Merge pull request #195 from VirtualFlyBrain/hotfix1

include symbols in templates
VirtualFlyBrain · Sep 4, 2024 · d556234 · d556234
2 parents a8ce672 + ec0deff
commit d556234
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/src/vfb_connect/cross_server_tools.py b/src/vfb_connect/cross_server_tools.py
@@ -260,6 +260,7 @@ def lookup_id(self, key, return_curie=False, allow_subsitutions=True, subsitutio
         print(f"\033[31mError:\033[0m Unrecognized value: \033[31m{key}\033[0m")
         return ''
 
+    @property
     def __version__(self):
         from importlib.metadata import version, PackageNotFoundError
         return version('vfb_connect')
@@ -742,13 +743,13 @@ def get_images(self, short_forms: iter, template=None, image_folder=None, image_
         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):
+    def get_templates(self, summary=True, return_dataframe=True, include_symbols=False):
         """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)
+        return self.neo_query_wrapper.get_templates(summary=summary, return_dataframe=return_dataframe, include_symbols=include_symbols)
 
     @batch_query
     def get_terms_by_xref(self, xrefs: iter, db='', summary=True, return_dataframe=True):

diff --git a/src/vfb_connect/neo/query_wrapper.py b/src/vfb_connect/neo/query_wrapper.py
@@ -384,7 +384,7 @@ def get_datasets(self, summary=True, return_dataframe=True):
             return pd.DataFrame.from_records(results)
         return results
 
-    def get_templates(self, summary=True, return_dataframe=True):
+    def get_templates(self, summary=True, return_dataframe=True, include_symbols=False):
         """Generate JSON report of all available templates.
 
             :param summary: Optional.  Returns summary reports if `True`. Default `True`
@@ -394,7 +394,12 @@ def get_templates(self, summary=True, return_dataframe=True):
         dc = self._query("MATCH (i:Individual:Template:Anatomy) "
                          "RETURN i.short_form as sf")
         short_forms = [d['sf'] for d in dc]
-        return self.get_anatomical_individual_TermInfo(short_forms, summary=summary)
+        if include_symbols:
+            dc = self._query("MATCH (i:Individual:Template:Anatomy) ",
+                             "WHERE exists(i.symbol) and not i.symbol[0] = '' "
+                             "RETURN i.symbol[0] as s")
+            short_forms.extend([d['s'] for d in dc if d['s']])
+        return self.get_anatomical_individual_TermInfo(short_forms, summary=summary, return_dataframe=return_dataframe)
 
     def vfb_id_2_xrefs(self, vfb_id: iter, db='', id_type='', reverse_return=False):
         """Map a list of short_form IDs in VFB to external DB IDs