for backward compatibility
The previous names are find_datasets and get_datasets
For example, a search for Datasets of a given proposalId would have
```python
Expand Down Expand Up @@ -585,13 +616,17 @@ def find_datasets(self, filter_fields=None) -> List[Dataset]:
find a set of datasets according to the simple filter provided
Original name, kept for for backward compatibility
"""
get_datasets = find_datasets
get_datasets = datasets_get_many
find_datasets = datasets_get_many


def find_published_data(self, filter=None) -> List[PublishedData]:
def published_data_get_many(self, filter=None) -> List[PublishedData]:
"""
retrieve all the published data using the simple fiter mechanism. This
is appropriate when you do not require paging or text search, but
want to be able to limit results based on items in the Dataset object.
This function has been renamed and the old name has been maintained for backward compatibility
The previous name are find_published_data and get_published_data
For example, a search for published data of a given doi would have
```python
Expand Down Expand Up @@ -623,10 +658,15 @@ def find_published_data(self, filter=None) -> List[PublishedData]:
find a set of published data according to the simple filter provided
Original name, kept for for backward compatibility
"""
get_published_data = find_published_data
get_published_data = published_data_get_many
find_published_data = published_data_get_many

def get_dataset_by_pid(self, pid=None) -> Dataset:
"""Gets dataset with the pid provided.

def datasets_get_one(self, pid=None) -> Dataset:
"""
Gets dataset with the pid provided.
This function has been renamed. Provious name has been maintained for backward compatibility.
Previous names was get_dataset_by_pid
Parameters
----------
Expand All @@ -643,6 +683,9 @@ def get_dataset_by_pid(self, pid=None) -> Dataset:
return None
return response.json()

get_dataset_by_pid = datasets_get_one


# this method is future, needs testing.
# def update_dataset(self, pid, fields: Dict):
# response = self._send_to_scicat(
Expand All @@ -654,11 +697,14 @@ def get_dataset_by_pid(self, pid=None) -> Dataset:
# return None
# return response.json()

def get_instrument(self, pid: str = None, name: str = None) -> dict:
def instruments_get_one(self, pid: str = None, name: str = None) -> dict:
"""
Get an instrument by pid or by name.
If pid is provided it takes priority over name.
This function has been renamed. Previous name has been maintained for backward compatibility.
Previous name was get_instrument
Parameters
----------
pid : str
Expand Down Expand Up @@ -694,9 +740,15 @@ def get_instrument(self, pid: str = None, name: str = None) -> dict:
return None
return response.json()

def get_sample(self, pid: str = None) -> dict:
get_instrument = instruments_get_one


def samples_get_one(self, pid: str = None) -> dict:
"""
Get an sample by pid.
Get a sample by pid.
This function has been renamed. Previous name has been maintained for backward compatibility.
Previous name was get_sample
Parameters
----------
Expand All @@ -719,9 +771,14 @@ def get_sample(self, pid: str = None) -> dict:
return None
return response.json()

def get_proposal(self, pid: str = None) -> dict:
get_sample = samples_get_one


def proposals_get_one(self, pid: str = None) -> dict:
"""
Get proposal by pid.
This function has been renamed. Previous name has been maintained for backward compatibility.
Previous name was get_proposal
Parameters
----------
Expand All @@ -743,9 +800,14 @@ def get_proposal(self, pid: str = None) -> dict:
return None
return response.json()

def get_dataset_origdatablocks(self, pid: str = None) -> dict:
get_proposal = proposals_get_one


def datasets_origdatablocks_get_one(self, pid: str = None) -> dict:
"""
Get dataset orig datablocks by dataset pid.
This function has been renamed. Previous name has been maintained for backward compatibility.
Previous name was get_dataset_origdatablocks
Parameters
----------
Expand All @@ -767,9 +829,14 @@ def get_dataset_origdatablocks(self, pid: str = None) -> dict:
return None
return response.json()

def delete_dataset(self, pid: str = None) -> dict:
get_dataset_origdatablocks = datasets_origdatablocks_get_one


def datasets_delete(self, pid: str = None) -> dict:
"""
Delete dataset by pid
This function has been renamed. Previous name has been maintained for backward compatibility.
Previous name was delete_dataset
Parameters
----------
Expand All @@ -792,6 +859,8 @@ def delete_dataset(self, pid: str = None) -> dict:
return None
return response.json()

delete_dataset = datasets_delete


def get_file_size(pathobj):
filesize = pathobj.lstat().st_size
Expand Down

0 comments on commit 08d524a

Please sign in to comment.