diff options
| author | Frederick Muriuki Muriithi | 2024-02-09 05:29:08 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-02-12 18:17:39 +0300 |
| commit | 34eab8a50ce185aaf786fd7138a3bd0b7c5b0576 (patch) | |
| tree | 0c020a6852289b747a85767a3571680ba8ccb69b /qc_app | |
| parent | 4c077c01db19e8adc01d9559677ad5693a1db909 (diff) | |
| download | gn-uploader-34eab8a50ce185aaf786fd7138a3bd0b7c5b0576.tar.gz | |
Retrive and display generic bundle errors
Implement the first QC check for generic errors e.g. missing files in
bundle, etc. Display retrieved errors on UI.
Diffstat (limited to 'qc_app')
| -rw-r--r-- | qc_app/static/css/styles.css | 8 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/rqtl2-qc-job-error.html | 14 | ||||
| -rw-r--r-- | qc_app/upload/rqtl2.py | 13 |
3 files changed, 29 insertions, 6 deletions
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css index f6e829f..474c7f7 100644 --- a/qc_app/static/css/styles.css +++ b/qc_app/static/css/styles.css @@ -198,3 +198,11 @@ form fieldset legend { width: 90%; overflow: scroll; } + +.qc-error-display { + border-radius: 0.8em; + padding-top: 0.5em; + padding-bottom: 0.5em; + max-height: 250px; + overflow: scroll; +} diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html index 5d2ebee..f9a912c 100644 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html +++ b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html @@ -12,9 +12,19 @@ be uploaded onto GeneNetwork.</p> </div> -<h2 class="heading">Errors</h2> +{%if errorsgeneric | length > 0%} +<h2 class="heading">Generic Errors ({{errorsgeneric | length}})</h3> +<div class="explainer"> + We found the following generic errors in your R/qtl2 bundle: +</div> +<ul class="alert-error qc-error-display"> + {%for msg in errorsgeneric%} + <li>{{msg}}</li> + {%endfor%} +</ul> +{%endif%} -<p><emph>list errors here by file type, I think …</emph></p> +<p><emph>list other errors here by file type, I think …</emph></p> <h4>stdout</h4> {{cli_output(job, "stdout")}} diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py index b96d9f0..c20bd8f 100644 --- a/qc_app/upload/rqtl2.py +++ b/qc_app/upload/rqtl2.py @@ -175,12 +175,15 @@ def upload_rqtl2_bundle(species_id: int, population_id: int): jobs.jobsnamespace(), jobid, [sys.executable, "-m", "scripts.qc_on_rqtl2_bundle", - app.config["SQL_URI"], app.config["REDIS_URL"], - jobs.jobsnamespace(), jobid, "--redisexpiry", - str(redis_ttl_seconds)], + app.config["SQL_URI"], app.config["REDIS_URL"], + jobs.jobsnamespace(), jobid, "--redisexpiry", + str(redis_ttl_seconds)], "rqtl2-bundle-qc-job", redis_ttl_seconds, - {}), + {"job-metadata": json.dumps({ + "speciesid": species_id, + "populationid": population_id, + "rqtl2-bundle-file": str(the_file.absolute())})}), redisuri, f"{app.config['UPLOAD_FOLDER']}/job_errors") return redirect(url_for( @@ -200,6 +203,8 @@ def rqtl2_bundle_qc_status(jobid: UUID): if jobstatus == "error": return render_template("rqtl2/rqtl2-qc-job-error.html", job=thejob, + errorsgeneric=json.loads( + thejob.get("errors-generic", "[]")), messages=logmessages) if jobstatus == "success": return render_template("rqtl2/rqtl2-qc-job-results.html", |