deleted Xiao Feng's SNP additions to RNA-seq data NOT because of code quality but because provided SNP data was inaccurate and could not reach author's to get resolution (BnIR; Yang et al., 2023), kept brassica verification util methods; I may re-add these files with bnasnpdb with further verification

Author: VinLau

api/models/brassica_rapa.py

@@ -7,7 +7,6 @@
 from api import db
 from api.models.arachis import SampleData as Arachis
 from api.models.cannabis import SampleData as Cannabis
-from api.models.brassica_rapa import SampleData as BrassicaRapa
 from api.models.dna_damage import SampleData as DNADamage
 from api.models.embryo import SampleData as Embryo
 from api.models.germination import SampleData as Germination
@@ -79,9 +78,6 @@ def get_data(species, database, gene_id, sample_ids=None):
         elif species == "arachis":
             if not BARUtils.is_arachis_gene_valid(gene_id):
                 return {"success": False, "error": "Invalid gene id", "error_code": 400}
-        elif species == "brassica_rapa":
-            if not BARUtils.is_brassica_rapa_gene_valid(gene_id):
-                return {"success": False, "error": "Invalid gene id", "error_code": 400}
         elif species == "cannabis":
             if not BARUtils.is_cannabis_gene_valid(gene_id):
                 return {"success": False, "error": "Invalid gene id", "error_code": 400}
@@ -121,11 +117,6 @@ def get_data(species, database, gene_id, sample_ids=None):
             # Example: PK-PFLW
             sample_regex = re.compile(r"^PK-\D{1,4}|MED_CTRL$", re.I)
 
-        elif database == "brassica_rapa":
-            table = BrassicaRapa
-            # Example: E1
-            sample_regex = re.compile(r"^\D{1,2}\d{0,2}|MED_CTRL$", re.I)
-
         elif database == "dna_damage":
             table = DNADamage
             # Another insane regex!

api/resources/rnaseq_gene_expression.py

@@ -13,7 +13,6 @@ SQLALCHEMY_BINDS = {
     'annotations_lookup': 'mysql://root:root@localhost/annotations_lookup',
     'arabidopsis_ecotypes': 'mysql://root:root@localhost/arabidopsis_ecotypes',
     'arachis': 'mysql://root:root@localhost/arachis',
-    'brassica_rapa': 'mysql://root:root@localhost/brassica_rapa',
     'cannabis': 'mysql://root:root@localhost/cannabis',
     'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp',
     'dna_damage': 'mysql://root:root@localhost/dna_damage',

config/BAR_API.cfg

@@ -12,7 +12,6 @@ echo "Welcome to the BAR API. Running init!"
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/annotations_lookup.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_ecotypes.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/arachis.sql
-mysql -u $DB_USER -p$DB_PASS < ./config/databases/brassica_rapa.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/cannabis.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/dna_damage.sql

config/databases/brassica_rapa.sql

@@ -187,17 +187,6 @@ def test_get_rna_expression_data(self):
         expected = {"wasSuccessful": False, "error": "Invalid gene id"}
         self.assertEqual(response.json, expected)
 
-        # Brassica rapa
-        # Valid data
-        response = self.app_client.get("/rnaseq_gene_expression/brassica_rapa/brassica_rapa/BraA01g000010/UO")
-        expected = {"wasSuccessful": True, "data": {"UO": 7.93926}}
-        self.assertEqual(response.json, expected)
-
-        # Invalid gene id
-        response = self.app_client.get("/rnaseq_gene_expression/brassica_rapa/abc/UO")
-        expected = {"wasSuccessful": False, "error": "Invalid gene id"}
-        self.assertEqual(response.json, expected)
-
         # Cannabis
         # Valid data
         response = self.app_client.get("/rnaseq_gene_expression/cannabis/cannabis/AGQN03009284/PK-RT")