diff --git a/app-openbis-command-line/src/python/obis/dm/commands/download_physical.py b/app-openbis-command-line/src/python/obis/dm/commands/download_physical.py
index 1b5e94c4878e2d35613278acaa94125ba492e74e..eae1d7420be9bb8deb234619fa57f1a8d2f9aa40 100644
--- a/app-openbis-command-line/src/python/obis/dm/commands/download_physical.py
+++ b/app-openbis-command-line/src/python/obis/dm/commands/download_physical.py
@@ -60,15 +60,21 @@ class DownloadPhysical(OpenbisCommand):
return CommandResult(returncode=0, output="Download completed.")
def download_dataset(self, perm_id):
+ click_echo(f"Downloading dataset {perm_id}")
data_set = self.openbis.get_dataset(perm_id)
files = self.files if self.files is not None else data_set.file_list
with cd(self.data_mgmt.invocation_path):
- target_folder = data_set.download(files, destination=self.data_mgmt.invocation_path)
+ try:
+ target_folder = data_set.download(files, destination=self.data_mgmt.invocation_path)
+ except Exception as e:
+ print(e)
+ raise e
+
if self.skip_integrity_check is not True:
invalid_files = validate_checksum(self.openbis, files, data_set.permId,
target_folder, None)
self.redownload_invalid_files_on_demand(invalid_files, target_folder, perm_id)
- click_echo(f"Files from dataset {perm_id} has been downloaded to {target_folder}")
+ click_echo(f"Files from dataset {perm_id} has been downloaded to {target_folder}")
def redownload_invalid_files_on_demand(self, invalid_files, target_folder, perm_id):
if len(invalid_files) == 0:
diff --git a/app-openbis-command-line/src/python/obis/dm/commands/search.py b/app-openbis-command-line/src/python/obis/dm/commands/search.py
index d4b2ad454ed0b47011402a553240b5977f78c67b..bb41b68df36cba2320564cee77260d6f9e2c5368 100644
--- a/app-openbis-command-line/src/python/obis/dm/commands/search.py
+++ b/app-openbis-command-line/src/python/obis/dm/commands/search.py
@@ -24,43 +24,38 @@ class Search(OpenbisCommand):
Command to search data in openBIS.
"""
- def __init__(self, dm, type_code, space, project, experiment, property_code, property_value,
- save_path):
+ def __init__(self, dm, filters, save_path):
"""
:param dm: data management
- :param type_code: Filter by type code
- :param space: Filter by space path
- :param project: Filter by project path
- :param experiment: Filter by experiment
- :param property_code: Filter by property_code, needs to be set together with property_value
- :param property_value: Filter by property_value, needs to be set together with property_code
+ :param filters: Dictionary of filter to be used during search
:param save_path: Path to save results. If not set, results will not be saved.
"""
- self.property_value = property_value
- self.property_code = property_code
- self.experiment = experiment
- self.project = project
- self.space = space
- self.type_code = type_code
+ self.filters = filters
self.save_path = save_path
self.load_global_config(dm)
super(Search, self).__init__(dm)
def search_samples(self):
properties = None
- if self.property_code is not None and self.property_value is not None:
+ if self.filters['property_code'] is not None and self.filters['property_value'] is not None:
properties = {
- self.property_code: self.property_value,
+ self.filters['property_code']: self.filters['property_value'],
}
- search_results = self.openbis.get_samples(
- space=self.space,
- project=self.project, # Not Supported with Project Samples disabled
- experiment=self.experiment,
- type=self.type_code,
- where=properties,
- props="*" # Fetch all properties
- )
+ args = dict(space=self.filters['space'],
+ project=self.filters['project'], # Not Supported with Project Samples disabled
+ experiment=self.filters['experiment'],
+ type=self.filters['type_code'],
+ where=properties,
+ attrs=["parents", "children"],
+ props="*") # Fetch all properties
+
+ if self.filters['registration_date'] is not None:
+ args['registrationDate'] = self.filters['registration_date']
+ if self.filters['modification_date'] is not None:
+ args['modificationDate'] = self.filters['modification_date']
+
+ search_results = self.openbis.get_samples(**args)
click_echo(f"Objects found: {len(search_results)}")
if self.save_path is not None:
click_echo(f"Saving search results in {self.save_path}")
@@ -77,20 +72,24 @@ class Search(OpenbisCommand):
output="Configuration fileservice_url needs to be set for download.")
properties = None
- if self.property_code is not None and self.property_value is not None:
+ if self.filters['property_code'] is not None and self.filters['property_value'] is not None:
properties = {
- self.property_code: self.property_value,
+ self.filters['property_code']: self.filters['property_value'],
}
+ args = dict(space=self.filters['space'],
+ project=self.filters['project'], # Not Supported with Project Samples disabled
+ experiment=self.filters['experiment'],
+ type=self.filters['type_code'],
+ where=properties,
+ attrs=["parents", "children"],
+ props="*") # Fetch all properties
+
+ if self.filters['registration_date'] is not None:
+ args['registrationDate'] = self.filters['registration_date']
+ if self.filters['modification_date'] is not None:
+ args['modificationDate'] = self.filters['modification_date']
- datasets = self.openbis.get_datasets(
- space=self.space,
- project=self.project, # Not Supported with Project Samples disabled
- experiment=self.experiment,
- type=self.type_code,
- where=properties,
- attrs=["parents", "children"],
- props="*" # Fetch all properties
- )
+ datasets = self.openbis.get_datasets(**args)
click_echo(f"Data sets found: {len(datasets)}")
if self.save_path is not None:
diff --git a/app-openbis-command-line/src/python/obis/dm/data_mgmt.py b/app-openbis-command-line/src/python/obis/dm/data_mgmt.py
index 92c5a514662296f08e1d4eae3995624e1f0624f1..eacdecccc553ffb793bd2690b31ae1f66bd7e5e2 100644
--- a/app-openbis-command-line/src/python/obis/dm/data_mgmt.py
+++ b/app-openbis-command-line/src/python/obis/dm/data_mgmt.py
@@ -229,29 +229,17 @@ class AbstractDataMgmt(metaclass=abc.ABCMeta):
return
@abc.abstractmethod
- def search_object(self, type_code, space, project, experiment, property_code, property_value,
- save):
+ def search_object(self, filters, save):
"""Search for objects in openBIS using filtering criteria.
- :param type_code: Type of searched object.
- :param space: Space path to filter object.
- :param project: Project path to filter object.
- :param experiment: Experiment path to filter object.
- :param property_code: Custom property code to search by, property_value must be set as well.
- :param property_value: Custom property value to search by, property_code must be set as well.
+ :param filters: dictionary of filter parameters
:param save: File path to save results. If missing, search results will not be saved.
"""
return
@abc.abstractmethod
- def search_data_set(self, type_code, space, project, experiment, property_code, property_value,
- save):
+ def search_data_set(self, filters, save):
"""Search for datasets in openBIS using filtering criteria.
- :param type_code: Type of searched object.
- :param space: Space path to filter object.
- :param project: Project path to filter object.
- :param experiment: Experiment path to filter object.
- :param property_code: Custom property code to search by, property_value must be set as well.
- :param property_value: Custom property value to search by, property_code must be set as well.
+ :param filters: dictionary of filter parameters
:param save: File path to save results. If missing, search results will not be saved.
"""
return
@@ -654,16 +642,12 @@ class PhysicalDataMgmt(AbstractDataMgmt):
cmd = Upload(self, sample_id, data_set_type, files)
return cmd.run()
- def search_object(self, type_code, space, project, experiment, property_code, property_value,
- save):
- cmd = Search(self, type_code, space, project, experiment, property_code, property_value,
- save)
+ def search_object(self,filters, save):
+ cmd = Search(self, filters, save)
return cmd.search_samples()
- def search_data_set(self, type_code, space, project, experiment, property_code, property_value,
- save):
- cmd = Search(self, type_code, space, project, experiment, property_code, property_value,
- save)
+ def search_data_set(self, filters, save):
+ cmd = Search(self, filters, save)
return cmd.search_data_sets()
def config(self, category, is_global, is_data_set_property, operation_type, prop=None,
diff --git a/app-openbis-command-line/src/python/obis/scripts/cli.py b/app-openbis-command-line/src/python/obis/scripts/cli.py
index 3c626e9762e4f1df9d1da63a14add25f12497598..33cc94059f4712f7e5d8d54a4c7ca3a424ce105a 100644
--- a/app-openbis-command-line/src/python/obis/scripts/cli.py
+++ b/app-openbis-command-line/src/python/obis/scripts/cli.py
@@ -279,6 +279,10 @@ _search_params = [
click.option('-property', 'property_code', default=None, help='Property code'),
click.option('-property-value', 'property_value', default=None,
help='Property value'),
+ click.option('-registration-date', '--registration-date', 'registration_date', default=None,
+ help='Registration date, it can be in the format "oYYYY-MM-DD" (e.g. ">2023-01-01")'),
+ click.option('-modification-date', '--modification-date', 'modification_date', default=None,
+ help='Modification date, it can be in the format "oYYYY-MM-DD" (e.g. ">2023-01-01")'),
click.option('-save', '--save', default=None, help='Filename to save results'),
]
@@ -322,10 +326,11 @@ def data_set_clear(ctx, data_set_settings):
@data_set.command('search', short_help="Search for datasets using a filtering criteria.")
@add_params(_search_params)
@click.pass_context
-def data_set_search(ctx, type_code, space, project, experiment, property_code, property_value,
- save):
+def data_set_search(ctx, type_code, space, project, experiment, registration_date,
+ modification_date, property_code, property_value, save):
if all(v is None for v in
- [type_code, space, project, experiment, property_code, property_value]):
+ [type_code, space, project, experiment, registration_date, modification_date,
+ property_code, property_value]):
click_echo("You must provide at least one filtering criteria!")
return -1
if (property_code is None and property_value is not None) or (
@@ -333,19 +338,12 @@ def data_set_search(ctx, type_code, space, project, experiment, property_code, p
click_echo("Property code and property value need to be specified!")
return -1
ctx.obj['runner'] = DataMgmtRunner(ctx.obj, halt_on_error_log=False)
- ctx.invoke(_data_set_search, type_code=type_code, space=space,
- project=project, experiment=experiment, property_code=property_code,
- property_value=property_value, save=save)
-
-
-@add_params(_search_params)
-@click.pass_context
-def _data_set_search(ctx, type_code, space, project, experiment, property_code, property_value,
- save):
+ filters = dict(type_code=type_code, space=space,
+ project=project, experiment=experiment, property_code=property_code,
+ registration_date=registration_date, modification_date=modification_date,
+ property_value=property_value)
return ctx.obj['runner'].run("data_set_search",
- lambda dm: dm.search_data_set(type_code, space, project,
- experiment, property_code,
- property_value, save)),
+ lambda dm: dm.search_data_set(filters, save)),
# # object: object_id
@@ -387,9 +385,11 @@ def object_clear(ctx, object_settings):
@object.command('search', short_help="Search for samples using a filtering criteria.")
@add_params(_search_params)
@click.pass_context
-def object_search(ctx, type_code, space, project, experiment, property_code, property_value, save):
+def object_search(ctx, type_code, space, project, experiment, registration_date,
+ modification_date, property_code, property_value, save):
if all(v is None for v in
- [type_code, space, project, experiment, property_code, property_value]):
+ [type_code, space, project, experiment, registration_date, modification_date,
+ property_code, property_value]):
click_echo("You must provide at least one filtering criteria!")
return -1
if (property_code is None and property_value is not None) or (
@@ -397,17 +397,12 @@ def object_search(ctx, type_code, space, project, experiment, property_code, pro
click_echo("Property code and property value need to be specified!")
return -1
ctx.obj['runner'] = DataMgmtRunner(ctx.obj, halt_on_error_log=False)
- ctx.invoke(_object_search, type_code=type_code, space=space,
- project=project, experiment=experiment, property_code=property_code,
- property_value=property_value, save=save)
-
-
-@add_params(_search_params)
-@click.pass_context
-def _object_search(ctx, type_code, space, project, experiment, property_code, property_value, save):
+ filters = dict(type_code=type_code, space=space,
+ project=project, experiment=experiment, property_code=property_code,
+ registration_date=registration_date, modification_date=modification_date,
+ property_value=property_value)
return ctx.obj['runner'].run("object_search",
- lambda dm: dm.search_object(type_code, space, project, experiment,
- property_code, property_value, save)),
+ lambda dm: dm.search_object(filters, save))
# # collection: collection_id
@@ -764,7 +759,8 @@ _download_params = [
help='An output .CSV file from `obis data_set search` command with the list of' +
' objects to download datasets from'),
click.option(
- '-f', '--file', help='File in the data set to download - downloading all if not given.'),
+ '-f', '--file', 'file',
+ help='File in the data set to download - downloading all if not given.'),
click.option('-s', '--skip_integrity_check', default=False, is_flag=True,
help='Flag to skip file integrity check with checksums'),
]
diff --git a/docs/app-openbis-command-line/README.md b/docs/app-openbis-command-line/README.md
index 4b8b3566a277bbdb91be4ca2ed9fa6bcee055e38..ba345db59ff1a8f530213af8bef51f1e89c743c9 100644
--- a/docs/app-openbis-command-line/README.md
+++ b/docs/app-openbis-command-line/README.md
@@ -205,6 +205,12 @@ Options:
-project, --project TEXT Full project identification code
-experiment, --experiment TEXT Full experiment code
-type, --type TEXT Type code
+ -registration-date, --registration-date TEXT
+ Registration date, it can be in the format
+ "oYYYY-MM-DD" (e.g. ">2023-01-31", "=2023-01-31", "<2023-01-31")
+ -modification-date, --modification-date TEXT
+ Modification date, it can be in the format
+ "oYYYY-MM-DD" (e.g. ">2023-01-31", "=2023-01-31", "<2023-01-31")
-property TEXT Property code
-property-value TEXT Property value
-save, --save TEXT Directory name to save results
@@ -269,7 +275,13 @@ Options:
-type, --type TEXT Type code to filter by
-space, --space TEXT Space code
-project, --project TEXT Full project identification code
- -experiment, --experiment TEXT Full experiment code
+ -experiment, --experiment TEXT Full experiment
+ -registration-date, --registration-date TEXT
+ Registration date, it can be in the format
+ "oYYYY-MM-DD" (e.g. ">2023-01-31", "=2023-01-31", "<2023-01-31")
+ -modification-date, --modification-date TEXT
+ Modification date, it can be in the format
+ "oYYYY-MM-DD" (e.g. ">2023-01-31", "=2023-01-31", "<2023-01-31")
-property TEXT Property code
-property-value TEXT Property value
-save, --save TEXT File name to save results in csv format