diff options
Diffstat (limited to 'uploader/templates')
| -rw-r--r-- | uploader/templates/genotypes/create-dataset.html | 16 | ||||
| -rw-r--r-- | uploader/templates/genotypes/index.html | 32 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-genotypes.html | 228 | ||||
| -rw-r--r-- | uploader/templates/genotypes/select-population.html | 25 | ||||
| -rw-r--r-- | uploader/templates/genotypes/view-dataset.html | 5 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/create-dataset.html | 2 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/review-job-data.html | 37 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-dataset.html | 26 | ||||
| -rw-r--r-- | uploader/templates/publications/create-publication.html | 31 |
9 files changed, 250 insertions, 152 deletions
diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html index 10331c1..ff174fb 100644 --- a/uploader/templates/genotypes/create-dataset.html +++ b/uploader/templates/genotypes/create-dataset.html @@ -35,13 +35,15 @@ id="txt-geno-dataset-name" name="geno-dataset-name" required="required" - class="form-control" /> + class="form-control" + value="{{population.Name}}Geno" + readonly="readonly" /> <small class="form-text text-muted"> <p>This is a short representative, but constrained name for the genotype dataset.<br /> - The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens - and underscores. Any other character will cause the name to be - rejected.</p></small> + It is used internally by the Genenetwork system. Do not change this + value.</p> + </small> </div> <div class="form-group"> @@ -50,7 +52,8 @@ id="txt-geno-dataset-fullname" name="geno-dataset-fullname" required="required" - class="form-control" /> + class="form-control" + value="{{population.Name}} Genotypes" /> <small class="form-text text-muted"> <p>This is a longer, more descriptive name for your dataset.</p></small> </div> @@ -61,7 +64,8 @@ <input type="text" id="txt-geno-dataset-shortname" name="geno-dataset-shortname" - class="form-control" /> + class="form-control" + value="{{population.Name}}Geno" /> <small class="form-text text-muted"> <p>A short name for your dataset. If you leave this field blank, the short name will be set to the same value as the diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html deleted file mode 100644 index b50ebc5..0000000 --- a/uploader/templates/genotypes/index.html +++ /dev/null @@ -1,32 +0,0 @@ -{%extends "genotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-select-species.html" import select_species_form%} - -{%block title%}Genotypes{%endblock%} - -{%block pagetitle%}Genotypes{%endblock%} - - -{%block contents%} -{{flash_all_messages()}} - -<div class="row"> - <p> - This section allows you to upload genotype information for your experiments, - in the case that you have not previously done so. - </p> - <p> - We'll need to link the genotypes to the species and population, so do please - go ahead and select those in the next two steps. - </p> -</div> - -<div class="row"> - {{select_species_form(url_for("species.populations.genotypes.index"), - species)}} -</div> -{%endblock%} - -{%block javascript%} -<script type="text/javascript" src="/static/js/species.js"></script> -{%endblock%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index a2b98c8..131576f 100644 --- a/uploader/templates/genotypes/list-genotypes.html +++ b/uploader/templates/genotypes/list-genotypes.html @@ -9,19 +9,6 @@ {{flash_all_messages()}} <div class="row"> - <h2>Genetic Markers</h2> - <p>There are a total of {{total_markers}} currently registered genetic markers - for the "{{species.FullName}}" species. You can click - <a href="{{url_for('species.populations.genotypes.list_markers', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="View genetic markers for species '{{species.FullName}}"> - this link to view the genetic markers - </a>. - </p> -</div> - -<div class="row"> <h2>Genotype Encoding</h2> <p> The genotype encoding used for the "{{population.FullName}}" population from @@ -56,59 +43,101 @@ </table> {%if genocode | length < 1%} - <a href="#add-genotype-encoding" - title="Add a genotype encoding system for this population" - class="btn btn-primary not-implemented"> - add genotype encoding + <div class="col"> + <a href="#add-genotype-encoding" + title="Add a genotype encoding system for this population" + class="btn btn-primary not-implemented"> + define genotype encoding </a> + </div> {%endif%} </div> -<div class="row text-danger"> - <h3>Some Important Concepts to Consider/Remember</h3> - <ul> - <li>Reference vs. Non-reference alleles</li> - <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li> - </ul> - <h3>Possible references</h3> - <ul> - <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li> - <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li> - </ul> +<div class="row"> + <h2>Genotype Dataset</h2> +</div> + +{%if dataset is not none%} + +<div class="row"> + <h3>Dataset Details</h3> + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td><a href="{{url_for('species.populations.genotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="View details regarding and manage dataset '{{dataset.FullName}}'" + target="_blank"> + {{dataset.FullName}}</a></td> + </tr> + </tbody> + </table> + + <p> + To see more information regarding this dataset (e.g. which markers have + sample allele data, the allele data itself, etc) click on the "Full Name" + link above.</p> +</div> + +<div class="row"> + <h3>Genotype Markers</h3> + + <div class="row"> + <p> + The table below lists all of the markers that exist for species + {{species.SpeciesName}} ({{species.FullName}}), regardless of whether + (or not) we have corresponding sample allele data for a particular marker. + </p> + <table id="tbl-genetic-markers" class="table compact stripe cell-border"> + <thead> + <tr> + <th title="">#</th> + <th title="">Index</th> + <th title="">Marker Name</th> + <th title="Chromosome">Chr</th> + <th title="Physical location of the marker in megabasepairs"> + Location (Mb)</th> + <th title="">Source</th> + <th title="">Source2</th> + </thead> + + <tbody> + {%for marker in markers%} + <tr> + <td></td> + <td></td> + <td></td> + <td></td> + <td></td> + <td></td> + <td></td> + </tr> + {%endfor%} + </tbody> + </table> </div> +{%else%} + <div class="row"> - <h2>Genotype Datasets</h2> - - <p>The genotype data is organised under various genotype datasets. You can - click on the link for the relevant dataset to view a little more information - about it.</p> - - {%if dataset is not none%} - <table class="table"> - <thead> - <tr> - <th>Name</th> - <th>Full Name</th> - </tr> - </thead> - - <tbody> - <tr> - <td>{{dataset.Name}}</td> - <td><a href="{{url_for('species.populations.genotypes.view_dataset', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}" - title="View details regarding and manage dataset '{{dataset.FullName}}'"> - {{dataset.FullName}}</a></td> - </tr> - </tbody> - </table> - {%else%} + <p> + Your genotype data will need to be under a dataset. Unfortunately there is + currently no dataset defined for this population. + </p> + <p class="text-warning"> <span class="glyphicon glyphicon-exclamation-sign"></span> - There is no genotype dataset defined for this population. + Click the button below to define the genotype dataset for this population. </p> <p> <a href="{{url_for('species.populations.genotypes.create_dataset', @@ -117,16 +146,81 @@ title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species." class="btn btn-primary"> create new genotype dataset</a></p> - {%endif%} </div> -<div class="row text-warning"> - <p> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a - single genotype dataset. If there is more than one, the system apparently - fails in unpredictable ways. - </p> - <p>Fix this to allow multiple datasets, each with a different assembly from - all the rest.</p> + +{%endif%} + +<div class="row"> + <h2>Notes</h2> + <div class="row text-danger"> + <h3>Genetic Markers: Some Important Concepts to Consider/Remember</h3> + <ul> + <li>Reference vs. Non-reference alleles</li> + <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li> + </ul> + <h3>Possible references</h3> + <ul> + <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li> + <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li> + </ul> + </div> + + <div class="row text-warning"> + <h3>Genotype Dataset</h3> + <p> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a + single genotype dataset per population. If there is more than one, the + system apparently fails in unpredictable ways. + </p> + </div> </div> + +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + + $(function() { + var dtGeneticMarkers = buildDataTable( + "#tbl-genetic-markers", + [], + [ + { + data: function(marker) { + return `<input type="checkbox" name="selected-markers" ` + + `id="chk-selected-markers-${marker.Id}-${marker.GenoFreezeId}" ` + + `value="${marker.Id}_${marker.GenoFreezeId}" ` + + `class="chk-row-select" />`; + } + }, + {data: 'index'}, + {data: "Name", searchable: true}, + {data: "Chr", searchable: true}, + {data: "Mb", searchable: true}, + {data: "Source", searchable: true}, + {data: "Source2", searchable: true} + ], + { + ajax: { + url: "{{url_for('species.populations.genotypes.list_markers', species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id)}}", + dataSrc: "markers" + }, + paging: true, + scroller: true, + scrollY: "50vh", + scrollCollapse: true, + layout: { + top: "info", + topStart: null, + topEnd: null, + bottom: null, + bottomStart: null, + bottomEnd: null + } + }); + }); + +</script> {%endblock%} diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html deleted file mode 100644 index acdd063..0000000 --- a/uploader/templates/genotypes/select-population.html +++ /dev/null @@ -1,25 +0,0 @@ -{%extends "genotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-display-species-card.html" import display_species_card%} -{%from "populations/macro-select-population.html" import select_population_form%} - -{%block title%}Genotypes{%endblock%} - -{%block pagetitle%}Genotypes{%endblock%} - - -{%block contents%} -{{flash_all_messages()}} - -<div class="row"> - {{select_population_form(url_for("species.populations.genotypes.select_population", species_id=species.SpeciesId), species, populations)}} -</div> -{%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} - -{%block javascript%} -<script type="text/javascript" src="/static/js/populations.js"></script> -{%endblock%} diff --git a/uploader/templates/genotypes/view-dataset.html b/uploader/templates/genotypes/view-dataset.html index 1c4eccf..d95a8e3 100644 --- a/uploader/templates/genotypes/view-dataset.html +++ b/uploader/templates/genotypes/view-dataset.html @@ -46,8 +46,9 @@ <div class="row"> <h2>Genotype Data</h2> - <p class="text-danger"> - Provide link to enable uploading of genotype data here.</p> + <div class="col" style="margin-bottom: 3px;"> + <a href="#" class="btn btn-primary not-implemented">upload genotypes</a> + </div> </div> {%endblock%} diff --git a/uploader/templates/phenotypes/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html index 6eced05..9963953 100644 --- a/uploader/templates/phenotypes/create-dataset.html +++ b/uploader/templates/phenotypes/create-dataset.html @@ -49,7 +49,7 @@ class="form-control" {%endif%} required="required" - disabled="disabled" /> + readonly="readonly" /> <small class="form-text text-muted"> <p>A short representative name for the dataset.</p> <p>Recommended: Use the population name and append "Publish" at the end. diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html index c8355b2..0e8f119 100644 --- a/uploader/templates/phenotypes/review-job-data.html +++ b/uploader/templates/phenotypes/review-job-data.html @@ -70,6 +70,9 @@ {%endif%} {%endfor%} </ul> +</div> + +<div class="row"> <form id="frm-review-phenotype-data" method="POST" @@ -78,10 +81,38 @@ population_id=population.Id, dataset_id=dataset.Id)}}"> <input type="hidden" name="data-qc-job-id" value="{{job.jobid}}" /> - <input type="submit" - value="continue" - class="btn btn-primary" /> + <div class="form-group"> + <label for="txt-data-name">data name</label> + <input type="text" + id="txt-data-name" + class="form-control" + name="data_name" + title="A short, descriptive name for this data." + placeholder="{{user.email}} - {{dataset.Name}} - {{timestamp}}" + value="{{user.email}} - {{dataset.Name}} - {{timestamp}}" + required="required"> + <span class="form-text text-muted"> + This is a short, descriptive name for the data. It is useful to humans, + enabling them identify what traits each data "resource" wraps around. + </span> + </div> + + {%if view_under_construction%} + <div class="form-group"> + <label for="txt-data-description">data description</label> + <textarea id="txt-data-description" + class="form-control" + name="data_description" + title="A longer description for this data." + rows="5"></textarea> + <span class="form-text text-muted"> + </span> + </div> + {%endif%} + + <button type="submit" class="btn btn-primary">continue</button> </form> + </div> {%else%} <div class="row"> diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index 3bb2586..fc84757 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -148,14 +148,36 @@ return `<a href="${url.toString()}" target="_blank">` + `${pheno.InbredSetCode}_${pheno.xref_id}` + `</a>`; - } + }, + title: "Record", + visible: true, + searchable: true }, { data: function(pheno) { return (pheno.Post_publication_description || pheno.Original_description || pheno.Pre_publication_description); - } + }, + title: "Description", + visible: true, + searchable: true + }, + { + data: function(pheno) { + return pheno.publication.Title; + }, + title: "Publication Title", + visible: false, + searchable: true + }, + { + data: function(pheno) { + return pheno.publication.Authors; + }, + title: "Authors", + visible: false, + searchable: true } ], { diff --git a/uploader/templates/publications/create-publication.html b/uploader/templates/publications/create-publication.html index fb0127d..da5889e 100644 --- a/uploader/templates/publications/create-publication.html +++ b/uploader/templates/publications/create-publication.html @@ -91,22 +91,22 @@ class="col-sm-2 col-form-label"> Month</label> <div class="col-sm-4"> - <select class="form-control" + <select class="form-select" id="select-publication-month" name="publication-month"> <option value="">Select a month</option> - <option value="january">January</option> - <option value="february">February</option> - <option value="march">March</option> - <option value="april">April</option> - <option value="may">May</option> - <option value="june">June</option> - <option value="july">July</option> - <option value="august">August</option> - <option value="september">September</option> - <option value="october">October</option> - <option value="november">November</option> - <option value="december">December</option> + <option {%if current_month | lower == "january"%}selected="selected"{%endif%}value="january">January</option> + <option {%if current_month | lower == "february"%}selected="selected"{%endif%}value="february">February</option> + <option {%if current_month | lower == "march"%}selected="selected"{%endif%}value="march">March</option> + <option {%if current_month | lower == "april"%}selected="selected"{%endif%}value="april">April</option> + <option {%if current_month | lower == "may"%}selected="selected"{%endif%}value="may">May</option> + <option {%if current_month | lower == "june"%}selected="selected"{%endif%}value="june">June</option> + <option {%if current_month | lower == "july"%}selected="selected"{%endif%}value="july">July</option> + <option {%if current_month | lower == "august"%}selected="selected"{%endif%}value="august">August</option> + <option {%if current_month | lower == "september"%}selected="selected"{%endif%}value="september">September</option> + <option {%if current_month | lower == "october"%}selected="selected"{%endif%}value="october">October</option> + <option {%if current_month | lower == "november"%}selected="selected"{%endif%}value="november">November</option> + <option {%if current_month | lower == "december"%}selected="selected"{%endif%}value="december">December</option> </select> <span class="form-text text-muted">Month of publication</span> </div> @@ -119,7 +119,10 @@ id="txt-publication-year" name="publication-year" class="form-control" - min="1960" /> + min="1960" + max="{{current_year}}" + value="{{current_year or ''}}" + required="required" /> <span class="form-text text-muted">Year of publication</span> </div> </div> |