From 0385626fd9ce1014ad35b7e16973b55d1f484378 Mon Sep 17 00:00:00 2001
From: ianlongden <ianlongden@morgan.harvard.edu>
Date: Fri, 1 Nov 2024 12:10:11 -0400
Subject: [PATCH] new chemicals to test renames with no chembi, already set

---
 Load/chemical.py    | 25 +++++++++++++++++++++++++
 data/cv_cvterm.yaml |  1 -
 data/db_dbxref.yaml |  1 +
 3 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/Load/chemical.py b/Load/chemical.py
index 3da46ad..0c6ced1 100644
--- a/Load/chemical.py
+++ b/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))
diff --git a/data/cv_cvterm.yaml b/data/cv_cvterm.yaml
index d916024..b624de0 100644
--- a/data/cv_cvterm.yaml
+++ b/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']
diff --git a/data/db_dbxref.yaml b/data/db_dbxref.yaml
index 9b9f419..cbe571d 100644
--- a/data/db_dbxref.yaml
+++ b/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']