Merge branch 'master' into new_canto_stuff

Load/add_dbxref_to_cvterms.py

@@ -0,0 +1,22 @@
+def add_dbxref_data_to_cvterms(cursor, cv_cvterm_id, db_id, dbxref_id):
+
+    # NOTE: these may not be correct but can be used to create some for testing.
+    # The FBxx may not match the actual production ones
+    cv_to_FB = {
+        "FlyBase anatomy CV": "FBbt",
+        "FlyBase development CV": "FBdv",
+        "FlyBase miscellaneous CV": "FBcv"
+    }
+    dbx_sql = """ INSERT INTO dbxref (db_id, accession) VALUES (%s, %s) RETURNING dbxref_id """
+    add_to_cvterm = """ UPDATE cvterm SET dbxref_id = %s where cvterm_id = %s """
+    for cv in (cv_to_FB.keys()):
+        fb_id = db_id[cv_to_FB[cv]]
+        count = 1
+        for cvterm in cv_cvterm_id[cv]:
+
+            print("Adding CV %s to type %s" % (cvterm, cv_to_FB[cv]))
+            print(cv_cvterm_id[cv][cvterm])
+            cursor.execute(dbx_sql, (fb_id, count))
+            dbx_id = cursor.fetchone()[0]
+            cursor.execute(add_to_cvterm, (dbx_id, cv_cvterm_id[cv][cvterm]))
+            count += 1

add-test_data.py

@@ -24,6 +24,7 @@
 from Load.drivers import add_driver_data
 from Load.geneproduct import create_geneproducts
 from Load.teis import create_teis
+from Load.add_dbxref_to_cvterms import add_dbxref_data_to_cvterms
 
 conn = psycopg2.connect(database="fb_test")
 cursor = conn.cursor()
@@ -566,6 +567,8 @@ def load_pub_author_pubprop(parsed_yaml):
 # transposable_element_insertion_site (teis)
 create_teis(cursor, organism_id, feature_id, cvterm_id, dbxref_id, db_id, pub_id)
 
+add_dbxref_data_to_cvterms(cursor, cv_cvterm_id, db_id, dbxref_id)
+
 conn.commit()
 conn.close()
 print("SUCCESS")

data/cv_cvterm.yaml

@@ -46,7 +46,7 @@ FlyBase: ['FlyBase analysis']
 FlyBase_internal: ['pubprop type:curated_by']
 
 FlyBase development CV: ['late embryonic stage', 'embryonic stage', 'adult stage', 'development 1', 'development 2', 'development 3',
-                         'wandering third instar larval stage']
+                         'wandering third instar larval stage', 'laval stage']
 FlyBase miscellaneous CV: [
     'CRISPR/Cas9', 'amorphic allele - molecular evidence', 'assay', 'biosample', 'biotic stimulus study', 'cell isolation', 'chemical entity',
     'conditional', 'colocalizes_with', 'comment',

data/db_dbxref.yaml

@@ -1,9 +1,9 @@
 testdb: ['hh-1']
 testdb2: []
 EMBL-EBI Single Cell Expression Atlas Datasets:  []
-FBbt: ['dissociated larval fat cell', 'CP1 lineage neuron']
-FBcv: []
-FBdv: []
+FBbt: ['dissociated larval fat cell', 'CP1 lineage neuron', 'eye']
+FBcv: ['maternal effect', 'eye', 'visible']
+FBdv: ['adult stage', 'larval stage', 'embryonic stage']
 GB: ['GB1', 'GB2']
 GO: []
 DOI: []