diff options
Diffstat (limited to 'uploader/templates/genotypes')
| -rw-r--r-- | uploader/templates/genotypes/base.html | 18 | ||||
| -rw-r--r-- | uploader/templates/genotypes/create-dataset.html | 86 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-genotypes.html | 226 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-markers.html | 99 | ||||
| -rw-r--r-- | uploader/templates/genotypes/view-dataset.html | 54 |
5 files changed, 483 insertions, 0 deletions
diff --git a/uploader/templates/genotypes/base.html b/uploader/templates/genotypes/base.html new file mode 100644 index 0000000..8d1b951 --- /dev/null +++ b/uploader/templates/genotypes/base.html @@ -0,0 +1,18 @@ +{%extends "populations/base.html"%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} + +{%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> +{%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/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html new file mode 100644 index 0000000..131576f --- /dev/null +++ b/uploader/templates/genotypes/list-genotypes.html @@ -0,0 +1,226 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Genotypes{%endblock%} + +{%block pagetitle%}Genotypes{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <h2>Genotype Encoding</h2> + <p> + The genotype encoding used for the "{{population.FullName}}" population from + the "{{species.FullName}}" species is as shown in the table below. + </p> + <table class="table"> + + <thead> + <tr> + <th>Allele Type</th> + <th>Allele Symbol</th> + <th>Allele Value</th> + </tr> + </thead> + + <tbody> + {%for row in genocode%} + <tr> + <td>{{row.AlleleType}}</td> + <td>{{row.AlleleSymbol}}</td> + <td>{{row.DatabaseValue if row.DatabaseValue is not none else "NULL"}}</td> + </tr> + {%else%} + <tr> + <td colspan="7" class="text-info"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There is no explicit genotype encoding defined for this population. + </td> + </tr> + {%endfor%} + </tbody> + </table> + + {%if genocode | length < 1%} + <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"> + <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"> + <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> + Click the button below to define the genotype dataset for this population. + </p> + <p> + <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> +</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 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 new file mode 100644 index 0000000..22189c7 --- /dev/null +++ b/uploader/templates/genotypes/list-markers.html @@ -0,0 +1,99 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Genotypes: List Markers{%endblock%} + +{%block pagetitle%}Genotypes: List Markers{%endblock%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.populations.genotypes.list_markers', + species_id=species['SpeciesId'], + population_id=population['Id'])}}"> + markers + </a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +{%if markers | length > 0%} +<div class="row"> + <p> + There are a total of {{total_markers}} genotype markers for this species. + </p> + <div class="row"> + <div class="col-md-2" style="text-align: start;"> + {%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> + Previous + </a> + {%endif%} + </div> + <div class="col-md-8" style="text-align: center;"> + Displaying markers {{start_from+1}} to {{start_from+count if start_from+count < total_markers else total_markers}} of + {{total_markers}} + </div> + <div class="col-md-2" style="text-align: end;"> + {%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 + <span class="glyphicon glyphicon-forward"></span> + </a> + {%endif%} + </div> + </div> + <table class="table"> + <thead> + <tr> + <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>{{marker.sequence_number}}</td> + <td>{{marker.Marker_Name}}</td> + <td>{{marker.Chr}}</td> + <td>{{marker.Mb}}</td> + <td>{{marker.Source}}</td> + <td>{{marker.Source2}}</td> + </tr> + {%endfor%} + </tbody> + </table> +</div> +{%else%} +<div class="row"> + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + This species does not currently have any genetic markers uploaded, therefore, + there is nothing to display here. + </p> + <p> + <a href="#add-genetic-markers-for-species-{{species.SpeciesId}}" + title="Add genetic markers for this species" + class="btn btn-primary"> + add genetic markers + </a> + </p> +</div> +{%endif%} +{%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%} |