Add regex switch expression tool#7314
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Other regex tools and other expression tools are located in the category "Text Manipulation", so I changed "Expression tools" to that. |
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I don't see why it fails.. |
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Is it because the tool doesn't generate a real output (only booleans?)? @mvdbeek |
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| **Regex switch** | ||
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| Matches a regular expression against an element name. It emits two booleans: |
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Guess "element name" needs better explanation. I guess you assume that the tool is mapped over a collection.
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It's the name of the dict element (job["input"]["name"]) of cwl (?), which looks like that:
"engineConfig": [],
"job": {
"input": {
"file_ext": "tabular",
"file_size": 14,
"name": "table.tsv",
"metadata": {
"dbkey": "?",
"data_lines": 2,
"comment_lines": 0,
"columns": 2,
"column_types": [
"int",
"int"
],
"column_names": [],
"delimiter": "__tc__"
},
"src": {
"src": "hda",
"id": 4
}
},
"pattern": "\.csv$"
},
"context": null,
"outdir": null,
"tmpdir": null,
Not sure if this name comes either of the element identifier or the element name (I guessed the latter).
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@bernt-matthias any idea why the testing fails? |
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@bernt-matthias looks like tests are green now :) |
| var matched = false; | ||
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| try { | ||
| if (pat !== "") { |
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Should we add a empty_field validator instead to the param?
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Testing fails again with the same cryptic error as before (..which turned green at some point :) ) |
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Let me use the opportunity to debug the failure. I guess the problem is due to #7293 |
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Fix is coming #7348 (I hope) |
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sorry for bump, but looks like it worked :) thank you @bernt-matthias |
`get_last_workflow_invocation_step_update_time()` returns UTC time (it's set by galaxy.model.orm.now.now()) while datetime.now() is your local time. If your system is not on UTC time this caused 5 minute scheduling delays for steps depending on expression tools that only produce parameters. Fixes the delay observed in galaxyproject/tools-iuc#7314
`get_last_workflow_invocation_step_update_time()` returns UTC time (it's set by galaxy.model.orm.now.now()) while datetime.now() is your local time. If your system is not on UTC time this caused 5 minute scheduling delays for steps depending on expression tools that only produce parameters. Fixes the delay observed in galaxyproject/tools-iuc#7314
`get_last_workflow_invocation_step_update_time()` returns UTC time (it's set by galaxy.model.orm.now.now()) while datetime.now() is your local time. If your system is not on UTC time this caused 5 minute scheduling delays for steps depending on expression tools that only produce parameters. Fixes the delay observed in galaxyproject/tools-iuc#7314
`get_last_workflow_invocation_step_update_time()` returns UTC time (it's set by galaxy.model.orm.now.now()) while datetime.now() is your local time. If your system is not on UTC time this caused 5 minute scheduling delays for steps depending on expression tools that only produce parameters. Fixes the delay observed in galaxyproject/tools-iuc#7314
`get_last_workflow_invocation_step_update_time()` returns UTC time (it's set by galaxy.model.orm.now.now()) while datetime.now() is your local time. If your system is not on UTC time this caused 5 minute scheduling delays for steps depending on expression tools that only produce parameters. Fixes the delay observed in galaxyproject/tools-iuc#7314
`get_last_workflow_invocation_step_update_time()` returns UTC time (it's set by galaxy.model.orm.now.now()) while datetime.now() is your local time. If your system is not on UTC time this caused 5 minute scheduling delays for steps depending on expression tools that only produce parameters. Fixes the delay observed in galaxyproject/tools-iuc#7314
`get_last_workflow_invocation_step_update_time()` returns UTC time (it's set by galaxy.model.orm.now.now()) while datetime.now() is your local time. If your system is not on UTC time this caused 5 minute scheduling delays for steps depending on expression tools that only produce parameters. Fixes the delay observed in galaxyproject/tools-iuc#7314
`get_last_workflow_invocation_step_update_time()` returns UTC time (it's set by galaxy.model.orm.now.now()) while datetime.now() is your local time. If your system is not on UTC time this caused 5 minute scheduling delays for steps depending on expression tools that only produce parameters. Fixes the delay observed in galaxyproject/tools-iuc#7314
As discussed here galaxyproject/galaxy#20966 I added the regex switch module as an expression tool.
Workflow example:

Workflow route 1:

Workflow route 2:

@mvdbeek mentioned there is a Galaxy bug regarding the workflow invocation. Tool works but "Attempting to schedule workflow invocation" takes 5 min to pipe the boolean to the target tools.
FOR CONTRIBUTOR: