adding wrapped methods

VirtualFlyBrain · Aug 13, 2024 · 5be15a7 · 5be15a7
1 parent 0798b15
commit 5be15a7
Show file tree

Hide file tree

Showing 7 changed files with 2,410 additions and 3,391 deletions.
diff --git a/docs/source/tutorials/connectomics.ipynb b/docs/source/tutorials/connectomics.ipynb
diff --git a/docs/source/tutorials/discovery.ipynb b/docs/source/tutorials/discovery.ipynb
diff --git a/docs/source/tutorials/overview.ipynb b/docs/source/tutorials/overview.ipynb
diff --git a/requirements.txt b/requirements.txt
@@ -3,7 +3,8 @@ psycopg2
 pandas
 pandasql
 jsonpath_rw
-setuptools~=50.3.2
+setuptools
 neuprint-python
 pysolr
-bottleneck<=1.3.6
+bottleneck<=1.3.6
+backports.tarfile
diff --git a/src/vfb_connect.egg-info/PKG-INFO b/src/vfb_connect.egg-info/PKG-INFO
@@ -1,56 +1,58 @@
 Metadata-Version: 2.1
-Name: vfb-connect
-Version: 1.2.20.dev45+fcedd60.dirty
+Name: vfb_connect
+Version: 1.3.0.dev2+0798b15.dirty
 Summary: Wrapper for querying VirtualFlyBrain servers.
 Home-page: https://github.com/VirtualFlyBrain/VFB_connect
 Author: David Osumi-Sutherland
 Author-email: [email protected]
-License: UNKNOWN
 Project-URL: Bug Reports, https://github.com/VirtualFlyBrain/VFB_connect/issues
 Project-URL: Source, https://github.com/VirtualFlyBrain/VFB_connect
 Project-URL: Documentation, https://vfb-connect.readthedocs.io/en/stable/
-Description: # VFB_connect [![test_vfb-connect](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/test_vfb-connect.yml/badge.svg)](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/test_vfb-connect.yml) [![publish-to-pypi](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/publish-to-pypi.yml/badge.svg)](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/publish-to-pypi.yml) [![PyPI version](https://badge.fury.io/py/vfb-connect.svg)](https://pypi.org/project/vfb-connect/)
-        [![test_notebooks](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/test_notebooks.yml/badge.svg)](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/test_notebooks.yml) [![Documentation Status](https://readthedocs.org/projects/vfb-connect/badge/?version=stable)](https://vfb-connect.readthedocs.io/en/stable/?badge=latest)
-
-        VFB_connect is a Python lib that wraps data/knowledgeBase query endpoints and returns VFB_json.
-
-
-        Available on PyPi:
-
-        ` pip install vfb_connect `
-
-
-          ## Some examples:
-
-         ```python
-
-        from vfb_connect.cross_server_tools import VfbConnect
-
-        # VFB connect object wraps connections and queries to public VFB servers.
-
-        vc=VfbConnect()
-
-        # Get TermInfo for Types/Classes, DataSets and anatomical individuals.
-
-        vc.neo_query_wrapper.get_type_TermInfo(['FBbt_00003686'])
-
-        vc.neo_query_wrapper.get_DataSet_TermInfo(['Ito02013'])
-
-        vc.neo_query_wrapper.get_anatomical_individual_TermInfo(['VFB_00010001'])
-
-        # Get all terms relevant to a brain region (all parts and all overlapping cells.  Query by label supported by default.
-
-        vc.get_terms_by_region('fan-shaped body')
-
-        ```
-
-        TermInfo return values conform to [VFB_json_schema](https://virtualflybrain.github.io/schema_doc.html)
-
-        For more examples see our [Quick Guide Jupyter Notebook](https://github.com/VirtualFlyBrain/VFB_connect/blob/master/snippets/VFB_connect_Quick_Guide.ipynb)
-
-Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Programming Language :: Python :: 3
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: pandas
+Requires-Dist: jsonpath_rw
+
+# VFB_connect [![test_vfb-connect](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/test_vfb-connect.yml/badge.svg)](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/test_vfb-connect.yml) [![publish-to-pypi](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/publish-to-pypi.yml/badge.svg)](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/publish-to-pypi.yml) [![PyPI version](https://badge.fury.io/py/vfb-connect.svg)](https://pypi.org/project/vfb-connect/)
+[![test_notebooks](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/test_notebooks.yml/badge.svg)](https://github.com/VirtualFlyBrain/VFB_connect/actions/workflows/test_notebooks.yml) [![Documentation Status](https://readthedocs.org/projects/vfb-connect/badge/?version=stable)](https://vfb-connect.readthedocs.io/en/stable/?badge=latest)
+
+VFB_connect is a Python lib that wraps data/knowledgeBase query endpoints and returns VFB_json.
+
+
+Available on PyPi:
+
+` pip install vfb_connect `
+
+
+  ## Some examples:
+
+ ```python
+
+from vfb_connect.cross_server_tools import VfbConnect
+
+# VFB connect object wraps connections and queries to public VFB servers.
+
+vc=VfbConnect()
+
+# Get TermInfo for Types/Classes, DataSets and anatomical individuals.
+
+vc.neo_query_wrapper.get_type_TermInfo(['FBbt_00003686'])
+
+vc.neo_query_wrapper.get_DataSet_TermInfo(['Ito02013'])
+
+vc.neo_query_wrapper.get_anatomical_individual_TermInfo(['VFB_00010001'])
+
+# Get all terms relevant to a brain region (all parts and all overlapping cells.  Query by label supported by default.
+
+vc.get_terms_by_region('fan-shaped body')
+
+```
+
+TermInfo return values conform to [VFB_json_schema](https://virtualflybrain.github.io/schema_doc.html)
+
+For more examples see our [Quick Guide Jupyter Notebook](https://github.com/VirtualFlyBrain/VFB_connect/blob/master/snippets/VFB_connect_Quick_Guide.ipynb)
diff --git a/src/vfb_connect/cross_server_tools.py b/src/vfb_connect/cross_server_tools.py
@@ -432,4 +432,74 @@ def get_transcriptomic_profile(self, cell_type, gene_type=False, return_datafram
             return pd.DataFrame.from_records(dc)
         else:
             return dc
+
+    #  Wrapped neo_query_wrapper methods
+    def get_datasets(self, summary=True, return_dataframe=True):
+        """Get all datasets in the database.
 
+        :return: List of datasets in the database.
+        :rtype: list
+        """
+        return self.neo_query_wrapper.get_datasets(summary=summary, return_dataframe=return_dataframe)
+
+    def get_images(self, short_forms, template=None, image_folder=None, image_type='swc', stomp=False):
+        """Get images for a list of individuals.
+
+        :param short_forms: List of short_form IDs for individuals.
+        :param template: Optional. Template name.
+        :param image_folder: Optional. Folder to save image files & manifest to.
+        :param image_type: Optional. Image type (file extension).
+        :param stomp: Optional. Overwrite image_folder if already exists.
+        :return: Manifest as Pandas DataFrame
+        """
+        return self.neo_query_wrapper.get_images(short_forms, template=template, image_folder=image_folder,
+                                                 image_type=image_type, stomp=stomp)
+
+    def get_templates(self, summary=True, return_dataframe=True):
+        """Get all templates in the database.
+
+        :return: List of templates in the database.
+        :rtype: list
+        """
+        return self.neo_query_wrapper.get_templates(summary=summary, return_dataframe=return_dataframe)
+
+    def get_terms_by_xref(self, xrefs, db, summary=True, return_dataframe=True):
+        """Get terms by cross-reference.
+
+        :param xrefs: List of cross-references.
+        :param db: Database name.
+        :return: List of terms.
+        :rtype: list
+        """
+        return self.neo_query_wrapper.get_terms_by_xref(xrefs, db=db, summary=summary, return_dataframe=return_dataframe)
+
+    def get_vfb_id_by_xref(self, xrefs, db, summary=True, return_dataframe=True):
+        """Get VFB ID by cross-reference.
+
+        :param xrefs: List of cross-references.
+        :param db: Database name.
+        :return: List of VFB IDs.
+        :rtype: list
+        """
+        return self.neo_query_wrapper.xref_2_vfb_id(xrefs, db=db, summary=summary, return_dataframe=return_dataframe)
+
+    def get_xref_by_vfbid(self, vfbids, db, summary=True, return_dataframe=True):
+        """Get cross-reference by VFB ID.
+
+        :param vfbids: List of VFB IDs.
+        :param db: Database name.
+        :return: List of cross-references.
+        :rtype: list
+        """
+        return self.neo_query_wrapper.vfb_id_2_xrefs(vfbids, db=db, summary=summary, return_dataframe=return_dataframe)
+
+    def get_images_by_filename(self, filenames, dataset=None, summary=True, return_dataframe=True):
+        """Get images by filename.
+
+        :param filenames: List of filenames.
+        :param dataset: Optional. Dataset name.
+        :return: List of images.
+        :rtype: list
+        """
+        return self.neo_query_wrapper.get_images_by_filename(filenames, dataset=dataset, summary=summary,
+                                                             return_dataframe=return_dataframe)
diff --git a/src/vfb_connect/neo/query_wrapper.py b/src/vfb_connect/neo/query_wrapper.py
@@ -313,7 +313,7 @@ def get_dbs(self):
                 "return i.short_form"
         return [d['i.short_form'] for d in self._query(query)]
 
-    def get_datasets(self, summary=True):
+    def get_datasets(self, summary=True, return_datasets=True):
         """Generate JSON report of all datsets.
 
             :param summary: Optional. Returns summary reports if `True`. Default `True`
@@ -324,7 +324,10 @@ def get_datasets(self, summary=True):
         dc = self._query("MATCH (ds:DataSet) "
                          "RETURN ds.short_form AS sf")
         short_forms = [d['sf'] for d in dc]
-        return self.get_DataSet_TermInfo(short_forms, summary=summary)
+        results = self.get_DataSet_TermInfo(short_forms, summary=summary)
+        if return_datasets and summary:
+            return pd.DataFrame.from_records(results)
+        return results
 
     def get_templates(self, summary=True):
         """Generate JSON report of all available templates.