From 4285cc10e24d6410206329ba079406e9aa21cc30 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 23 Sep 2024 14:30:15 -0500
Subject: Move R/qtl2 upload code under the populations package.

---
 .../rqtl2/select-probeset-study-id.html            | 143 +++++++++++++++++++++
 1 file changed, 143 insertions(+)
 create mode 100644 uploader/templates/populations/rqtl2/select-probeset-study-id.html

(limited to 'uploader/templates/populations/rqtl2/select-probeset-study-id.html')

diff --git a/uploader/templates/populations/rqtl2/select-probeset-study-id.html b/uploader/templates/populations/rqtl2/select-probeset-study-id.html
new file mode 100644
index 0000000..e3fd9cc
--- /dev/null
+++ b/uploader/templates/populations/rqtl2/select-probeset-study-id.html
@@ -0,0 +1,143 @@
+{%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('expression-data.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('expression-data.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%}
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