Move R/qtl2 upload code under the populations package.

1 files changed, 115 insertions, 0 deletions

diff --git a/uploader/templates/populations/rqtl2/select-tissue.html b/uploader/templates/populations/rqtl2/select-tissue.html
new file mode 100644
index 0000000..fe3080a
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+++ b/uploader/templates/populations/rqtl2/select-tissue.html
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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">Tissue</h2>
+
+<div class="row">
+  <p>The data you are uploading concerns a tissue, cell, organ, or other
+    biological material used in an experiment.</p>
+  <p>Select the appropriate biological material below</p>
+</div>
+
+{%if tissues | length > 0%}
+<div class="row">
+  <form method="POST"
+        action="{{url_for('expression-data.rqtl2.select_tissue',
+	        species_id=species.SpeciesId, population_id=population.Id)}}"
+        id="frm:select-probeset-dataset">
+    <legend class="heading">Select from existing ProbeSet datasets</legend>
+    {{flash_messages("error-select-tissue")}}
+
+    <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}}" />
+
+    <div class="form-group">
+      <label class="form-label" for="select-tissue">Tissue</label>
+      <select id="select-tissue"
+	      name="tissueid"
+	      required="required"
+	      {%if tissues | length == 0%}disabled="disabled"{%endif%}
+              class="form-control"
+              aria-describedby="help-select-tissue">
+        <option value="">Select a tissue</option>
+        {%for tissue in tissues%}
+        <option value={{tissue.Id}}>
+	  {{tissue.Name}}
+	  {%if tissue.Short_Name%}
+	  -- ({{tissue.Short_Name}})
+	  {%endif%}
+        </option>
+        {%endfor%}
+      </select>
+
+      <span id="help-select-tissue" class="form-text text-muted">
+        Select from existing biological material.</span>
+    </div>
+
+    <button type="submit" class="btn btn-primary">use selected</button>
+  </form>
+</div>
+
+<div class="row">
+  <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+</div>
+{%endif%}
+
+<div class="row">
+  <p>If you cannot find the biological material in the drop-down above, add it
+    to the system below.</p>
+
+  <form method="POST"
+        action="{{url_for('expression-data.rqtl2.create_tissue',
+	        species_id=species.SpeciesId, population_id=population.Id)}}"
+        id="frm:create-probeset-dataset">
+    <legend class="heading">Add new tissue, organ or biological material</legend>
+    {{flash_messages("error-create-tissue")}}
+
+    <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}}" />
+
+    <div class="form-group">
+      <label class="form-label" for="tissue-name">name</label>
+      <input type="text"
+             id="txt-tissuename"
+             name="tissuename"
+             required="required"
+             title = "A name to identify the tissue, organ or biological material."
+             class="form-control"
+             aria-describedby="help-tissue-name" />
+
+      <span class="form-text text-muted" id="help-tissue-name">
+        A name to identify the tissue, organ or biological material.
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-shortname" class="form-label">short name</label>
+      <input type="text" id="txt-tissueshortname" name="tissueshortname"
+	     required="required"
+	     maxlength="7"
+	     title="A short name (e.g. 'Mam') for the biological material."
+             class="form-control"
+             aria-describedby="help-tissue-short-name" />
+
+      <span class="form-text text-muted" id="help-tissue-short-name">
+        Provide a short name for the tissue, organ or biological material used in
+        the experiment.
+      </span>
+    </div>
+
+    <button type="submit" class="btn btn-primary" />add new material</button>
+</form>
+</div>
+
+{%endblock%}