Finish updating other mapping databases

biopragmatics · Apr 30, 2024 · 8592f25 · 8592f25
1 parent 32662ba
commit 8592f25
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Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/src/semra/landscape/diseases.py b/src/semra/landscape/diseases.py
@@ -86,6 +86,7 @@
     priority_pickle_path=MODULE.join(name="priority.pkl"),
     priority_sssom_path=MODULE.join(name="priority.sssom.tsv"),
     configuration_path=MODULE.join(name="configuration.json"),
+    zenodo_record=11091885,
 )
 
 
@@ -94,6 +95,7 @@ def main():
     """Build the mapping database for disease terms."""
     # Takes about 2 hours
     CONFIGURATION.get_mappings(refresh_raw=True, refresh_processed=True)
+    CONFIGURATION.upload_zenodo()
 
 
 if __name__ == "__main__":

diff --git a/src/semra/landscape/genes.py b/src/semra/landscape/genes.py
@@ -59,23 +59,25 @@
         Mutation(source="umls", confidence=0.8),
         Mutation(source="ncit", confidence=0.8),
     ],
-    raw_pickle_path=MODULE.join(name="raw.pkl"),
-    raw_sssom_path=MODULE.join(name="raw.sssom.tsv"),
+    raw_pickle_path=MODULE.join(name="raw.pkl.gz"),
+    raw_sssom_path=MODULE.join(name="raw.sssom.tsv.gz"),
     # raw_neo4j_path=MODULE.join("neo4j_raw"),
-    processed_pickle_path=MODULE.join(name="processed.pkl"),
-    processed_sssom_path=MODULE.join(name="processed.sssom.tsv"),
+    processed_pickle_path=MODULE.join(name="processed.pkl.gz"),
+    processed_sssom_path=MODULE.join(name="processed.sssom.tsv.gz"),
     processed_neo4j_path=MODULE.join("neo4j"),
     processed_neo4j_name="semra-gene",
-    priority_pickle_path=MODULE.join(name="priority.pkl"),
-    priority_sssom_path=MODULE.join(name="priority.sssom.tsv"),
+    priority_pickle_path=MODULE.join(name="priority.pkl.gz"),
+    priority_sssom_path=MODULE.join(name="priority.sssom.tsv.gz"),
     configuration_path=MODULE.join(name="configuration.json"),
+    zenodo_record=11092012,
 )
 
 
 @click.command()
 def main():
     """Build the mapping database for gene terms."""
     CONFIGURATION.get_mappings(refresh_raw=True, refresh_processed=True)
+    CONFIGURATION.upload_zenodo()
 
 
 if __name__ == "__main__":