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+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages %}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Phenotype(ProbeSet) Study</h2>
+
+<div class="row">
+ <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
+ file(s). This data needs to be organised under a study.</p>
+ <p>In this page, you can either select from a existing dataset:</p>
+
+ <form method="POST"
+ action="{{url_for('upload.rqtl2.select_probeset_study',
+ species_id=species.SpeciesId, population_id=population.Id)}}"
+ id="frm:select-probeset-study">
+ <legend class="heading">Select from existing ProbeSet studies</legend>
+ {{flash_messages("error-rqtl2-select-probeset-study")}}
+
+ <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+ <input type="hidden" name="population_id"
+ value="{{population.InbredSetId}}" />
+ <input type="hidden" name="rqtl2_bundle_file"
+ value="{{rqtl2_bundle_file}}" />
+ <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+ <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+
+ <div>
+ <label for="select:probe-study" class="form-label">Study</label>
+ <select id="select:probe-study"
+ name="probe-study-id"
+ required="required"
+ aria-describedby="help-select-probeset-study"
+ {%if studies | length == 0%}disabled="disabled"{%endif%}
+ class="form-control">
+ <option value="">Select a study</option>
+ {%for study in studies%}
+ <option value={{study.Id}}>
+ {{study.Name}}
+ {%if study.FullName%}
+ -- ({{study.FullName}})
+ {%endif%}
+ </option>
+ {%endfor%}
+ </select>
+ <small id="help-select-probeset-study" class="form-text text-muted">
+ Select from existing ProbeSet studies.
+ </small>
+ </div>
+
+ <button type="submit" class="btn btn-primary">select study</button>
+ </form>
+</div>
+
+<div class="row">
+ <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+</div>
+
+<div class="row">
+
+ <p>Create a new ProbeSet dataset below:</p>
+
+ <form method="POST"
+ action="{{url_for('upload.rqtl2.create_probeset_study',
+ species_id=species.SpeciesId, population_id=population.Id)}}"
+ id="frm:create-probeset-study">
+ <legend class="heading">Create new ProbeSet study</legend>
+
+ {{flash_messages("error-rqtl2-create-probeset-study")}}
+
+ <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+ <input type="hidden" name="population_id"
+ value="{{population.InbredSetId}}" />
+ <input type="hidden" name="rqtl2_bundle_file"
+ value="{{rqtl2_bundle_file}}" />
+ <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+ <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+
+ <div>
+ <label for="select:platform" class="form-label">Platform</label>
+ <select id="select:platform"
+ name="platformid"
+ required="required"
+ aria-describedby="help-select-platform"
+ {%if platforms | length == 0%}disabled="disabled"{%endif%}
+ class="form-control">
+ <option value="">Select a platform</option>
+ {%for platform in platforms%}
+ <option value="{{platform.GeneChipId}}">
+ {{platform.GeneChipName}} ({{platform.Name}})
+ </option>
+ {%endfor%}
+ </select>
+ <small id="help-select-platform" class="form-text text-muted">
+ Select from a list of known genomics platforms.
+ </small>
+ </div>
+
+ <div class="form-group">
+ <label for="txt:studyname" class="form-label">Study name</label>
+ <input type="text" id="txt:studyname" name="studyname"
+ placeholder="Name of the study. (Required)"
+ required="required"
+ maxlength="100"
+ class="form-control" />
+ <span class="form-text text-muted" id="help-study-name">
+ Provide a name for the study.</span>
+ </div>
+
+ <div class="form-group">
+ <label for="txt:studyfullname" class="form-label">Full Study Name</label>
+ <input type="text"
+ id="txt:studyfullname"
+ name="studyfullname"
+ placeholder="Longer name of the study. (Optional)"
+ maxlength="100"
+ class="form-control" />
+ <span class="form-text text-muted" id="help-study-full-name">
+ Provide a longer, more descriptive name for the study. This is optional
+ and you can leave it blank.
+ </span>
+ </div>
+
+ <div class="form-group">
+ <label for="txt:studyshortname" class="form-label">Short Study Name</label>
+ <input type="text"
+ id="txt:studyshortname"
+ name="studyshortname"
+ placeholder="Shorter name of the study. (Optional)"
+ maxlength="100"
+ class="form-control" />
+ <span class="form-text text-muted" id="help-study-short-name">
+ Provide a shorter name for the study. This is optional and you can leave
+ it blank.
+ </span>
+ </div>
+
+ <button type="submit" class="btn btn-primary">create study</button>
+ </form>
+</div>
+
+{%endblock%}