Minor fixes

logicmoo · Jul 12, 2022 · 3f0f7d5 · 3f0f7d5
1 parent b63cc6e
commit 3f0f7d5
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Showing 2 changed files with 30 additions and 1 deletion.
diff --git a/bio-mongo-load b/bio-mongo-load
@@ -0,0 +1,24 @@
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/biogrid_gene_gene_4.1.190_2020-10-19.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/ChEBI2Reactome_PE_Pathway.txt_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/codingRNA_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/COVID-19-biogrid_LATEST.tab3.zip_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/entrez_to_protein_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/GO_2020-10-21.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/NCBI2Reactome_PE_Pathway.txt_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/noncodingRNA_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/PA_gene2celltype_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/reactome_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/smpdb_chebi_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/smpdb_protein_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/uniprot2GO_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/UniProt2Reactome_PE_Pathway.txt_2020-10-20.metta
+docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/uniprot2taxonomy.metta
+
+#docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/GO_annotation_2020-10-20.metta
+#docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/concept-inhr-member.metta
+#docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/patient_gene_under_expr.metta
+#docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/Go-Plus-GO_with_definition_2020-10-20.metta
+#docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/GTEx_median_tissue_expression.metta
+#docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/string_ggi_2020-10-20.metta
+#docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/string_ppi_2020-10-20.metta
+#docker-compose exec app python das/das_upload_to_mongo.py -d BIO ./data/annotation_service/patient_gene_over_expr.metta
diff --git a/das/atomese2metta/translator.py b/das/atomese2metta/translator.py
@@ -106,6 +106,7 @@ class Translator:
     "MemberLink",
     "SetLink",
     "SimilarityLink",
+    "LazyExecutionOutputLink",
   )
 
   _ALLOWED_NODES = (
@@ -126,6 +127,9 @@ class Translator:
     "EnstNode",
     "UniprotNode",
     "RefseqNode",
+    "PharmGkbNode",
+    "SchemaNode",
+    "PatientNode",
   )
 
   IGNORED_SYMBOLS = ("stv",)
@@ -189,7 +193,8 @@ def translate(self, expressions) -> Union[Symbol, Expression, None]:
       mtype = self.symbol_name2metta(first)
       if self.is_node(first):
         if len(rest) > 1:
-          raise ValueError(f"Node rest len is greater than 1: {rest}")
+          rest = rest[0:1]
+          #raise ValueError(f"Node rest len is greater than 1: {rest}")
 
         symbol = self.replace_nodesymbol(mtype, rest[0])