fix-3064 #3080

antgonza · 2021-02-25T15:38:35Z

No description provided.

ElDeveloper

Looks great, @antgonza just a few small suggestions.

ElDeveloper · 2021-03-02T21:56:28Z

.github/workflows/qiita-ci.yml

+          - cover_package: "qiita_db"
+          - cover_package: "qiita_pet qiita_core qiita_ware"


Should have the same effect, so just in case you are interested in containing everything in one line.

Suggested change

- cover_package: "qiita_db"

- cover_package: "qiita_pet qiita_core qiita_ware"

- cover_package: ["qiita_db", "qiita_pet qiita_core qiita_ware"]

ElDeveloper · 2021-03-02T21:57:27Z

.github/workflows/qiita-ci.yml

+
+      - name: Basic dependencies install
+        env:
+          COVER_PACKAGE: ${{ matrix.COVER_PACKAGE }}


Shouldn't this be:

Suggested change

COVER_PACKAGE: ${{ matrix.COVER_PACKAGE }}

COVER_PACKAGE: ${{ matrix.cover_package }}

Sure, note that it works as expected so my guess is case insensitive

ElDeveloper · 2021-03-02T21:57:41Z

.github/workflows/qiita-ci.yml

+          COVER_PACKAGE: ${{ matrix.COVER_PACKAGE }}
+        shell: bash -l {0}
+        run: |
+          echo "Testing: " $COVER_PACKAGE


Same as above.

ElDeveloper · 2021-03-02T21:58:29Z

.github/workflows/qiita-ci.yml

+          echo "StrictModes no" > sshd_config
+          sudo mv sshd_config /etc/ssh/sshd_config
+          sudo systemctl restart ssh
+          ps -elf | grep ssh


Is this still needed or is it a command for debugging?

ElDeveloper · 2021-03-02T22:01:17Z

.github/workflows/qiita-ci.yml

+          pushd webdis
+          ./webdis &
+          popd


Suggested change

pushd webdis

./webdis &

popd

$PWD/webdis/webdis &

In my own experience the webdis expects and looks for files in the folder; if you run from outside the folder the expected files are not where they should be

ElDeveloper · 2021-03-02T22:02:29Z

.github/workflows/qiita-ci.yml

+          export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg
+          export REDBIOM_HOST="http://localhost:7379"
+
+          echo "1. Setting up redis"


Instead of using echo, another alternative is to put each of these sections under a -name: Setting up redis tag so that the UI summarizes which step failed, etc.

I'm OK with echos! :)

ElDeveloper · 2021-03-02T22:09:02Z

.github/workflows/qiita-ci.yml

+         file: codecov.yml
+         fail_ci_if_error: true
+
+  lint:


Up to you but maybe the main job could depend on the lint job so that the full test suite isn't run before you find there's a syntax error or something like that. That would also mean that the tests aren't run if there are linting errors which might be undesirable.

ElDeveloper · 2021-03-02T22:19:51Z

.github/workflows/qiita-ci.yml

+      run: python -m pip install --upgrade pip
+    - name: lint
+      run: |
+        pip install -q flake8


Isn't this missing the command that lints the code?

ElDeveloper · 2021-03-03T00:37:41Z

Looks great, thanks @antgonza!

@wasade

* adding creation and modification timestamps to prep_templates (#3066) * adding creation and modification timestamps to prep_templates * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * fix #3068 (#3069) * minor improvements (#3067) * minor improvements * fix test * adding @wasade suggestion * minor fixes (#3073) * fix #3072 (#3074) * fix #3072 * flake8 * fix #3076 (#3077) * fix #3076 * addressing @ElDeveloper comments * fix #3070 (#3075) * fix #3070 * Apply suggestions from code review Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * flake8 Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * fix-3064 (#3080) * Create qiita-ci.yml * add passwd to psql * nginx + redis * redis via conda * redis-server - -> redis-server -- * daemonize -> daemonize * conda libevent * apt-get libevent-dev * adding multiple sections * rm travis_retry * add missing activagte * onfig_test.cfg * rm indent * add 1 indent * pgport * add drop * change db name * redis version * redis -> redbiom version * split tests * source .profile * adding ssh command * mkdir ~/.ssh/ * only ssh * pushing to retrigger * add run * split ssh conf/run * 60367309 * add bash * fix ident * rm ssh cmd * strict=no * localhost * mod permissions * user ssh * rm keys * echos * start ssh service * ssh -vvv * split setup/test * localhost -> 127 * localhost -> 127 * rm ssh setup * -o StrictHostKeyChecking=no * change key creation * echo sshd_config * readd ssh config * cp sshd_config and then move * rm echos * extra qiita folder * ls test_data * rm qiita folder * use key in .ssh * more ssh params * tee -> > * chmod * fullpath * ls key * rm localhost * params * rsa -> rsa-sha2-256 * rm root login * readd -o StrictHostKeyChecking=no * minimizing params * permissions * cleaning up * comments => echo * -o StrictHostKeyChecking=no * export REDBIOM_HOST=http://127.0.0.1:7379 * localhost -> 127.0.0.1 * add runner * cover package * cleaning env vars * renaming jobs * redbiom host * add env vars via export * changing echo * add env COVER_PACKAGE * rm user sftp * just qiita_db * open_sftp -> SFTPClient * +1 worker * only SCPClient * ssh.SCPClient -> SCPClient * return sftp/ssh back * just qiita_db * rm sftp * add all tests * BASE_URL = https://127.0.0.1:8383 * bash -c * start_biom * start_biom 127 * populate QIITA_SERVER_CERT * nginx 127 * adding ports to conf * lowering ports * service qiita * 8383 postgres * curl test * mkdir nginx * moving tests around * moving curl up * echos for curl * sleep 10 * 127.0.0.1 -> localhost * returning some localhost to 127... * qiita_pet! * final clean up * kill qiita first * addreesing @ElDeveloper comments * checkout repo for flake8 * split cover_package * Workflows GUI (#3078) * fix #3076 * addressing @ElDeveloper comments * adding workflows GUI * improve HTML * db changes and improvements * comment out new db changes * rm default_workflows from PluginHandler.get * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * fix #3081 (#3082) * fix #3081 * generate_analysis_list_per_study to speed up retrival * minor modifications * split sql * addressing @ElDeveloper comments * add Command.processing_jobs (#3085) * add Command.processing_jobs * Update qiita_db/software.py [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * Improve workflows (#3083) * fix #3076 * addressing @ElDeveloper comments * adding workflows GUI * improve HTML * db changes and improvements * comment out new db changes * rm default_workflows from PluginHandler.get * improving workflows after deployment * fix error * clean up * minor fixes * improving html * comments from @justinshaffer * addressing @ElDeveloper comments * 2021.03 (#3084) * 2021.03 * add Command.processing_jobs to changelog * codecov * codecov required * codecov token Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu>

antgonza added 30 commits February 25, 2021 08:38

Create qiita-ci.yml

987c6c1

add passwd to psql

393dcbb

nginx + redis

6de0a09

redis via conda

3dc47b8

redis-server - -> redis-server --

07f6aed

daemonize -> daemonize

14b3713

conda libevent

94a839f

apt-get libevent-dev

d058a33

adding multiple sections

74b99c0

rm travis_retry

e3abf08

add missing activagte

421f40b

onfig_test.cfg

2ba53ce

rm indent

c447bfa

add 1 indent

d425d9e

pgport

ab7bd26

add drop

cb9903a

change db name

5ac15b2

redis version

e659e51

redis -> redbiom version

e733ae4

split tests

86ad303

source .profile

5a34101

adding ssh command

70b51cc

mkdir ~/.ssh/

8bbbc45

only ssh

1c3b8be

pushing to retrigger

8fbd6f8

add run

f8e4e34

split ssh conf/run

d665766

60367309

1bf7a9d

add bash

a627559

fix ident

04b7794

antgonza added 20 commits March 1, 2021 18:11

BASE_URL = https://127.0.0.1:8383

851a528

bash -c

cc3ba29

start_biom

c6dcfa0

start_biom 127

f54279a

populate QIITA_SERVER_CERT

a3f6d18

nginx 127

dac1750

adding ports to conf

60ad191

lowering ports

7d3d4be

service qiita

b704d89

8383 postgres

70b6d90

curl test

f92a0cf

mkdir nginx

3aa7f11

moving tests around

1128a05

moving curl up

9002cf4

echos for curl

84af8da

sleep 10

7a64717

127.0.0.1 -> localhost

ce1e30b

returning some localhost to 127...

023c075

qiita_pet!

ba77bdd

final clean up

3df0ca7

antgonza changed the title ~~[WIP] fix-3064~~ fix-3064 Mar 2, 2021

kill qiita first

9c2c49c

ElDeveloper suggested changes Mar 2, 2021

View reviewed changes

antgonza added 3 commits March 2, 2021 15:26

addreesing @ElDeveloper comments

317a650

checkout repo for flake8

f455ce6

split cover_package

25542f8

ElDeveloper merged commit a6578bc into dev Mar 3, 2021

antgonza deleted the fix-3064 branch March 19, 2021 01:56

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fix-3064 #3080

fix-3064 #3080

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antgonza commented Feb 25, 2021

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ElDeveloper commented Mar 3, 2021

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		- cover_package: "qiita_db"
		- cover_package: "qiita_pet qiita_core qiita_ware"

	- cover_package: "qiita_db"
	- cover_package: "qiita_pet qiita_core qiita_ware"
	- cover_package: ["qiita_db", "qiita_pet qiita_core qiita_ware"]

	COVER_PACKAGE: ${{ matrix.COVER_PACKAGE }}
	COVER_PACKAGE: ${{ matrix.cover_package }}

fix-3064 #3080

fix-3064 #3080

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antgonza commented Feb 25, 2021

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ElDeveloper commented Mar 3, 2021

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