From e9972eed006d43e29aa1451798663f23bac4fb7d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@pasteur.fr>
Date: Wed, 6 Nov 2019 23:12:27 +0100
Subject: [PATCH] fix the last commit about missing gene names
(commit 7143e9d0 on #139)
---
ippisite/ippidb/models.py | 7 +++++--
ippisite/ippidb/tests.py | 20 +++++++++++++++++---
2 files changed, 22 insertions(+), 5 deletions(-)
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 872e3751..f2e01079 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -251,7 +251,10 @@ class Protein(AutoFillableModel):
gene_names = info["gene_names"]
# put whatever name it find
- self.gene_name = gene_names[0]["name"]
+ try:
+ self.gene_name = gene_names[0]["name"]
+ except IndexError:
+ pass
# then try to find the primary, if present
for gene_name in gene_names:
if gene_name["type"] == "primary":
@@ -283,7 +286,7 @@ class Protein(AutoFillableModel):
return len(self.entry_name) > 0
def __str__(self):
- return "{} ({})".format(self.uniprot_id, self.recommended_name_long)
+ return "{} ({})".format(self.uniprot_id, self.recommended_name_long or self.short_name)
class Domain(AutoFillableModel):
diff --git a/ippisite/ippidb/tests.py b/ippisite/ippidb/tests.py
index 832dd501..dec2ff7e 100644
--- a/ippisite/ippidb/tests.py
+++ b/ippisite/ippidb/tests.py
@@ -17,7 +17,7 @@ from .models import (
create_tanimoto,
update_compound_cached_properties,
)
-from .models import DrugBankCompound
+from .models import DrugBankCompound, Protein
from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey
@@ -433,7 +433,7 @@ class TestGetDoiInfo(TestCase):
class TestGetPfamInfo(TestCase):
- def test_create_protein(self):
+ def test_get_pfam_info(self):
target = {"id": "bZIP_1", "description": "bZIP transcription factor"}
resp = ws.get_pfam_info("PF00170")
self.assertEqual(resp, target)
@@ -461,8 +461,22 @@ class TestGetGooglePatentInfo(TestCase):
)
+class TestProtein(TestCase):
+ def test_create_protein_no_gene_name(self):
+ # this test ensures that we can save a protein with no gene name
+ # in the DB
+ p = Protein()
+ p.uniprot_id= 'P00784'
+ try:
+ p.save()
+ except Exception as exc:
+ self.fail("exception {exc} raised while saving protein P00784")
+
+
+
+
class TestGetPubMEDIdInfo(TestCase):
- def test_create_protein(self):
+ def test_get_pubmed_info(self):
target = {
"title": "Gene List significance at-a-glance with" " GeneValorization.",
"journal_name": "Bioinformatics (Oxford, England)",
--
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