Merge pull request #313 from azneto/master

updates retrieve_feature_id to ignore case
lmb-embrapa · Jun 8, 2021 · 7a99773 · 7a99773
2 parents 5e0ae62 + 55b5084
commit 7a99773
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Showing 3 changed files with 24 additions and 14 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -4,18 +4,18 @@ os: linux
 
 jobs:
   include:
-    - dist: bionic
-      python: "3.6"
     - dist: bionic
       python: "3.7"
     - dist: bionic
       python: "3.8"
-    - dist: xenial
-      python: "3.6"
+    - dist: bionic
+      python: "3.9"
     - dist: xenial
       python: "3.7"
     - dist: xenial
       python: "3.8"
+    - dist: xenial
+      python: "3.9"
 
 services:
   - postgresql

diff --git a/machado/loaders/common.py b/machado/loaders/common.py
@@ -162,22 +162,31 @@ def retrieve_feature_id(accession: str, soterm: str) -> int:
     # feature.name
     try:
         return Feature.objects.get(
-            name=accession, type__cv__name="sequence", type__name=soterm
+            name__iexact=accession, type__cv__name="sequence", type__name=soterm
         ).feature_id
     except (MultipleObjectsReturned, ObjectDoesNotExist):
         pass
 
     # feature.dbxref.accession
     try:
         return Feature.objects.get(
-            dbxref__accession=accession, type__cv__name="sequence", type__name=soterm
+            dbxref__accession__iexact=accession,
+            type__cv__name="sequence",
+            type__name=soterm,
         ).feature_id
     except (MultipleObjectsReturned, ObjectDoesNotExist):
         pass
 
     # featuredbxref.dbxref.accession
-    return FeatureDbxref.objects.get(
-        dbxref__accession=accession,
-        feature__type__cv__name="sequence",
-        feature__type__name=soterm,
-    ).feature_id
+    try:
+        return FeatureDbxref.objects.get(
+            dbxref__accession__iexact=accession,
+            feature__type__cv__name="sequence",
+            feature__type__name=soterm,
+        ).feature_id
+    except ObjectDoesNotExist:
+        raise ObjectDoesNotExist("{} {} does not exist".format(soterm, accession))
+    except MultipleObjectsReturned:
+        raise MultipleObjectsReturned(
+            "{} {} matches multiple features".format(soterm, accession)
+        )
diff --git a/setup.py b/setup.py
@@ -30,10 +30,11 @@
     ],
     scripts=["bin/fixChadoModel.py"],
     install_requires=[
-        "django==3.1.8",
+        "numpy>=1.19",
+        "django==3.1.12",
         "psycopg2-binary==2.8.6",
-        "biopython==1.78",
-        "obonet==0.2.6",
+        "obonet==0.3.0",
+        "biopython==1.79",
         "tqdm==4.47.0",
         "typing==3.7.4.3",
         "bibtexparser==1.2.0",