From f184e2b4762d1ec5608d600dcb87406679212e39 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 22 Sep 2020 04:27:43 +0300 Subject: Add unittesting github action * .github/workflows/main.yml: Add it. --- .github/workflows/main.yml | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 .github/workflows/main.yml (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 00000000..4c8db1c4 --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,31 @@ +name: tests + +# Run actions when pushing to the testing branch or when you create a +# PR against it +on: + push: + branches: [ testing ] + pull_request: + branches: [ testing ] + +jobs: + unittest: + runs-on: ubuntu-latest + container: bonfacekilz/python2-genenetwork2:latest + + steps: + # Use v1 of checkout since v2 fails + - name: Checkout Project + uses: actions/checkout@v1 + + # Redis is required by some of the tests + - name: Start Redis + run: | + redis-server --daemonize yes + + - name: Run the unit tests + run: | + mkdir -p /genotype_files/genotype/json + env GN2_PROFILE=/usr/gn2-profile TMPDIR=/tmp SERVER_PORT=5004 \ + GENENETWORK_FILES=/genotype_files/ bash bin/genenetwork2 \ + etc/default_settings.py -c -m unittest discover -v -- cgit v1.2.3 From 855558084a538ebdfec0bd43f829ba8d0d314a21 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 23 Sep 2020 03:05:42 +0300 Subject: Update github action to include mariadb service * .github/workflows/main.yml: Add mariadb service. This makes the build pass because somewhere(because of cyclic imports), a connection to mariadb is required. --- .github/workflows/main.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 4c8db1c4..94b0db75 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -13,6 +13,19 @@ jobs: runs-on: ubuntu-latest container: bonfacekilz/python2-genenetwork2:latest + services: + mariadb: + image: mariadb:latest + ports: + - 3306:3306 + env: + MYSQL_USER: gn2 + MYSQL_PASSWORD: mysql_password + MYSQL_ALLOW_EMPTY_PASSWORD: yes + MYSQL_DATABASE: db_webqtl_s + MYSQL_ROOT_PASSWORD: mysql_password + options: --health-cmd="mysqladmin ping" --health-interval=5s --health-timeout=2s --health-retries=3 + steps: # Use v1 of checkout since v2 fails - name: Checkout Project -- cgit v1.2.3 From 1907457a00f0f7a9f7e74d8955265c8635f03bce Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 25 Sep 2020 03:55:33 +0300 Subject: Update github action * .github/workflows/main.yml: Set up a mariadb and redis within the GH action. (services): Remove mariadb service. --- .github/workflows/main.yml | 40 ++++++++++++++++++++++------------------ 1 file changed, 22 insertions(+), 18 deletions(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 94b0db75..2fd9a886 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -13,32 +13,36 @@ jobs: runs-on: ubuntu-latest container: bonfacekilz/python2-genenetwork2:latest - services: - mariadb: - image: mariadb:latest - ports: - - 3306:3306 - env: - MYSQL_USER: gn2 - MYSQL_PASSWORD: mysql_password - MYSQL_ALLOW_EMPTY_PASSWORD: yes - MYSQL_DATABASE: db_webqtl_s - MYSQL_ROOT_PASSWORD: mysql_password - options: --health-cmd="mysqladmin ping" --health-interval=5s --health-timeout=2s --health-retries=3 - steps: + # First start with mariadb set then checkout. The checkout gives + # the mysqld enough time to start + - name: Set up mariadb + run: | + mysql_install_db --user=mysql --datadir=/usr/local/mysql + # Wait for the mysqld_safe process to start + mysqld_safe --user=mysql --datadir=/usr/local/mysql & + # Use v1 of checkout since v2 fails - name: Checkout Project uses: actions/checkout@v1 - # Redis is required by some of the tests + # Redis is required by some of the tests 6379 - name: Start Redis run: | - redis-server --daemonize yes + /gn2-profile/bin/screen -dmLS redisconn /gn2-profile/bin/redis-server + + # Redis is required by some of the tests 6379 + - name: Bootstrap tables + run: | + mysql -u root -e "SHOW DATABASES;" + mysql -u root -e "CREATE DATABASE db_webqtl_s;" + mysql -u root -e "CREATE USER 'gn2'@'localhost' IDENTIFIED BY 'mysql_password';" + mysql -u root -e "GRANT ALL PRIVILEGES ON *.* TO 'gn2'@'localhost';FLUSH PRIVILEGES;" - name: Run the unit tests run: | - mkdir -p /genotype_files/genotype/json - env GN2_PROFILE=/usr/gn2-profile TMPDIR=/tmp SERVER_PORT=5004 \ - GENENETWORK_FILES=/genotype_files/ bash bin/genenetwork2 \ + env GN2_PROFILE=/gn2-profile \ + TMPDIR=/tmp SERVER_PORT=5004 \ + WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ + GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ etc/default_settings.py -c -m unittest discover -v -- cgit v1.2.3 From cde844b7de1875bda37c6672acf712c4a8bf2b79 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sat, 26 Sep 2020 01:22:47 +0300 Subject: Use Python3 image to run tests --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2fd9a886..f27feb5f 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -11,7 +11,7 @@ on: jobs: unittest: runs-on: ubuntu-latest - container: bonfacekilz/python2-genenetwork2:latest + container: bonfacekilz/python3-genenetwork2:latest steps: # First start with mariadb set then checkout. The checkout gives -- cgit v1.2.3 From b526fc6f6b6f450e169c01db5ffea92f94512393 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 3 Nov 2020 21:54:36 +0300 Subject: Use python3-genenetwork2 on commit bdce85d in container * .github/workflows/main.yml: Update gn2 container. --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f27feb5f..d76a5433 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -11,7 +11,7 @@ on: jobs: unittest: runs-on: ubuntu-latest - container: bonfacekilz/python3-genenetwork2:latest + container: bonfacekilz/python3-genenetwork2:bdce85d steps: # First start with mariadb set then checkout. The checkout gives -- cgit v1.2.3 From 13db311203483f5ef6082e49e15158840ce072ef Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 4 Nov 2020 02:24:47 +0300 Subject: Use python3-genenetwork2 docker image on commit 0bf4ee6 --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d76a5433..c78f6d85 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -11,7 +11,7 @@ on: jobs: unittest: runs-on: ubuntu-latest - container: bonfacekilz/python3-genenetwork2:bdce85d + container: bonfacekilz/python3-genenetwork2:0bf4ee6 steps: # First start with mariadb set then checkout. The checkout gives -- cgit v1.2.3 From 4a16262f1f8097122ed0bedf2e92211627ad223a Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sat, 21 Nov 2020 09:58:14 +0300 Subject: Use docker image with markdown packaged * .github/workflows/main.yml (jobs): [container]: Use image that is on python3-genenetwork "ad741c1" which has python-markdown packaged. --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c78f6d85..2342796a 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -11,7 +11,7 @@ on: jobs: unittest: runs-on: ubuntu-latest - container: bonfacekilz/python3-genenetwork2:0bf4ee6 + container: bonfacekilz/python3-genenetwork2:ad741c1 steps: # First start with mariadb set then checkout. The checkout gives -- cgit v1.2.3 From cd5b32a69215bf5c168b7619ebc881908845204c Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Wed, 10 Feb 2021 08:11:33 +0300 Subject: add broken links checker to workflow --- .github/workflows/main.yml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2342796a..79c69699 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -46,3 +46,22 @@ jobs: WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ etc/default_settings.py -c -m unittest discover -v + + - name: Start Genenetwork as a Background Task + run: | + env GN2_PROFILE=/gn2-profile \ + TMPDIR=/tmp SERVER_PORT=5004 \ + WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ + GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ + etc/default_settings.py + + - name: Test for Broken Links + run: | + + env GN2_PROFILE=/gn2-profile \ + TMPDIR=/tmp\ + WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ + GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ + etc/default_settings.py -c -m\ + /__w/genenetwork/genenetwork/test/requests/links_scraper/genelinks.py + -- cgit v1.2.3 From 02ac2fd38fea7f85b3ef89464157a7c0d1ffcac7 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Wed, 10 Feb 2021 08:14:03 +0300 Subject: fix:starting genenetwork on the background --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 79c69699..a8642806 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -53,7 +53,7 @@ jobs: TMPDIR=/tmp SERVER_PORT=5004 \ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py + etc/default_settings.py& - name: Test for Broken Links run: | -- cgit v1.2.3 From e67e6d7f88ffb21e4101147c5abadb2b7c78e5ae Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Wed, 10 Feb 2021 08:18:47 +0300 Subject: fix error --- .github/workflows/main.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a8642806..d4649d4f 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -62,6 +62,5 @@ jobs: TMPDIR=/tmp\ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py -c -m\ - /__w/genenetwork/genenetwork/test/requests/links_scraper/genelinks.py + etc/default_settings.py -c -m /__w/genenetwork/genenetwork/test/requests/links_scraper/genelinks.py -- cgit v1.2.3 From f3a8fdc660504e0ea74ae63d5ed7c891db6e3963 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Wed, 10 Feb 2021 08:20:18 +0300 Subject: fix paths issues --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d4649d4f..5d46ccb9 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -62,5 +62,5 @@ jobs: TMPDIR=/tmp\ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py -c -m /__w/genenetwork/genenetwork/test/requests/links_scraper/genelinks.py + etc/default_settings.py -c -m /__w/genenetwork2/genenetwork2/test/requests/links_scraper/genelinks.py -- cgit v1.2.3 From 6f3273429482dea1aaaa4e5fe61b178485e271b8 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 11 Feb 2021 07:26:04 +0300 Subject: edit workflow --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5d46ccb9..a36abc0a 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -62,5 +62,5 @@ jobs: TMPDIR=/tmp\ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py -c -m /__w/genenetwork2/genenetwork2/test/requests/links_scraper/genelinks.py + etc/default_settings.py -c /__w/genenetwork2/genenetwork2/test/requests/links_scraper/genelinks.py -- cgit v1.2.3 From a3ea9cb840bc8dbc9e5e0940ec72a36712e13a2a Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 11 May 2021 10:47:51 +0300 Subject: workflows: main.yml: Update container image --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a36abc0a..64c0fdb2 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -11,7 +11,7 @@ on: jobs: unittest: runs-on: ubuntu-latest - container: bonfacekilz/python3-genenetwork2:ad741c1 + container: bonfacekilz/python3-genenetwork2:00ba1f8 steps: # First start with mariadb set then checkout. The checkout gives -- cgit v1.2.3 From 5e3e8e5847fe994652e3c6675ce96312fd9dc16a Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 11 May 2021 11:09:36 +0300 Subject: workflows: main.yml: Remove hard-coded path --- .github/workflows/main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 64c0fdb2..2b7c3b16 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -57,10 +57,10 @@ jobs: - name: Test for Broken Links run: | - env GN2_PROFILE=/gn2-profile \ TMPDIR=/tmp\ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py -c /__w/genenetwork2/genenetwork2/test/requests/links_scraper/genelinks.py + etc/default_settings.py -c \ + $PWD/test/requests/links_scraper/genelinks.py -- cgit v1.2.3 From 232148b1304ae531df6d9157f6d574d5c944830e Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 11 May 2021 11:30:53 +0300 Subject: workflows: main.yml: Use screen to run gn2 --- .github/workflows/main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2b7c3b16..f9a3fa13 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -49,11 +49,11 @@ jobs: - name: Start Genenetwork as a Background Task run: | - env GN2_PROFILE=/gn2-profile \ + /gn2-profile/bin/screen -dmL bash -c "env GN2_PROFILE=/gn2-profile \ TMPDIR=/tmp SERVER_PORT=5004 \ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py& + etc/default_settings.py" - name: Test for Broken Links run: | -- cgit v1.2.3 From 4538c0ad693ae94ebda5f0bf39678d776c0c8297 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 11 May 2021 11:47:20 +0300 Subject: workflows: main.yml: Set up gn2 before running the unit tests --- .github/workflows/main.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f9a3fa13..b09f2f1d 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -39,21 +39,21 @@ jobs: mysql -u root -e "CREATE USER 'gn2'@'localhost' IDENTIFIED BY 'mysql_password';" mysql -u root -e "GRANT ALL PRIVILEGES ON *.* TO 'gn2'@'localhost';FLUSH PRIVILEGES;" - - name: Run the unit tests + - name: Start Genenetwork as a Background Task run: | - env GN2_PROFILE=/gn2-profile \ + /gn2-profile/bin/screen -dmL bash -c "env GN2_PROFILE=/gn2-profile \ TMPDIR=/tmp SERVER_PORT=5004 \ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py -c -m unittest discover -v + etc/default_settings.py" - - name: Start Genenetwork as a Background Task + - name: Run the unit tests run: | - /gn2-profile/bin/screen -dmL bash -c "env GN2_PROFILE=/gn2-profile \ + env GN2_PROFILE=/gn2-profile \ TMPDIR=/tmp SERVER_PORT=5004 \ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py" + etc/default_settings.py -c -m unittest discover -v - name: Test for Broken Links run: | -- cgit v1.2.3 From 75b378f757979af1d6fdaff3f3abde0599c5f744 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 11 May 2021 12:10:37 +0300 Subject: workflows: main.yml: Use mariadb as a service --- .github/workflows/main.yml | 30 +++++++++++++----------------- 1 file changed, 13 insertions(+), 17 deletions(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index b09f2f1d..a2925e08 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -12,16 +12,19 @@ jobs: unittest: runs-on: ubuntu-latest container: bonfacekilz/python3-genenetwork2:00ba1f8 + services: + mysql: + image: mariadb:15.1 + env: + MYSQL_ALLOW_EMPTY_PASSWORD: yes + MYSQL_USER: gn2 + MYSQL_PASSWORD: mysql_password + MYSQL_DATABASE: db_webqtl_s + ports: + - 3306:3306 + options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3 steps: - # First start with mariadb set then checkout. The checkout gives - # the mysqld enough time to start - - name: Set up mariadb - run: | - mysql_install_db --user=mysql --datadir=/usr/local/mysql - # Wait for the mysqld_safe process to start - mysqld_safe --user=mysql --datadir=/usr/local/mysql & - # Use v1 of checkout since v2 fails - name: Checkout Project uses: actions/checkout@v1 @@ -31,17 +34,10 @@ jobs: run: | /gn2-profile/bin/screen -dmLS redisconn /gn2-profile/bin/redis-server - # Redis is required by some of the tests 6379 - - name: Bootstrap tables - run: | - mysql -u root -e "SHOW DATABASES;" - mysql -u root -e "CREATE DATABASE db_webqtl_s;" - mysql -u root -e "CREATE USER 'gn2'@'localhost' IDENTIFIED BY 'mysql_password';" - mysql -u root -e "GRANT ALL PRIVILEGES ON *.* TO 'gn2'@'localhost';FLUSH PRIVILEGES;" - - name: Start Genenetwork as a Background Task run: | - /gn2-profile/bin/screen -dmL bash -c "env GN2_PROFILE=/gn2-profile \ + /gn2-profile/bin/screen -dmLS gn2conn + bash -c "env GN2_PROFILE=/gn2-profile \ TMPDIR=/tmp SERVER_PORT=5004 \ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ -- cgit v1.2.3 From c4ec08c1b544c05cce1c1247b8bc1afb741643e4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 11 May 2021 13:38:47 +0300 Subject: workflows: main.yml: Remove mysql service and update gn2 b/g task --- .github/workflows/main.yml | 31 +++++++++++++++++-------------- 1 file changed, 17 insertions(+), 14 deletions(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a2925e08..c6b56a81 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -12,19 +12,16 @@ jobs: unittest: runs-on: ubuntu-latest container: bonfacekilz/python3-genenetwork2:00ba1f8 - services: - mysql: - image: mariadb:15.1 - env: - MYSQL_ALLOW_EMPTY_PASSWORD: yes - MYSQL_USER: gn2 - MYSQL_PASSWORD: mysql_password - MYSQL_DATABASE: db_webqtl_s - ports: - - 3306:3306 - options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3 steps: + # First start with mariadb set then checkout. The checkout gives + # the mysqld enough time to start + - name: Set up mariadb + run: | + mysql_install_db --user=mysql --datadir=/usr/local/mysql + # Wait for the mysqld_safe process to start + mysqld_safe --user=mysql --datadir=/usr/local/mysql & + # Use v1 of checkout since v2 fails - name: Checkout Project uses: actions/checkout@v1 @@ -34,10 +31,17 @@ jobs: run: | /gn2-profile/bin/screen -dmLS redisconn /gn2-profile/bin/redis-server + # Initialise the tables + - name: Bootstrap tables + run: | + mysql -u root -e "SHOW DATABASES;" + mysql -u root -e "CREATE DATABASE db_webqtl_s;" + mysql -u root -e "CREATE USER 'gn2'@'localhost' IDENTIFIED BY 'mysql_password';" + mysql -u root -e "GRANT ALL PRIVILEGES ON *.* TO 'gn2'@'localhost';FLUSH PRIVILEGES;" + - name: Start Genenetwork as a Background Task run: | - /gn2-profile/bin/screen -dmLS gn2conn - bash -c "env GN2_PROFILE=/gn2-profile \ + /gn2-profile/bin/screen -dm bash -c "env GN2_PROFILE=/gn2-profile \ TMPDIR=/tmp SERVER_PORT=5004 \ WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ @@ -59,4 +63,3 @@ jobs: GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ etc/default_settings.py -c \ $PWD/test/requests/links_scraper/genelinks.py - -- cgit v1.2.3 From 43d4e9b42f9ebcb9012bc791aa4ac34a15f290a7 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 May 2021 18:31:40 +0300 Subject: workflows: main: Use "bonfacekilz/genenetwork2:latest" docker image --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c6b56a81..f279a7e5 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -11,7 +11,7 @@ on: jobs: unittest: runs-on: ubuntu-latest - container: bonfacekilz/python3-genenetwork2:00ba1f8 + container: bonfacekilz/genenetwork2:latest steps: # First start with mariadb set then checkout. The checkout gives -- cgit v1.2.3 From c1b23a1b01071c252ddae6dbea14500e4c248d84 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 6 Oct 2021 21:01:54 +0300 Subject: workflows: main.yml: Disable link checking --- .github/workflows/main.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to '.github/workflows') diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f279a7e5..8e2c7966 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -55,11 +55,11 @@ jobs: GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ etc/default_settings.py -c -m unittest discover -v - - name: Test for Broken Links - run: | - env GN2_PROFILE=/gn2-profile \ - TMPDIR=/tmp\ - WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ - GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ - etc/default_settings.py -c \ - $PWD/test/requests/links_scraper/genelinks.py + # - name: Test for Broken Links + # run: | + # env GN2_PROFILE=/gn2-profile \ + # TMPDIR=/tmp\ + # WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ + # GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \ + # etc/default_settings.py -c \ + # $PWD/test/requests/links_scraper/genelinks.py -- cgit v1.2.3