new chemicals to test renames with no chembi, already set

Load/chemical.py

@@ -203,3 +203,28 @@ def add_chemical_data(cursor, cvterm_id, organism_id, dbxref_id, pub_id, db_id,
         cursor.execute(dbxref_sql, (db_id['CHEBI'], chem[2]))
         dbxref_id = cursor.fetchone()[0]
         cursor.execute(f_dbx, (chem_id, dbxref_id))
+
+    # create pubchem only chemicals for renaming tests
+    chems = (['p-carbon dioxide', '116526'],
+             ['p-hydrogen peroxide', '116240'])
+    obsolete = False
+    for chem in chems:
+        cursor.execute(dbxref_sql, (db_id['FlyBase'], f"FBch00{chem[1]}"))
+        dbxref_id = cursor.fetchone()[0]
+        cursor.execute(chemical_sql, (chem[0], 'FBch0{}'.format(chem[1]),
+                       organism_id['Dmel'], cvterm_id['chemical entity'], dbxref_id, obsolete))
+        chem_id = cursor.fetchone()[0]
+
+        cursor.execute(syn_sql, ("PUBCHEM:{}".format(chem[1]), cvterm_id['symbol'], "PUBCHEM:{}".format(chem[1])))
+        syn_id = cursor.fetchone()[0]
+        cursor.execute(fs_sql, (syn_id, chem_id, pub_id, True))
+
+        cursor.execute(syn_sql, ("PUBCHEM:{}".format(chem[1]), cvterm_id['fullname'], "PUBCHEM:{}".format(chem[1])))
+        syn_id = cursor.fetchone()[0]
+        cursor.execute(fs_sql, (syn_id, chem_id, pub_id, True))
+
+        cursor.execute(dbxref_sql, (db_id['PubChem'], chem[1]))
+        dbxref_id = cursor.fetchone()[0]
+        # Add feature_dbxref.
+        cursor.execute(f_dbx, (chem_id, dbxref_id))
+        cursor.execute(feat_pub_sql, (chem_id, pubchem_pub_id))

data/cv_cvterm.yaml

@@ -13,7 +13,6 @@ cell_lineprop type: ['internalnotes', 'lab_of_origin', 'comment', 'source_genoty
                      'source_strain', 'source_cross', 'karyotype']
 cell_line_libraryprop type: ['member_of_reagent_collection', 'experimental_attribute']
 cell_line_relationship: ['targeted_mutant_from']
-CHEBI: []
 
 DOID: []
 disease_ontology: ['hh-1']

data/db_dbxref.yaml

@@ -1,5 +1,6 @@
 testdb: ['hh-1']
 testdb2: []
+CHEBI: []
 EMBL-EBI Single Cell Expression Atlas Datasets:  []
 FBbt: ['dissociated larval fat cell', 'CP1 lineage neuron', 'eye']
 FBcv: ['maternal effect', 'eye', 'visible']