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{%extends "base.html"%}
{%from "flash_messages.html" import flash_messages, flash_all_messages%}
{%block title%}Upload R/qtl2 Bundle{%endblock%}
{%block contents%}
<h2 class="heading">Phenotype(ProbeSet) Study</h2>
<div class="explainer">
<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>
</div>
{{flash_all_messages()}}
<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>
<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}}" />
<fieldset>
<label for="select:probe-study">Study</label>
<select id="select:probe-study"
name="probe-study-id"
required="required"
{%if studies | length == 0%}disabled="disabled"{%endif%}>
<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>
<span class="form-col-2">Select from existing ProbeSet studies.</span>
</fieldset>
<fieldset>
<input type="submit"
value="select study"
class="btn btn-main form-col-2" />
</fieldset>
</form>
<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
<div class="explainer">
<p>Create a new ProbeSet dataset below:</p>
</div>
<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>
<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}}" />
<fieldset>
<label for="select:platform">Platform</label>
<select id="select:platform"
name="platformid"
required="required"
{%if platforms | length == 0%}disabled="disabled"{%endif%}>
<option value="">Select a platform</option>
{%for platform in platforms%}
<option value="{{platform.GeneChipId}}">
{{platform.GeneChipName}} ({{platform.Name}})
</option>
{%endfor%}
</select>
<span class="form-col-2">Select from a list of known genomics platforms.
</span>
</fieldset>
<fieldset>
<label for="select:tissue">Tissue</label>
<select id="select:tissue"
name="tissueid"
required="required"
{%if tissues | length == 0%}disabled="disabled"{%endif%}>
<option value="">Select tissue</option>
{%for tissue in tissues%}
<option value="{{tissue.Id}}">
{{tissue.TissueName}} ({{tissue.Short_Name}})
</option>
{%endfor%}
</select>
<span class="form-col-2">
Select the Tissue to which the data is concerned.
</span>
</fieldset>
<fieldset>
<label for="txt:studyname">Study name</label>
<input type="text" id="txt:studyname" name="studyname"
placeholder="Name of the study. (Required)"
required="required"
maxlength="100" />
<span class="form-col-2">Provide a name for the study.</span>
</fieldset>
<fieldset>
<label for="txt:studyfullname">Full Study Name</label>
<input type="text" id="txt:studyfullname" name="studyfullname"
placeholder="Longer name of the study. (Optional)"
maxlength="100" />
<span class="form-col-2">
Provide a longer, more descriptive name for the study. This is optional
and you can leave it blank.
</span>
</fieldset>
<fieldset>
<label for="txt:studyshortname">Short Study Name</label>
<input type="text" id="txt:studyshortname" name="studyshortname"
placeholder="Shorter name of the study. (Optional)"
maxlength="100" />
<span class="form-col-2">
Provide a shorter name for the study. This is optional and you can leave
it blank.
</span>
</fieldset>
<fieldset>
<input type="submit"
value="create study"
class="btn btn-main form-col-2" />
</fieldset>
</form>
{%endblock%}
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