From cddd0045d11a850a009d4a9be746fb558e3ded00 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Mon, 22 Aug 2022 17:05:24 -0400 Subject: [PATCH 1/6] BAR upgrade. --- .github/workflows/bar-api.yml | 2 +- Dockerfile | 2 +- api/resources/efp_image.py | 8 +-- .../summarization_gene_expression.py | 15 ++++- docker-compose.yml | 4 +- requirements.txt | 66 +++++++++---------- 6 files changed, 53 insertions(+), 44 deletions(-) diff --git a/.github/workflows/bar-api.yml b/.github/workflows/bar-api.yml index 2884d104..f3207df9 100644 --- a/.github/workflows/bar-api.yml +++ b/.github/workflows/bar-api.yml @@ -13,7 +13,7 @@ jobs: runs-on: Ubuntu-20.04 strategy: matrix: - python-version: [3.7, 3.8, 3.9, 3.10.4] + python-version: [3.7, 3.8, 3.9, 3.10.6] services: redis: diff --git a/Dockerfile b/Dockerfile index fe8d3478..6bb64463 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.10.4-bullseye +FROM python:3.10.6-bullseye WORKDIR /usr/src/app diff --git a/api/resources/efp_image.py b/api/resources/efp_image.py index 2c02f4b8..dfd7228f 100644 --- a/api/resources/efp_image.py +++ b/api/resources/efp_image.py @@ -83,7 +83,7 @@ def get(self, efp="", view="", mode="", gene_1="", gene_2=""): # Request is not cached # Run eFP. Note, this is currently running from home directory! efp_url = ( - "https://bar.utoronto.ca/~asher/python3/" + "https://bar.utoronto.ca/" + efp + "/cgi-bin/efpWeb.cgi?dataSource=" + view @@ -95,6 +95,8 @@ def get(self, efp="", view="", mode="", gene_1="", gene_2=""): + gene_2 + "&grey_low=None&grey_stddev=None&navbar=0" ) + # This is important to fix the eFP Url which as & instead of & + efp_url = re.sub(r"amp;", "", efp_url) efp_html = requests.get(efp_url) # Now search for something like Date: Mon, 22 Aug 2022 17:07:24 -0400 Subject: [PATCH 2/6] Fixed numpy version. --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 3d64728d..9682f560 100644 --- a/requirements.txt +++ b/requirements.txt @@ -36,7 +36,7 @@ mccabe==0.7.0 more-itertools==8.14.0 mypy-extensions==0.4.3 mysqlclient==2.1.1 -numpy==1.23.2 +numpy==1.21.6 packaging==21.3 pandas==1.4.3 pathspec==0.9.0 From 491ca0ec884454ef3cbfc4ddf9fea40eee6fe846 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Mon, 22 Aug 2022 17:09:55 -0400 Subject: [PATCH 3/6] Fixed pandas version. --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 9682f560..2a99b490 100644 --- a/requirements.txt +++ b/requirements.txt @@ -38,7 +38,7 @@ mypy-extensions==0.4.3 mysqlclient==2.1.1 numpy==1.21.6 packaging==21.3 -pandas==1.4.3 +pandas==1.3.5 pathspec==0.9.0 platformdirs==2.5.2 pluggy==1.0.0 From ebbc03381f0ba6eca3126697d37112b056ef0d83 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Mon, 22 Aug 2022 17:13:17 -0400 Subject: [PATCH 4/6] Loosen the range of package versions. --- requirements.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index 2a99b490..5d172a31 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,13 +8,13 @@ certifi==2022.6.15 cffi==1.15.1 chardet==5.0.0 charset-normalizer==2.1.1 -click==8.1.3 +click commonmark==0.9.1 coverage==6.4.4 cryptography==37.0.4 Deprecated==1.2.13 docopt==0.6.2 -flake8==5.0.4 +flake8 Flask==2.1.2 Flask-Caching==2.0.1 Flask-Cors==3.0.10 @@ -24,7 +24,7 @@ flask-restx==0.5.1 Flask-SQLAlchemy==2.5.1 greenlet==1.1.2 idna==3.3 -importlib-metadata==4.12.0 +importlib-metadata iniconfig==1.1.1 itsdangerous==2.1.2 Jinja2==3.1.2 From 75de60ba0d877ddb3ebf17896f9b74c366ea56b0 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Mon, 22 Aug 2022 17:15:54 -0400 Subject: [PATCH 5/6] Update Ubuntu. --- .github/workflows/bar-api.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/bar-api.yml b/.github/workflows/bar-api.yml index f3207df9..290039b9 100644 --- a/.github/workflows/bar-api.yml +++ b/.github/workflows/bar-api.yml @@ -10,7 +10,7 @@ on: jobs: test: - runs-on: Ubuntu-20.04 + runs-on: ubuntu-22.04 strategy: matrix: python-version: [3.7, 3.8, 3.9, 3.10.6] From cd4aa1175c44d087f8486bcd019d82697eb833d4 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Mon, 22 Aug 2022 17:24:13 -0400 Subject: [PATCH 6/6] Updated documentation requirements. --- docs/requirements.txt | 35 ++++++++++++++++++----------------- docs/source/conf.py | 2 +- 2 files changed, 19 insertions(+), 18 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index b37cd8a3..c636d2b0 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,27 +1,28 @@ alabaster==0.7.12 -Babel==2.9.1 -beautifulsoup4==4.10.0 -certifi==2021.10.8 -charset-normalizer==2.0.10 -docutils==0.17.1 -furo==2022.1.2 +Babel==2.10.3 +beautifulsoup4==4.11.1 +certifi==2022.6.15 +charset-normalizer==2.1.1 +docutils==0.19 +furo==2022.6.21 idna==3.3 -imagesize==1.3.0 -Jinja2==3.0.3 -MarkupSafe==2.0.1 +imagesize==1.4.1 +Jinja2==3.1.2 +MarkupSafe==2.1.1 packaging==21.3 -Pygments==2.11.2 -pyparsing==3.0.6 -pytz==2021.3 -requests==2.27.1 +Pygments==2.13.0 +pyparsing==3.0.9 +pytz==2022.2.1 +requests==2.28.1 snowballstemmer==2.2.0 -soupsieve==2.3.1 -Sphinx==4.3.2 -sphinx-copybutton==0.4.0 +soupsieve==2.3.2.post1 +Sphinx==5.1.1 +sphinx-basic-ng==0.0.1a12 +sphinx-copybutton==0.5.0 sphinxcontrib-applehelp==1.0.2 sphinxcontrib-devhelp==1.0.2 sphinxcontrib-htmlhelp==2.0.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -urllib3==1.26.8 +urllib3==1.26.12 diff --git a/docs/source/conf.py b/docs/source/conf.py index 9121f1c3..0184bb47 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -18,7 +18,7 @@ # -- Project information ----------------------------------------------------- project = "BAR API" -copyright = "2021, BAR Developers" +copyright = "2022, BAR Developers" author = "BAR Developers" # The full version, including alpha/beta/rc tags