diff options
Diffstat (limited to 'uploader/templates/genotypes')
| -rw-r--r-- | uploader/templates/genotypes/base.html | 22 | ||||
| -rw-r--r-- | uploader/templates/genotypes/create-dataset.html | 86 | ||||
| -rw-r--r-- | uploader/templates/genotypes/index.html | 28 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-genotypes.html | 236 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-markers.html | 23 | ||||
| -rw-r--r-- | uploader/templates/genotypes/select-population.html | 31 | ||||
| -rw-r--r-- | uploader/templates/genotypes/view-dataset.html | 54 |
7 files changed, 327 insertions, 153 deletions
diff --git a/uploader/templates/genotypes/base.html b/uploader/templates/genotypes/base.html index 1b274bf..8d1b951 100644 --- a/uploader/templates/genotypes/base.html +++ b/uploader/templates/genotypes/base.html @@ -1,12 +1,18 @@ {%extends "populations/base.html"%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} -{%block lvl3_breadcrumbs%} -<li {%if activelink=="genotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.genotypes.index')}}">Genotypes</a> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.populations.genotypes.list_genotypes', + species_id=species['SpeciesId'], + population_id=population['Id'])}}"> + genotype + </a> </li> -{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} + + +{%block sidebarcontents%} +{{display_sui_population_card(species, population)}} {%endblock%} diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html new file mode 100644 index 0000000..ff174fb --- /dev/null +++ b/uploader/templates/genotypes/create-dataset.html @@ -0,0 +1,86 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes — Create Dataset{%endblock%} + +{%block pagetitle%}Genotypes — Create Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="create-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}">Create Dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-geno-create-dataset" + method="POST" + action="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}"> + <legend>Create a new Genotype Dataset</legend> + + <div class="form-group"> + <label for="txt-geno-dataset-name" class="form-label">Name</label> + <input type="text" + id="txt-geno-dataset-name" + name="geno-dataset-name" + required="required" + 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 /> + It is used internally by the Genenetwork system. Do not change this + value.</p> + </small> + </div> + + <div class="form-group"> + <label for="txt-geno-dataset-fullname" class="form-label">Full Name</label> + <input type="text" + id="txt-geno-dataset-fullname" + name="geno-dataset-fullname" + required="required" + 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> + + <div class="form-group"> + <label for="txt-geno-dataset-shortname" + class="form-label">Short Name</label> + <input type="text" + id="txt-geno-dataset-shortname" + name="geno-dataset-shortname" + 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 + "<strong>Name</strong>" field above.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + class="btn btn-primary" + value="create dataset" /> + </div> + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html deleted file mode 100644 index e749f5a..0000000 --- a/uploader/templates/genotypes/index.html +++ /dev/null @@ -1,28 +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%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index 3780f85..131576f 100644 --- a/uploader/templates/genotypes/list-genotypes.html +++ b/uploader/templates/genotypes/list-genotypes.html @@ -1,39 +1,14 @@ {%extends "genotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Genotypes{%endblock%} {%block pagetitle%}Genotypes{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="list-genotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.genotypes.list_genotypes', - species_id=species.SpeciesId, - population_id=population.Id)}}">List genotypes</a> -</li> -{%endblock%} - {%block contents%} {{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)}}" - 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 @@ -68,69 +43,184 @@ </table> {%if genocode | length < 1%} - <a href="#add-genotype-encoding" - title="Add a genotype encoding system for this population" - class="btn btn-primary"> - 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 defined %} - <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="#create-new-genotype-dataset" + <a href="{{url_for('species.populations.genotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" 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> + +{%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 sidebarcontents%} -{{display_population_card(species, population)}} + +{%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/list-markers.html b/uploader/templates/genotypes/list-markers.html index 9198b44..22189c7 100644 --- a/uploader/templates/genotypes/list-markers.html +++ b/uploader/templates/genotypes/list-markers.html @@ -1,19 +1,18 @@ {%extends "genotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-display-species-card.html" import display_species_card%} {%block title%}Genotypes: List Markers{%endblock%} {%block pagetitle%}Genotypes: List Markers{%endblock%} -{%block lvl4_breadcrumbs%} -<li {%if activelink=="list-markers"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.genotypes.list_markers', - species_id=species.SpeciesId)}}">List markers</a> + species_id=species['SpeciesId'], + population_id=population['Id'])}}"> + markers + </a> </li> {%endblock%} @@ -30,6 +29,7 @@ {%if start_from > 0%} <a href="{{url_for('species.populations.genotypes.list_markers', species_id=species.SpeciesId, + population_id=population.Id, start_from=start_from-count, count=count)}}"> <span class="glyphicon glyphicon-backward"></span> @@ -45,6 +45,7 @@ {%if start_from + count < total_markers%} <a href="{{url_for('species.populations.genotypes.list_markers', species_id=species.SpeciesId, + population_id=population.Id, start_from=start_from+count, count=count)}}"> Next @@ -56,7 +57,7 @@ <table class="table"> <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"> @@ -96,7 +97,3 @@ </div> {%endif%} {%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html deleted file mode 100644 index 7c81943..0000000 --- a/uploader/templates/genotypes/select-population.html +++ /dev/null @@ -1,31 +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"> - <p> - You have indicated that you intend to upload the genotypes for species - '{{species.FullName}}'. We now just require the population for your - experiment/study, and you should be good to go. - </p> -</div> - -<div class="row"> - {{select_population_form(url_for("species.populations.genotypes.select_population", - species_id=species.SpeciesId), - populations)}} -</div> -{%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} diff --git a/uploader/templates/genotypes/view-dataset.html b/uploader/templates/genotypes/view-dataset.html new file mode 100644 index 0000000..d95a8e3 --- /dev/null +++ b/uploader/templates/genotypes/view-dataset.html @@ -0,0 +1,54 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Genotypes: View Dataset{%endblock%} + +{%block pagetitle%}Genotypes: View Dataset{%endblock%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.populations.genotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">dataset</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Genotype Dataset Details</h2> + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + </tr> + </thead> + + <tbody> + <tr> + <td>{{dataset.Name}}</td> + <td>{{dataset.FullName}}</td> + </tr> + </tbody> + </table> +</div> + +<div class="row text-warning"> + <h2>Assembly Details</h2> + + <p>Maybe include the assembly details here if found to be necessary.</p> +</div> + +<div class="row"> + <h2>Genotype Data</h2> + + <div class="col" style="margin-bottom: 3px;"> + <a href="#" class="btn btn-primary not-implemented">upload genotypes</a> + </div> +</div> + +{%endblock%} |