From 2de954fe0ac5877d214521e92dccf4fb2799b89a Mon Sep 17 00:00:00 2001 From: tatjana Date: Thu, 29 Oct 2020 18:38:44 +0100 Subject: [PATCH 1/5] Update to newest HGNC --- public_recipes.yml | 2 +- recipes/public.yml | 2 +- solvebio/test/helper.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/public_recipes.yml b/public_recipes.yml index a5ab8961..49cf9f2a 100644 --- a/public_recipes.yml +++ b/public_recipes.yml @@ -359,7 +359,7 @@ recipes: ordering: 12 expression: |- dataset_query( - 'solvebio:public:/HGNC/3.1.0-2017-06-29/HGNC', + 'solvebio:public:/HGNC/3.3.0-2020-10-29/HGNC', fields=['synonyms'], entities=[('gene', record.gene)], limit=1 diff --git a/recipes/public.yml b/recipes/public.yml index a5ab8961..49cf9f2a 100644 --- a/recipes/public.yml +++ b/recipes/public.yml @@ -359,7 +359,7 @@ recipes: ordering: 12 expression: |- dataset_query( - 'solvebio:public:/HGNC/3.1.0-2017-06-29/HGNC', + 'solvebio:public:/HGNC/3.3.0-2020-10-29/HGNC', fields=['synonyms'], entities=[('gene', record.gene)], limit=1 diff --git a/solvebio/test/helper.py b/solvebio/test/helper.py index 54514177..8f29d21b 100644 --- a/solvebio/test/helper.py +++ b/solvebio/test/helper.py @@ -14,7 +14,7 @@ class SolveBioTestCase(unittest.TestCase): - TEST_DATASET_FULL_PATH = 'solvebio:public:/HGNC/3.3.0-2019-07-22/HGNC' + TEST_DATASET_FULL_PATH = 'solvebio:public:/HGNC/3.3.0-2020-10-29/HGNC' TEST_DATASET_FULL_PATH_2 = 'solvebio:public:/ClinVar/5.1.0-20200720/Variants-GRCH38' def setUp(self): From ee577d3eb8b9575d4a36cdfb9250f03b3dccc77b Mon Sep 17 00:00:00 2001 From: tatjana Date: Tue, 3 Nov 2020 17:28:06 +0100 Subject: [PATCH 2/5] update tests --- solvebio/test/test_query.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/solvebio/test/test_query.py b/solvebio/test/test_query.py index a8f1734d..737a72f6 100644 --- a/solvebio/test/test_query.py +++ b/solvebio/test/test_query.py @@ -294,14 +294,14 @@ def test_get_by_index(self): def test_field_filters(self): limit = 1 results = self.dataset.query(limit=limit) - self.assertEqual(len(results[0].keys()), 54) + self.assertEqual(len(results[0].keys()), 55) results = self.dataset.query(limit=limit, fields=['entrez_id']) self.assertEqual(len(results[0].keys()), 1) results = self.dataset.query( limit=limit, exclude_fields=['entrez_id']) - self.assertEqual(len(results[0].keys()), 53) + self.assertEqual(len(results[0].keys()), 54) self.assertTrue('entrez_id' not in results[0].keys()) def test_entity_filters(self): From 9d42d0a88b736921452555b1cd73c0d18c50071b Mon Sep 17 00:00:00 2001 From: tatjana Date: Wed, 4 Nov 2020 14:26:22 +0100 Subject: [PATCH 3/5] Try ubuntu 18.04 on travis --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index f08904ad..9c60b42e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,3 +1,4 @@ +dist: bionic language: python python: - '2.7' From 7e2af35f265dad03af626dec359f72fec993a729 Mon Sep 17 00:00:00 2001 From: tatjana Date: Wed, 4 Nov 2020 17:17:56 +0100 Subject: [PATCH 4/5] travis pypy to pypy2 update --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 9c60b42e..8327a571 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,7 +5,7 @@ python: - '3.6' - '3.7' - '3.8' -- 'pypy' +- 'pypy2' - 'pypy3' before_install: - export PYTHONPATH=$PYTHONPATH:$(pwd) From 13a7037316cc1910d0f254479974cb7b864dfdfb Mon Sep 17 00:00:00 2001 From: tatjana Date: Wed, 4 Nov 2020 19:10:56 +0100 Subject: [PATCH 5/5] Revert travis changes - moved to another PR --- .travis.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 8327a571..f08904ad 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,11 +1,10 @@ -dist: bionic language: python python: - '2.7' - '3.6' - '3.7' - '3.8' -- 'pypy2' +- 'pypy' - 'pypy3' before_install: - export PYTHONPATH=$PYTHONPATH:$(pwd)