v0.3.7

CHANGELOG.md

@@ -1,5 +1,16 @@
 # Change log
 
+## v0.3.7
+
+### Main changes
+
+- Separate `Dataset.from_dataseries` and `Dataset.from_flexilims` to avoid confusion
+
+### Minor
+
+- `get_children` output is filtered to contain only relevant columns when   `children_datatype` is not None
+
+### Bugfixes
 ## v0.3.6
 
 ### Main changes

flexiznam/main.py

@@ -968,11 +968,14 @@ def get_children(
     if parent_id is None:
         assert parent_name is not None, "Must provide either parent_id or parent_name"
         parent_id = get_id(parent_name, flexilims_session=flexilims_session)
-    results = format_results(flexilims_session.get_children(parent_id))
+    results = format_results(
+        flexilims_session.get_children(parent_id), return_list=True
+    )
     if not len(results):
-        return results
+        return pd.DataFrame(results)
     if children_datatype is not None:
-        results = results.loc[results.type == children_datatype, :]
+        results = [r for r in results if r["type"] == children_datatype]
+    results = pd.DataFrame(results)
     results.set_index("name", drop=False, inplace=True)
     return results
 
@@ -1046,8 +1049,8 @@ def get_datasets(
                 datapath_dict[recording_id] = datapaths
         else:
             datapath_dict[recording_id] = [
-                flexiznam.Dataset.from_flexilims(
-                    data_series=ds, flexilims_session=flexilims_session
+                flexiznam.Dataset.from_dataseries(
+                    dataseries=ds, flexilims_session=flexilims_session
                 )
                 for _, ds in datasets.iterrows()
             ]
@@ -1085,7 +1088,7 @@ def generate_name(datatype, name, flexilims_session=None, project_id=None):
     return name
 
 
-def format_results(results):
+def format_results(results, return_list=False):
     """Make request output a nice DataFrame
 
     This will crash if any attribute is also present in the flexilims reply,
@@ -1095,6 +1098,7 @@ def format_results(results):
 
     Args:
         results (:obj:`list` of :obj:`dict`): Flexilims reply
+        return_list (bool): if True, return a list of dicts instead of a DataFrame
 
     Returns:
         :py:class:`pandas.DataFrame`: Reply formatted as a DataFrame
@@ -1108,5 +1112,6 @@ def format_results(results):
                 )
             result[attr_name] = attr_value
         result.pop("attributes")
-    df = pd.DataFrame(results)
-    return df
+    if return_list:
+        return results
+    return pd.DataFrame(results)

flexiznam/schema/datasets.py

@@ -56,44 +56,57 @@ def from_flexilims(
         project=None,
         name=None,
         id=None,
-        data_series=None,
         flexilims_session=None,
     ):
-        """Loads a dataset from flexilims.
+        """Loads a dataset from flexilims
 
         If the dataset_type attribute of the flexilims entry defined in
         Dataset.SUBCLASSES,this subclass will be used. Otherwise a generic Dataset is
         returned
 
         Args:
-            project: Name of the project or hexadecimal project_id
-            name: Unique name of the dataset on flexilims
-            id: Hexadecimal id of the dataset on flexilims
-            data_series: default to None. pd.Series as returned by flz.get_entities.
-                If provided, supersedes project, name and id.
-            flexilims_session: authentication session to access flexilims
+            project (str, optional): Name of the project or hexadecimal project_id. If
+                not provided, can be read from flexilims_session
+            name (str, optional): Unique name of the dataset on flexilims. Ignored if
+                `dataseries` is provided
+            id (str, optional): Hexadecimal id of the dataset on flexilims. Ignored if
+                `dataseries` is provided
+            flexilims_session (flexilims.Session, optional): authentication session to
+                access flexilims.
         """
-        if data_series is not None:
-            if (project is not None) or (name is not None):
-                raise AttributeError("Specify either data_series OR project + name/id")
-        else:
-            data_series = flz.get_entity(
-                project_id=project,
-                datatype="dataset",
-                name=name,
-                id=id,
-                flexilims_session=flexilims_session,
+        dataseries = flz.get_entity(
+            project_id=project,
+            datatype="dataset",
+            name=name,
+            id=id,
+            flexilims_session=flexilims_session,
+        )
+
+        if dataseries is None:
+            if project is None:
+                project = flexilims_session.project_id
+            raise FlexilimsError(
+                "No dataset named {} in project {}".format(name, project)
             )
+        ds = Dataset.from_dataseries(dataseries, flexilims_session=flexilims_session)
+        return ds
 
-            if data_series is None:
-                if project is None:
-                    project = flexilims_session.project_id
-                raise FlexilimsError(
-                    "No dataset named {} in project {}".format(name, project)
-                )
-        dataset_type = data_series.dataset_type
+    @staticmethod
+    def from_dataseries(
+        dataseries,
+        flexilims_session=None,
+    ):
+        """Create dataset from a flexilims dataseries
+
+        This function does not call flexilims, but uses the dataseries object directly.
+        Args:
+            dataseries (flexilims.DataSeries): flexilims dataseries object
+            flexilims_session (flexilims.Session, optional): authentication session to
+                access flexilims. Will be added to dataset object.
+        """
+        dataset_type = dataseries.dataset_type
 
-        kwargs = Dataset._format_series_to_kwargs(data_series)
+        kwargs = Dataset._format_series_to_kwargs(dataseries)
         name = kwargs.pop("name")
         kwargs["flexilims_session"] = flexilims_session
         if dataset_type in Dataset.SUBCLASSES:
@@ -204,7 +217,7 @@ def from_origin(
                 )
             elif conflicts == "skip" or conflicts == "overwrite":
                 if len(processed) == 1:
-                    return Dataset.from_flexilims(data_series=processed.iloc[0])
+                    return Dataset.from_dataseries(dataseries=processed.iloc[0])
                 else:
                     raise flz.errors.NameNotUniqueError(
                         "{} {} datasets with name starting by {} exists for {}, "

flexiznam/utils.py

@@ -465,8 +465,8 @@ def _check_path(output, element, flexilims_session, recursive, error_only):
             output.append([element.name, element.type, "Folder found", " ".join(ok), 0])
     else:
         try:
-            ds = Dataset.from_flexilims(
-                flexilims_session=flexilims_session, data_series=element
+            ds = Dataset.from_dataseries(
+                flexilims_session=flexilims_session, dataseries=element
             )
             if not ds.path_full.exists():
                 output.append(

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="flexiznam",
-    version="v0.3.6",
+    version="v0.3.7",
     url="https://github.com/znamlab/flexznam",
     license="MIT",
     author="Antonin Blot",

tests/test-results/pytest_in_tests.xml

@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="51" time="508.400" timestamp="2023-07-04T17:50:17.000292" hostname="FM70R4W0XG"><testcase classname="tests.test_2p" name="test_create_yaml" time="6.411" /><testcase classname="tests.test_2p" name="test_parse_yaml" time="2.847" /><testcase classname="tests.test_2p" name="test_flm" time="16.873" /><testcase classname="tests.test_barseq" name="test_create_yaml" time="1.543" /><testcase classname="tests.test_barseq" name="test_parse_yaml" time="5.873" /><testcase classname="tests.test_barseq" name="test_flm" time="31.002" /><testcase classname="tests.test_components.test_cli" name="test_config" time="0.212" /><testcase classname="tests.test_components.test_cli" name="test_add_password" time="0.017" /><testcase classname="tests.test_components.test_cli" name="test_create_yaml" time="0.525" /><testcase classname="tests.test_components.test_cli" name="test_make_full_yaml" time="6.748" /><testcase classname="tests.test_components.test_cli" name="test_upload" time="20.516" /><testcase classname="tests.test_components.test_cli" name="test_flm_issues" time="51.080" /><testcase classname="tests.test_components.test_main" name="test_get_flexilims_session" time="0.226" /><testcase classname="tests.test_components.test_main" name="test_format_results" time="0.013" /><testcase classname="tests.test_components.test_main" name="test_get_experimental_sessions" time="0.696" /><testcase classname="tests.test_components.test_main" name="test_get_entities" time="1.038" /><testcase classname="tests.test_components.test_main" name="test_get_entity" time="0.055" /><testcase classname="tests.test_components.test_main" name="test_get_mouse_id" time="0.219" /><testcase classname="tests.test_components.test_main" name="test_get_datasets" time="3.037" /><testcase classname="tests.test_components.test_main" name="test_add_mouse" time="2.969" /><testcase classname="tests.test_components.test_main" name="test_generate_name" time="2.836" /><testcase classname="tests.test_components.test_main" name="test_get_children" time="2.332" /><testcase classname="tests.test_components.test_main" name="test_add_entity" time="1.769" /><testcase classname="tests.test_components.test_main" name="test_update_entity" time="4.204" /><testcase classname="tests.test_components.test_mcms" name="test_get_mouse_df" time="0.508" /><testcase classname="tests.test_components.test_mcms" name="test_get_procedures" time="0.328" /><testcase classname="tests.test_components.test_utils" name="test_create_config" time="0.053" /><testcase classname="tests.test_components.test_utils" name="test_update_config" time="0.227" /><testcase classname="tests.test_components.test_utils" name="test_passwd_creation" time="0.038" /><testcase classname="tests.test_components.test_utils" name="test_check_flexilims_paths" time="59.582" /><testcase classname="tests.test_components.test_utils" name="test_check_flexilims_names" time="58.108" /><testcase classname="tests.test_components.test_utils" name="test_add_genealogy" time="118.553" /><testcase classname="tests.test_components.test_utils" name="test_clean_recursively" time="0.012" /><testcase classname="tests.test_components.test_utils" name="test_add_missing_paths" time="28.553" /><testcase classname="tests.test_components.test_utils" name="test_check_attribute" time="63.925" /><testcase classname="tests.test_components.tests_schema.test_camera_data" name="test_create_directly" time="0.010" /><testcase classname="tests.test_components.tests_schema.test_camera_data" name="test_create_from_folder" time="1.135" /><testcase classname="tests.test_components.tests_schema.test_camera_data" name="test_create_from_flexilims" time="0.898" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_dataset" time="0.011" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_constructor" time="0.008" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_dataset_flexilims_integration" time="0.936" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_from_flexilims" time="0.939" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_from_origin" time="2.929" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_update_flexilims" time="7.092" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_dataset_paths" time="0.217" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_project_project_id" time="0.012" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_dataset_type_enforcer" time="0.010" /><testcase classname="tests.test_components.tests_schema.test_harp" name="test_harp" time="0.304" /><testcase classname="tests.test_components.tests_schema.test_microscopy_data" name="test_from_folder" time="0.093" /><testcase classname="tests.test_components.tests_schema.test_scanimage_data" name="test_scanimage" time="0.298" /><testcase classname="tests.test_components.tests_schema.test_sequencing_data" name="test_from_folder" time="0.244" /></testsuite></testsuites>
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="52" time="1217.486" timestamp="2023-07-06T16:21:50.352629" hostname="FM70R4W0XG"><testcase classname="tests.test_2p" name="test_create_yaml" time="5.630" /><testcase classname="tests.test_2p" name="test_parse_yaml" time="4.056" /><testcase classname="tests.test_2p" name="test_flm" time="37.068" /><testcase classname="tests.test_barseq" name="test_create_yaml" time="3.134" /><testcase classname="tests.test_barseq" name="test_parse_yaml" time="9.162" /><testcase classname="tests.test_barseq" name="test_flm" time="57.617" /><testcase classname="tests.test_components.test_cli" name="test_config" time="0.168" /><testcase classname="tests.test_components.test_cli" name="test_add_password" time="0.016" /><testcase classname="tests.test_components.test_cli" name="test_create_yaml" time="0.451" /><testcase classname="tests.test_components.test_cli" name="test_make_full_yaml" time="4.992" /><testcase classname="tests.test_components.test_cli" name="test_upload" time="35.318" /><testcase classname="tests.test_components.test_cli" name="test_flm_issues" time="110.427" /><testcase classname="tests.test_components.test_main" name="test_get_flexilims_session" time="0.210" /><testcase classname="tests.test_components.test_main" name="test_format_results" time="0.016" /><testcase classname="tests.test_components.test_main" name="test_get_experimental_sessions" time="1.185" /><testcase classname="tests.test_components.test_main" name="test_get_entities" time="2.557" /><testcase classname="tests.test_components.test_main" name="test_get_entity" time="0.055" /><testcase classname="tests.test_components.test_main" name="test_get_mouse_id" time="0.655" /><testcase classname="tests.test_components.test_main" name="test_get_datasets" time="6.716" /><testcase classname="tests.test_components.test_main" name="test_add_mouse" time="6.767" /><testcase classname="tests.test_components.test_main" name="test_generate_name" time="6.369" /><testcase classname="tests.test_components.test_main" name="test_get_children" time="10.536" /><testcase classname="tests.test_components.test_main" name="test_add_entity" time="2.100" /><testcase classname="tests.test_components.test_main" name="test_update_entity" time="9.515" /><testcase classname="tests.test_components.test_mcms" name="test_get_mouse_df" time="0.502" /><testcase classname="tests.test_components.test_mcms" name="test_get_procedures" time="0.308" /><testcase classname="tests.test_components.test_utils" name="test_create_config" time="0.034" /><testcase classname="tests.test_components.test_utils" name="test_update_config" time="0.231" /><testcase classname="tests.test_components.test_utils" name="test_passwd_creation" time="0.049" /><testcase classname="tests.test_components.test_utils" name="test_check_flexilims_paths" time="206.289" /><testcase classname="tests.test_components.test_utils" name="test_check_flexilims_names" time="136.485" /><testcase classname="tests.test_components.test_utils" name="test_add_genealogy" time="276.362" /><testcase classname="tests.test_components.test_utils" name="test_clean_recursively" time="0.008" /><testcase classname="tests.test_components.test_utils" name="test_add_missing_paths" time="63.834" /><testcase classname="tests.test_components.test_utils" name="test_check_attribute" time="147.412" /><testcase classname="tests.test_components.tests_schema.test_camera_data" name="test_create_directly" time="0.007" /><testcase classname="tests.test_components.tests_schema.test_camera_data" name="test_create_from_folder" time="1.996" /><testcase classname="tests.test_components.tests_schema.test_camera_data" name="test_create_from_flexilims" time="2.030" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_dataset" time="0.022" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_constructor" time="0.011" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_dataset_flexilims_integration" time="2.067" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_from_flexilims" time="2.082" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_from_dataseries" time="0.014" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_from_origin" time="46.158" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_update_flexilims" time="14.295" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_dataset_paths" time="0.803" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_project_project_id" time="0.011" /><testcase classname="tests.test_components.tests_schema.test_datasets" name="test_dataset_type_enforcer" time="0.013" /><testcase classname="tests.test_components.tests_schema.test_harp" name="test_harp" time="0.571" /><testcase classname="tests.test_components.tests_schema.test_microscopy_data" name="test_from_folder" time="0.064" /><testcase classname="tests.test_components.tests_schema.test_scanimage_data" name="test_scanimage" time="0.477" /><testcase classname="tests.test_components.tests_schema.test_sequencing_data" name="test_from_folder" time="0.385" /></testsuite></testsuites>

tests/test_components/test_main.py

@@ -4,7 +4,7 @@
 import flexiznam.main as flz
 from flexiznam.config import PARAMETERS, get_password
 from flexiznam.errors import FlexilimsError, NameNotUniqueError
-from tests.tests_resources.data_for_testing import MOUSE_ID
+from tests.tests_resources.data_for_testing import MOUSE_ID, SESSION
 
 # Test functions from main.py
 from flexiznam.schema import Dataset
@@ -180,6 +180,13 @@ def test_get_children(flm_sess):
     assert isinstance(res, pd.DataFrame)
     res = flz.get_children(parent_name="mouse_physio_2p", flexilims_session=flm_sess)
     assert len(res) == 1
+    res_all = flz.get_children(parent_name=SESSION, flexilims_session=flm_sess)
+    assert (res_all.type != "recording").sum() != 0
+    res_part = flz.get_children(
+        parent_name=SESSION, flexilims_session=flm_sess, children_datatype="recording"
+    )
+    assert (res_part.type != "recording").sum() == 0
+    assert res_all.shape[1] > res_part.shape[1]
 
 
 def test_add_entity(flm_sess):
@@ -251,7 +258,7 @@ def test_update_entity(flm_sess):
     assert dbval["attributes"]["acq_num"] is None
 
     # restore database state
-    ds = Dataset.from_flexilims(data_series=original_entity, flexilims_session=flm_sess)
+    ds = Dataset.from_dataseries(dataseries=original_entity, flexilims_session=flm_sess)
     ds.update_flexilims(mode="overwrite")
     new_entity = flz.get_entity(
         datatype="dataset", name=dataset_name, flexilims_session=flm_sess