fixed notebooks

docs/requirements.txt

@@ -1,6 +1,6 @@
 requests
 psycopg2
-pandas
+pandas==1.5.3
 pandasql
 jsonpath_rw
 setuptools~=50.3.2
@@ -11,5 +11,5 @@ sphinx-autodoc-typehints
 docutils
 myst-parser
 sphinx_rtd_theme
-
+neuprint-python
 numpy>=1.22.2 # not directly required, pinned by Snyk to avoid a vulnerability

src/vfb_connect.egg-info/PKG-INFO

@@ -1,55 +1,56 @@
 Metadata-Version: 2.1
 Name: vfb-connect
-Version: 1.2.12.dev34+0ddbd15.dirty
+Version: 1.2.20.dev7+f222e3e.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
-
-# 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)

src/vfb_connect/neo/neo4j_tools.py

@@ -229,7 +229,7 @@ def get_lookup(self, limit_by_prefix=None, include_individuals=False,
                 lookup_query = "MATCH (a:%s) %s AND EXISTS(a.synonyms) OR (a)-[:has_reference {typ:'syn'}]->(:pub:Individual) " \
                                "UNWIND a.synonyms AS synonym2 " \
                                "RETURN DISTINCT a.short_form AS id, synonym2 AS name " \
-                               "UNION ALL MATCH (n)-[r:has_reference {typ:'syn'}]->(:pub:Individual) " \
+                               "UNION ALL MATCH (a)-[r:has_reference {typ:'syn'}]->(:pub:Individual) " \
                                "UNWIND r.value AS synonym1 " \
                                "WITH a.short_form AS id, synonym1 AS synonym " \
                                "RETURN DISTINCT id, synonym AS name" % (l, where)