Treat each transcript id as an unique job identifier. #23
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… of github.com:cmbi/metadome into unique_job_id
metadome/domain/transcript.py
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| @@ -0,0 +1,8 @@ | |||
| import re | |||
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Please merge this into metadome/domains/services/helper_functions
metadome/presentation/api/routes.py
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| @@ -60,11 +67,31 @@ def submit_gene_analysis_job_for_transcript(transcript_id): | |||
| return jsonify({'job_id': job_id, | |||
| 'job_name': job_name,}) | |||
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| @bp.route('/submit_visualization/<transcript_id>/', methods=['GET']) | |||
| def submit_visualization_job_for_transcript(transcript_id): | |||
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Please remove the other endpoints that tried to do this
metadome/presentation/api/routes.py
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| @bp.route('/status', methods=['GET']) | ||
| def get_job_status_stub(): | ||
| """This endpoint is a stub, to ensure deeper endpoints may be used""" | ||
| pass | ||
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| @bp.route('/status/<transcript_id>/', methods=['GET']) | ||
| def get_visualization_status_for_transcript(transcript_id): |
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This is 'get_job_status(job_name, job_id)', please remove the code if it is no longer needed
metadome/presentation/api/routes.py
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| @@ -85,6 +112,22 @@ def get_job_result_stub(): | |||
| """This endpoint is a stub, to ensure deeper endpoints may be used""" | |||
| pass | |||
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| @bp.route('/result/<transcript_id>/', methods=['GET']) | |||
| def get_visualization_result_for_transcript(transcript_id): | |||
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This is 'get_job_result(job_name, job_id):', please remove that method if this is the new way to do this
| <span id="statusLabel"></span> | ||
| </div> | ||
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| <div id="errorDisplay" class="container is-hidden"> |
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I propose to remove this tag and use the templates/error.html
| @@ -137,7 +137,15 @@ | |||
| </div> | |||
| </div> | |||
| </div> | |||
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| <div id="statusDisplay" class="container is-hidden"> | |||
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Please remove this tag, instead use this:
when loading:
$("#loading_overlay").addClass('is-active');
when finished:
$("#loading_overlay").removeClass('is-active');
| if (this.readyState == 4 && this.status > 0) { | ||
| var response = JSON.parse(xhttp.responseText); | ||
| if (response.error !== undefined) | ||
| showErrorOnPage(response.error); |
| xhttp.send(); | ||
| } | ||
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| function hideStatusOnPage() { |
| $("#statusDisplay").addClass('is-hidden'); | ||
| } | ||
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| function showStatusOnPage(status) { |
| $("#statusLabel").text("status for transcript " + pageTranscriptID + ": " + status); | ||
| } | ||
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| function hideErrorOnPage() { |
metadome/controllers/job.py
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| _log.info("visualization job for transcript {} is already running as task {}" | ||
| .format(transcript_id, task_id)) | ||
| else: | ||
| from metadome.tasks import create_prebuild_visualization |
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I think you need to create the file here that you are about to lock, now multiple tasks for the same gene-transcript could be submitted by opening a second tab in the browser and performing the same query. Try the gene ZNF479 (will take a long time to run) for example.
| function getVisualizationStatus(transcript_id) { | ||
| $.get(Flask.url_for("api.get_visualization_status_for_transcript", | ||
| {'transcript_id': transcript_id}), | ||
| function(data) { |
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Please add a way to manipulate the text of this label: https://github.com/cmbi/metadome/blob/master/metadome/presentation/web/templates/dashboard.html#L32
And after 5 status checks of 10 ms, change the text to: "Loading ...
This is taking longer than usual, and may take up to an hour. You can choose to wait or check back later." and change the checks to 50ms
Also change the text back to 'Loading ...' after success, as the overlay is used at other points in the visualization as well.
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Tested changes and approved. Thanks @cbaakman this looks really good :) 👍
Makes sure that no two jobs can generate the same data file. The directory that holds the data is locked whenever modified and the celery id of the job is stored also.
The endpoints and javascript have been tested in the browser.