Added a more intelligeble class name in the memoization loading.

chiffa · Feb 3, 2016 · 0bc156a · 0bc156a
1 parent 0cca811
commit 0bc156a
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Showing 5 changed files with 29 additions and 28 deletions.
diff --git a/bioflow/analysis_pipeline_example.py b/bioflow/analysis_pipeline_example.py
@@ -19,10 +19,10 @@
 
 
 # first, let's clear logs:
-# clear_logs()
+clear_logs()
 
 # # setting static folders and urls for the databases
-# set_folders('/home/andrei/support')
+set_folders('/home/andrei/support')
 # # pulling the online databases
 # StructureGenerator.pull_online_dbs()
 # # setting the organism to yeast

diff --git a/bioflow/configs/sources.ini b/bioflow/configs/sources.ini
@@ -8,7 +8,7 @@ load = HumanBinaryHQ.txt
 location = /home/andrei/support/HiNT
 
 [BIOGRID]
-load = Homo_Sapiens
+load = Homo_sapiens
 location = /home/andrei/support/BioGRID
 
 [INTERNAL]

diff --git a/bioflow/configs_manager.py b/bioflow/configs_manager.py
@@ -60,7 +60,7 @@ class StructureGenerator(object):
         'shortname': 'human',
         'tax_id': '9606',
         'Reactome_name': 'Homo_sapiens.owl',
-        'Biogrid_name': 'Homo_Sapiens',
+        'Biogrid_name': 'Homo_sapiens',
         'HINT_name': 'HumanBinaryHQ.txt'}
 
     # default configuration elements for mice proteins analysis
@@ -243,8 +243,8 @@ def set_folders(file_directory, neo4jserver='http://localhost:7474',
 
 
 if __name__ == "__main__":
-    set_folders('/home/ank/datastore')
-    StructureGenerator.build_source_config('yeast')
+    set_folders('/home/andrei/support')
+    StructureGenerator.build_source_config('human')
     # pp = PrettyPrinter(indent=4)
     # pp.pprint(parse_configs())
     # StructureGenerator.pull_online_dbs()
diff --git a/bioflow/db_importers/import_main.py b/bioflow/db_importers/import_main.py
@@ -44,21 +44,21 @@ def destroy_db():
 if __name__ == "__main__":
     # clear_all(bulbs_names_dict)
     run_diagnostics(full_list)
-    # insert_reactome()
-    # run_diagnostics(full_list)
-    #
-    # # clear_all({'GO Term': (DatabaseGraph.GOTerm, "GOTerm")})
-    #
-    # go_terms, go_terms_structure = GOTermsParser().parse_go_terms(main_configs.GeneOntology)
-    # import_gene_ontology(go_terms, go_terms_structure)
-    #
-    # # memoize_go_terms()
-    #
-    # # clear_all({'UNIPROT': (DatabaseGraph.UNIPORT, "UNIPROT")})
-    #
-    # uniprot = UniProtParser(main_configs.up_tax_ids).parse_uniprot(main_configs.UNIPROT_source)
-    # reactome_acnum_bindings = pull_up_acc_nums_from_reactome()
-    # import_uniprots(uniprot, reactome_acnum_bindings)
+    insert_reactome()
+    run_diagnostics(full_list)
+
+    # clear_all({'GO Term': (DatabaseGraph.GOTerm, "GOTerm")})
+
+    go_terms, go_terms_structure = GOTermsParser().parse_go_terms(main_configs.GeneOntology)
+    import_gene_ontology(go_terms, go_terms_structure)
+
+    # memoize_go_terms()
+
+    # clear_all({'UNIPROT': (DatabaseGraph.UNIPORT, "UNIPROT")})
+
+    uniprot = UniProtParser(main_configs.up_tax_ids).parse_uniprot(main_configs.UNIPROT_source)
+    reactome_acnum_bindings = pull_up_acc_nums_from_reactome()
+    import_uniprots(uniprot, reactome_acnum_bindings)
 
     cross_ref_hint()
     cross_ref_bio_grid()

diff --git a/bioflow/neo4j_db/db_io_routines.py b/bioflow/neo4j_db/db_io_routines.py
@@ -68,13 +68,14 @@ def annotations_2_node_chars(node_generator):
             log.warning("%s is floating alone in the wild. He feels lonely. %s",
                         str(node), 'The database is most likely broken.')
 
-        for object_node in annotates_backlink_generator:
-            node_bulbs_id = get_bulbs_id(object_node)
-            node_legacy_id = object_node.ID
-            node_type = object_node.element_type
-            node_display_name = object_node.displayName
-            referenced_nodes.append((node_type, node_display_name,
-                                     node_bulbs_id, node_legacy_id))
+        else:
+            for object_node in annotates_backlink_generator:
+                node_bulbs_id = get_bulbs_id(object_node)
+                node_legacy_id = object_node.ID
+                node_type = object_node.element_type
+                node_display_name = object_node.displayName
+                referenced_nodes.append((node_type, node_display_name,
+                                         node_bulbs_id, node_legacy_id))
 
     return referenced_nodes