Improve workflows #3083

antgonza · 2021-03-09T15:07:09Z

First review/merge #3078.

These are improvements after the qiita-rc deployment.

ElDeveloper

Thanks @antgonza. The default workflows UI looks great, thanks for deploying to qiita-rc. Do you think scrolling to zoom should be disabled by default in this page like in the main processing network UI?

ElDeveloper · 2021-03-16T21:01:30Z

qiita_db/software.py

+
+        Returns
+        -------
+        description : str


Suggested change

description : str

str

qiita_db/software.py

ElDeveloper · 2021-03-16T23:34:19Z

qiita_db/software.py

+
+        Returns
+        -------
+        description : str


Suggested change

description : str

str

qiita_db/software.py

ElDeveloper · 2021-03-16T23:35:30Z

qiita_db/software.py

    @property
    def data_type(self):
-        """Retrieves all the data_types the workflow accepts
+        """Retrieves all the data_types of the default workflow


Suggested change

"""Retrieves all the data_types of the default workflow

"""Retrieves all the data_types accepted by the default workflow

ElDeveloper · 2021-03-16T23:39:36Z

qiita_pet/handlers/software.py

+            main_nodes = dict()
+            for x, y in graph.edges:
+                connections = []
+                for a, b, c in graph[x][y]['connections'].connections:


Suggested change

for a, b, c in graph[x][y]['connections'].connections:

for a, _, c in graph[x][y]['connections'].connections:

ElDeveloper · 2021-03-16T23:40:53Z

qiita_pet/templates/study_ajax/study_analyses.html

@@ -6,7 +6,8 @@
 </script>
 <h3>Analyses that have used this study</h3>

-Note that if an analysis doesn't have a link, it means that is a "User default analysis"; which means that the analysis belongs to that user but the user has only selected artifacts and hasn't created the actual analysis. Please contact the user and ask them to delete that artifact from their analysis creation page.
+Note that if an analysis doesn't have a link, it means that it is a "User default analysis". This means that the analysis belongs to the indicated user but the user has only selected artifacts and the actual analysis has not been created. Please contact the user and ask them to delete that artifact from their analysis creation page.
+page.


Suggested change

page.

ElDeveloper · 2021-03-16T23:53:39Z

qiita_pet/handlers/software.py

+            #                   output_type: output_node_name}, ...}
+            # for easy look up and merge of output_names
+            main_nodes = dict()
+            for x, y in graph.edges:


I don't think I follow all that is going on in this loop. But my general comment would be to move this into a separate function that can be tested. Maybe as a class method or a function in the DefaultWorfklow module.

ElDeveloper · 2021-03-16T23:57:21Z

qiita_pet/templates/workflows.html

@@ -63,16 +64,26 @@
    <h3>Recommended Workflows</h3>
    ~~ Click on the spheres to get more information ~~


What do you think about this:

Suggested change

~~ Click on the spheres to get more information ~~

<h5>Click on the circles to get more information</h5>

ElDeveloper

Thanks so much @antgonza! Looks great.

@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 <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 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 <[email protected]> * flake8 Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 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 <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 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 <[email protected]> Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * 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 <[email protected]>

antgonza added 16 commits February 19, 2021 12:42

fix qiita-spots#3076

3b934a1

addressing @ElDeveloper comments

fb17bd5

Merge branch 'dev' of github.com:biocore/qiita into workflows-GUI

be9848a

adding workflows GUI

51cc864

improve HTML

d7655ae

db changes and improvements

aa82154

Merge branch 'dev' of github.com:biocore/qiita into workflows-GUI

189ffd0

comment out new db changes

35ed05e

rm default_workflows from PluginHandler.get

e0a05c0

improving workflows after deployment

e6be223

fix error

d4c5153

merging dev

fbcaa6f

clean up

400e07a

Merge branch 'dev' of github.com:biocore/qiita into improve-workflows

d8f2cf4

minor fixes

090610d

improving html

1426f7d

antgonza changed the title ~~[WIP] Improve workflows~~ Improve workflows Mar 13, 2021

antgonza requested a review from ElDeveloper March 13, 2021 20:35

comments from @justinshaffer

3df3dc6

ElDeveloper suggested changes Mar 16, 2021

View reviewed changes

addressing @ElDeveloper comments

b8adbbb

ElDeveloper approved these changes Mar 17, 2021

View reviewed changes

ElDeveloper merged commit 8e6d250 into qiita-spots:dev Mar 17, 2021

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Improve workflows #3083

Improve workflows #3083

antgonza commented Mar 9, 2021

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ElDeveloper Mar 16, 2021

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ElDeveloper Mar 16, 2021

ElDeveloper Mar 16, 2021

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ElDeveloper left a comment

	"""Retrieves all the data_types of the default workflow
	"""Retrieves all the data_types accepted by the default workflow

	for a, b, c in graph[x][y]['connections'].connections:
	for a, _, c in graph[x][y]['connections'].connections:

		@@ -63,16 +64,26 @@
		<h3>Recommended Workflows</h3>
		~~ Click on the spheres to get more information ~~

	~~ Click on the spheres to get more information ~~
	<h5>Click on the circles to get more information</h5>

Improve workflows #3083

Improve workflows #3083

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antgonza commented Mar 9, 2021

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