diff options
Diffstat (limited to 'uploader')
| -rw-r--r-- | uploader/phenotypes/views.py | 99 | ||||
| -rw-r--r-- | uploader/static/css/styles.css | 14 | ||||
| -rw-r--r-- | uploader/templates/base.html | 2 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/job-status.html | 8 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/macro-display-resumable-elements.html | 60 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/review-job-data.html | 101 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-dataset.html | 3 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-phenotype.html | 89 |
8 files changed, 323 insertions, 53 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index ec4c840..8ecd305 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 @@ -44,7 +44,8 @@ from .models import (dataset_by_id, phenotypes_count, save_new_dataset, dataset_phenotypes, - datasets_by_population) + datasets_by_population, + phenotype_publication_data) phenotypesbp = Blueprint("phenotypes", __name__) render_template = make_template_renderer("phenotypes") @@ -220,16 +221,26 @@ def view_phenotype(# pylint: disable=[unused-argument] ): """View an individual phenotype from the dataset.""" def __render__(privileges): + phenotype = phenotype_by_id(conn, + species["SpeciesId"], + population["Id"], + dataset["Id"], + xref_id) return render_template( "phenotypes/view-phenotype.html", species=species, population=population, dataset=dataset, - phenotype=phenotype_by_id(conn, - species["SpeciesId"], - population["Id"], - dataset["Id"], - xref_id), + phenotype=phenotype, + has_se=all(bool(item.get("error")) for item in phenotype["data"]), + publish_data={ + key.replace("_", " "): val + for key,val in + (phenotype_publication_data(conn, phenotype["Id"]) or {}).items() + if (key in ("PubMed_ID", "Authors", "Title", "Journal") + and val is not None + and val.strip() is not "") + }, privileges=(privileges ### For demo! Do not commit this part + ("group:resource:edit-resource", @@ -502,3 +513,77 @@ 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/static/css/styles.css b/uploader/static/css/styles.css index f482c1b..1c3e677 100644 --- a/uploader/static/css/styles.css +++ b/uploader/static/css/styles.css @@ -3,7 +3,7 @@ body { box-sizing: border-box; display: grid; grid-template-columns: 1fr 6fr; - grid-template-rows: 5em 100%; + grid-template-rows: 4em 100%; grid-gap: 20px; font-family: Georgia, Garamond, serif; @@ -24,7 +24,7 @@ body { } #header .header { - font-size: 2em; + font-size: 1.7em; display: inline-block; text-align: start; } @@ -38,7 +38,7 @@ body { border-width: 1px; border-color: #FFFFFF; vertical-align: middle; - margin: 0.2em; + margin: 0.01em; border-style: solid; border-width: 2px; border-radius: 0.5em; @@ -66,7 +66,8 @@ body { } .pagetitle { - padding-top: 0.5em; + line-height: 1; + padding-top: 0.2em; /* background: pink; */ border-radius: 0.5em; /* background-color: #6699CC; */ @@ -74,10 +75,11 @@ body { background-color: #88BBEE; } -.pagetitle h1 { +.pagetitle .title { text-align: start; text-transform: capitalize; - padding-left: 0.25em; + padding-left: 0.5em; + font-size: 1.7em; } .pagetitle .breadcrumb { diff --git a/uploader/templates/base.html b/uploader/templates/base.html index 3a8ef16..c124b13 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -93,7 +93,7 @@ <main id="main" class="main container-fluid"> <div class="pagetitle row"> - <h1>GN Uploader: {%block pagetitle%}{%endblock%}</h1> + <span class="title">GN Uploader: {%block pagetitle%}{%endblock%}</span> <nav> <ol class="breadcrumb"> <li {%if activelink is not defined or activelink=="home"%} 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/macro-display-resumable-elements.html b/uploader/templates/phenotypes/macro-display-resumable-elements.html new file mode 100644 index 0000000..b0bf1b5 --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-resumable-elements.html @@ -0,0 +1,60 @@ +{%macro display_resumable_elements(id, title, help)%} +<div id="{{id}}" + class="resumable-elements hidden" + style="background:#D4D4EE;border-radius: 5px;;padding: 1em;border-left: solid #B2B2CC 1px;border-bottom: solid #B2B2CC 2px;margin-top:0.3em;"> + <strong style="line-height: 1.2em;">{{title | title}}</strong> + + <span class="form-text text-muted">{{help | safe}}</span> + + <div id="{{id}}-selected-files" + class="resumable-selected-files" + style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"> + <div class="panel panel-info file-display-template hidden"> + <div class="panel-heading filename">The Filename Goes Here!</div> + <div class="panel-body"> + <ul> + <li> + <strong>Name</strong>: + <span class="filename">the file's name</span></li> + + <li><strong>Size</strong>: <span class="filesize">0 MB</span></li> + + <li> + <strong>Unique Identifier</strong>: + <span class="fileuniqueid">brrr</span></li> + + <li> + <strong>Mime</strong>: + <span class="filemimetype">text/csv</span></li> + </ul> + </div> + </div> + </div> + + <a id="{{id}}-browse-button" + class="resumable-browse-button btn btn-info" + href="#" + style="margin-left: 80%;">Browse</a> + + <div id="{{id}}-progress-bar" class="progress hidden"> + <div class="progress-bar" + role="progress-bar" + aria-valuenow="60" + aria-valuemin="0" + aria-valuemax="100" + style="width: 0%;"> + Uploading: 60% + </div> + </div> + + <div id="{{id}}-cancel-resume-buttons"> + <a id="{{id}}-resume-button" + class="resumable-resume-button btn btn-info hidden" + href="#">resume upload</a> + + <a id="{{id}}-cancel-button" + class="resumable-cancel-button btn btn-danger hidden" + href="#">cancel upload</a> + </div> +</div> +{%endmacro%} 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%} diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index 66de5d8..011f8f6 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -79,7 +79,8 @@ population_id=population.Id, dataset_id=dataset.Id, xref_id=pheno['pxr.Id'])}}" - title="View phenotype details"> + title="View phenotype details" + target="_blank"> {{pheno.InbredSetCode}}_{{pheno["pxr.Id"]}}</a></td> <td>{{pheno.Post_publication_description or pheno.Pre_publication_abbreviation or pheno.Original_description}}</td> </tr> diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html index 99bb8e5..18ac202 100644 --- a/uploader/templates/phenotypes/view-phenotype.html +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -34,51 +34,66 @@ <td>{{phenotype.Post_publication_description or phenotype.Pre_publication_abbreviation or phenotype.Original_description}} </tr> <tr> - <td><strong>Cross-Reference ID</strong></td> - <td>{{phenotype.xref_id}}</td> - </tr> - <tr> - <td><strong>Collation</strong></td> + <td><strong>Database</strong></td> <td>{{dataset.FullName}}</td> </tr> <tr> <td><strong>Units</strong></td> <td>{{phenotype.Units}}</td> </tr> + {%for key,value in publish_data.items()%} + <tr> + <td><strong>{{key}}</strong></td> + <td>{{value}}</td> + </tr> + {%else%} + <tr> + <td colspan="2" class="text-muted"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + No publication data found. + </td> + </tr> + {%endfor%} </tbody> </table> + </div> +</div> - <form action="#edit-delete-phenotype" - method="POST" - id="frm-delete-phenotype"> +{%if "group:resource:edit-resource" in privileges +or "group:resource:delete-resource" in privileges%} +<div class="row"> + <form action="#edit-delete-phenotype" + method="POST" + id="frm-delete-phenotype"> - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" value="{{population.Id}}" /> - <input type="hidden" name="dataset_id" value="{{dataset.Id}}" /> - <input type="hidden" name="phenotype_id" value="{{phenotype.Id}}" /> + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" value="{{population.Id}}" /> + <input type="hidden" name="dataset_id" value="{{dataset.Id}}" /> + <input type="hidden" name="phenotype_id" value="{{phenotype.Id}}" /> - <div class="btn-group btn-group-justified"> - <div class="btn-group"> - {%if "group:resource:edit-resource" in privileges%} - <input type="submit" - title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values." - class="btn btn-primary not-implemented" - value="edit" /> - {%endif%} - </div> - <div class="btn-group"></div> - <div class="btn-group"> - {%if "group:resource:delete-resource" in privileges%} - <input type="submit" - title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype." - class="btn btn-danger not-implemented" - value="delete" /> - {%endif%} - </div> - </div> - </form> - </div> + <div class="btn-group btn-group-justified"> + <div class="btn-group"> + {%if "group:resource:edit-resource" in privileges%} + <input type="submit" + title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values." + class="btn btn-primary not-implemented" + value="edit" /> + {%endif%} + </div> + <div class="btn-group"></div> + <div class="btn-group"> + {%if "group:resource:delete-resource" in privileges%} + <input type="submit" + title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype." + class="btn btn-danger not-implemented" + disabled="disabled" + value="delete" /> + {%endif%} + </div> + </div> + </form> </div> +{%endif%} <div class="row"> <div class="panel panel-default"> @@ -90,9 +105,10 @@ <th>#</th> <th>Sample</th> <th>Value</th> - <th>Symbol</th> - <th>SE</th> + {%if has_se%} + <th>SE: {{has_se}}</th> <th>N</th> + {%endif%} </tr> </thead> @@ -102,9 +118,10 @@ <td>{{loop.index}}</td> <td>{{item.StrainName}}</td> <td>{{item.value}}</td> - <td>{{item.Symbol or "-"}}</td> + {%if has_se%} <td>{{item.error or "-"}}</td> <td>{{item.count or "-"}}</td> + {%endif%} </tr> {%endfor%} </tbody> |