diff options
Diffstat (limited to 'uploader')
| -rw-r--r-- | uploader/phenotypes/views.py | 76 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/job-status.html | 8 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/review-job-data.html | 101 |
3 files changed, 182 insertions, 3 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index ec4c840..53e68d1 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -5,7 +5,7 @@ import json import datetime from pathlib import Path from zipfile import ZipFile -from functools import wraps +from functools import wraps, reduce from logging import INFO, ERROR, DEBUG, FATAL, CRITICAL, WARNING from redis import Redis @@ -502,3 +502,77 @@ def job_status( metadata=jobs.job_files_metadata( rconn, jobs.jobsnamespace(), job['jobid']), activelink="add-phenotypes") + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/review-job/<uuid:job_id>", + 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 review_job_data( + species: dict, + population: dict, + dataset: dict, + job_id: uuid.UUID, + **kwargs +):# pylint: disable=[unused-argument] + """Review data one more time before entering it into the database.""" + with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: + try: + job = jobs.job(rconn, jobs.jobsnamespace(), str(job_id)) + except jobs.JobNotFound as _jnf: + job = None + + def __metadata_by_type__(by_type, item): + filetype = item[1]["filetype"] + return { + **by_type, + filetype: (by_type.get(filetype, tuple()) + + ({"filename": item[0], **item[1]},)) + } + metadata = reduce(__metadata_by_type__, + (jobs.job_files_metadata( + rconn, jobs.jobsnamespace(), job['jobid']) + if job else {}).items(), + {}) + + def __desc__(filetype): + match filetype: + case "phenocovar": + desc = "phenotypes" + case "pheno": + desc = "phenotypes data" + case "phenose": + desc = "phenotypes standard-errors" + case "phenonum": + desc = "phenotypes samples" + case _: + desc = f"unknown file type '{filetype}'." + + return desc + + def __summarise__(filetype, files): + return { + "filetype": filetype, + "number-of-files": len(files), + "total-data-rows": sum( + int(afile["linecount"]) - 1 for afile in files), + "description": __desc__(filetype) + } + + summary = { + filetype: __summarise__(filetype, meta) + for filetype,meta in metadata.items() + } + return render_template("phenotypes/review-job-data.html", + species=species, + population=population, + dataset=dataset, + job_id=job_id, + job=job, + summary=summary, + activelink="add-phenotypes") diff --git a/uploader/templates/phenotypes/job-status.html b/uploader/templates/phenotypes/job-status.html index 6f43d22..12963c1 100644 --- a/uploader/templates/phenotypes/job-status.html +++ b/uploader/templates/phenotypes/job-status.html @@ -62,8 +62,12 @@ {%if job.status in ("completed:success", "success")%} <p> {%if errors | length == 0%} - <a href="#" - class="not-implemented btn btn-primary" + <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)}}" + class="btn btn-primary" title="Continue to process data">Continue</a> {%else%} <span class="text-muted" diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html new file mode 100644 index 0000000..7bc8c62 --- /dev/null +++ b/uploader/templates/phenotypes/review-job-data.html @@ -0,0 +1,101 @@ +{%extends "phenotypes/base.html"%} +{%from "cli-output.html" import cli_output%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block extrameta%} +{%if not job%} +<meta http-equiv="refresh" + content="20; url={{url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" /> +{%endif%} +{%endblock%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="add-phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} + +{%if job%} +<div class="row"> + <h3 class="heading">Data Review</h3> + <p>The “<strong>{{dataset.FullName}}</strong>” dataset from the + “<strong>{{population.FullName}}</strong>” population of the + species “<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>” + will be updated as follows:</p> + + {%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%} + {%if summary.get(ftype, False)%} + <ul> + <li>A total of {{summary[ftype]["number-of-files"]}} files will be processed + adding {%if ftype == "phenocovar"%}(possibly){%endif%} + {{summary[ftype]["total-data-rows"]}} new + {%if ftype == "phenocovar"%} + phenotypes + {%else%} + {{summary[ftype]["description"]}} rows + {%endif%} + to the database. + </li> + </ul> + {%endif%} + {%endfor%} + + <a href="#" class="not-implemented btn btn-primary">continue</a> +</div> +{%else%} +<div class="row"> + <h4 class="subheading">Invalid Job</h3> + <p class="text-danger"> + Could not find a job with the ID: <strong>{{job_id}}.</p> + <p>You will be redirected in + <span id="countdown-element" class="text-info">20</span> second(s)</p> + <p class="text-muted"> + <small> + If you are not redirected, please + <a href="{{url_for( + 'species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">click here</a> to continue + </small> + </p> +</div> +{%endif%} +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(document).ready(function() { + var countdown = 20; + var countdown_element = $("#countdown-element"); + if(countdown_element.length === 1) { + intv = window.setInterval(function() { + countdown = countdown - 1; + countdown_element.html(countdown); + }, 1000); + } + }); +</script> +{%endblock%} |