diff options
Diffstat (limited to 'qc_app')
| -rw-r--r-- | qc_app/templates/rqtl2/rqtl2-qc-job-results.html | 62 | ||||
| -rw-r--r-- | qc_app/upload/rqtl2.py | 18 |
2 files changed, 75 insertions, 5 deletions
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html new file mode 100644 index 0000000..46a168f --- /dev/null +++ b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html @@ -0,0 +1,62 @@ +{%extends "base.html"%} +{%from "cli-output.html" import cli_output%} + +{%block title%}R/qtl2 bundle: QC job results{%endblock%} + +{%block contents%} +<h1 class="heading">R/qtl2 bundle: QC job results</h1> + +<div class="explainer"> + <p>The R/qtl2 bundle you uploaded has passed all automated quality-control + checks successfully.</p> + <p>You may now continue to load the data into GeneNetwork for the bundle, with + the following details:</p> +</div> + +<form id="form-qc-job-results" action="#implement-this" method="POST"> + <fieldset> + <legend>Species</legend> + <input type="hidden" name="speciesid" value="{{species.SpeciesId}}" /> + + <span class="form-col-1">Name</span> + <span class="form-col-2">{{species.Name | capitalize}}</span> + + <span class="form-col-1">Scientific</span> + <span class="form-col-2">{{species.FullName | capitalize}}</span> + </fieldset> + + <fieldset> + <legend>population</legend> + <input type="hidden" name="populationid" value="{{populationid}}" /> + + <span class="form-col-1">Name</span> + <span class="form-col-2">{{population.InbredSetName}}</span> + + <span class="form-col-1">Full Name</span> + <span class="form-col-2">{{population.FullName}}</span> + + <span class="form-col-1">Genetic Type</span> + <span class="form-col-2">{{population.GeneticType}}</span> + + <span class="form-col-1">Description</span> + <span class="form-col-2">{{population.Description or "-"}}</span> + </fieldset> + + <fieldset> + <legend>R/qtl2 Bundle File</legend> + <input type="hidden" name="rqtl2-bundle-file" value="{{rqtl2bundle}}" /> + <input type="hidden" name="original-filename" value="{{rqtl2bundleorig}}" /> + + <span class="form-col-1">Original Name</span> + <span class="form-col-2">{{rqtl2bundleorig}}</span> + + <span class="form-col-1">Internal Name</span> + <span class="form-col-2">{{rqtl2bundle.name[0:25]}}…</span> + </fieldset> + + <fieldset> + <input type="submit" value="continue" class="btn btn-main form-col-2" /> + </fieldset> +</form> + +{%endblock%} diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py index c20bd8f..4b00891 100644 --- a/qc_app/upload/rqtl2.py +++ b/qc_app/upload/rqtl2.py @@ -183,7 +183,8 @@ def upload_rqtl2_bundle(species_id: int, population_id: int): {"job-metadata": json.dumps({ "speciesid": species_id, "populationid": population_id, - "rqtl2-bundle-file": str(the_file.absolute())})}), + "rqtl2-bundle-file": str(the_file.absolute()), + "original-filename": request.files["rqtl2_bundle_file"].filename})}), redisuri, f"{app.config['UPLOAD_FOLDER']}/job_errors") return redirect(url_for( @@ -193,7 +194,8 @@ def upload_rqtl2_bundle(species_id: int, population_id: int): methods=["GET", "POST"]) def rqtl2_bundle_qc_status(jobid: UUID): """Check the status of the QC jobs.""" - with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: + with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn, + database_connection(app.config["SQL_URI"]) as dbconn): try: thejob = jobs.job(rconn, jobs.jobsnamespace(), jobid) messagelistname = thejob.get("log-messagelist") @@ -207,9 +209,15 @@ def rqtl2_bundle_qc_status(jobid: UUID): thejob.get("errors-generic", "[]")), messages=logmessages) if jobstatus == "success": - return render_template("rqtl2/rqtl2-qc-job-results.html", - job=thejob, - messages=logmessages) + jobmeta = json.loads(thejob["job-metadata"]) + species = species_by_id(dbconn, jobmeta["speciesid"]) + return render_template( + "rqtl2/rqtl2-qc-job-results.html", + species=species, + population=population_by_species_and_id( + dbconn, species["SpeciesId"], jobmeta["populationid"]), + rqtl2bundle=Path(jobmeta["rqtl2-bundle-file"]), + rqtl2bundleorig=jobmeta["original-filename"]) return render_template("rqtl2/rqtl2-qc-job-status.html", job=thejob, |