diff options
| -rw-r--r-- | uploader/__init__.py | 3 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 65 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/job-status.html | 30 |
3 files changed, 89 insertions, 9 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py index 46689c5..e00c726 100644 --- a/uploader/__init__.py +++ b/uploader/__init__.py @@ -136,7 +136,8 @@ def create_app(config: Optional[dict] = None): "uploader.flask_extensions", "uploader.publications.models", "uploader.publications.datatables", - "uploader.phenotypes.models")) + "uploader.phenotypes.models", + "uploader.phenotypes.views")) # setup jinja2 symbols app.add_template_global(user_logged_in) diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index ce73c89..23bc682 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -1,4 +1,6 @@ """Views handling ('classical') phenotypes."""# pylint: disable=[too-many-lines] +import io +import csv import sys import uuid import json @@ -21,12 +23,14 @@ from gn_libs import jobs as gnlibs_jobs from gn_libs.jobs.jobs import JobNotFound from gn_libs.mysqldb import database_connection +from werkzeug.datastructures import Headers from flask import (flash, request, jsonify, redirect, Blueprint, - current_app as app) + current_app as app, + Response as FlaskResponse) from r_qtl import r_qtl2_qc as rqc from r_qtl import exceptions as rqe @@ -522,6 +526,65 @@ def job_status( @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/job/<uuid:job_id>/download-errors", + methods=["GET"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def download_errors( + species: dict, + population: dict, + dataset: dict, + job_id: uuid.UUID, + **kwargs):# pylint: disable=[unused-argument] + """Download the list of errors as a CSV file.""" + with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: + try: + job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id)) + _prefix_ = jobs.jobsnamespace() + _jobid_ = job['jobid'] + def __generate_chunks__(): + _errors_ = ( + json.loads(error) + for key in rconn.keys( + f"{_prefix_}:{str(_jobid_)}:*:errors:*") + for error in rconn.lrange(key, 0, -1)) + _chunk_no_ = 0 + _all_errors_printed_ = False + while not _all_errors_printed_: + _chunk_ = [] + try: + for _ in range(0, 1000): + _chunk_.append(next(_errors_)) + except StopIteration: + _all_errors_printed_ = True + if len(_chunk_) <= 0: + raise + + _out_ = io.StringIO() + _writer_ = csv.DictWriter(_out_, fieldnames=tuple(_chunk_[0].keys())) + if _chunk_no_ == 0: + _writer_.writeheader() + _writer_.writerows(_chunk_) + _chunk_no_ += 1 + yield _out_.getvalue() + if _all_errors_printed_: + return + + headers = Headers() + headers.set("Content-Disposition", + "attachment", + filename=f"{job['job-type']}_{job['jobid']}.csv") + return FlaskResponse( + __generate_chunks__(), mimetype="text/csv", headers=headers) + except jobs.JobNotFound as _jnf: + return render_template("jobs/job-not-found.html", job_id=job_id) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" "/<int:dataset_id>/job/<uuid:job_id>/review", methods=["GET"]) @require_login diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html index 0bbe8e0..951907f 100644 --- a/uploader/templates/phenotypes/job-status.html +++ b/uploader/templates/phenotypes/job-status.html @@ -52,10 +52,10 @@ <p> {%if errors | length == 0%} <a href="{{url_for('species.populations.phenotypes.review_job_data', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - job_id=job_id)}}" + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + job_id=job_id)}}" class="btn btn-primary" title="Continue to process data">Continue</a> {%else%} @@ -70,13 +70,28 @@ </div> <h3 class="subheading">upload errors</h3> +{%if errors | length == 0 %} <div class="row" style="max-height: 20em; overflow: scroll;"> - {%if errors | length == 0 %} <p class="text-info"> <span class="glyphicon glyphicon-info-sign"></span> No errors found so far </p> - {%else%} +</div> +{%else%} +{%if errors | length > 0%} +<div class="row"> + <div class="col"> + <a href="{{url_for('species.populations.phenotypes.download_errors', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + job_id=job_id)}}" + class="btn btn-info" + title="Download the errors as a CSV file.">download errors CSV</a> + </div> +</div> +{%endif%} +<div class="row" style="max-height: 20em; overflow: scroll;"> <table class="table table-responsive"> <thead style="position: sticky; top: 0; background: white;"> <tr> @@ -111,7 +126,8 @@ {%endfor%} </tbody> </table> - {%endif%} +</div> +{%endif%} </div> <div class="row"> |