Select the platform (GeneChipId) first

5 files changed, 183 insertions, 9 deletions

diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 09dd3e1..ea47806 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -27,24 +27,57 @@ def make_menu_items_grouper(grouping_fn=lambda item: item):
         return {**acc, grouping: (acc[grouping] + (row_values,))}
     return __grouper__
 
+def species() -> tuple:
+    "Retrieve the species from the database."
+    with database_connection() as conn:
+        with conn.cursor(cursorclass=DictCursor) as cursor:
+            cursor.execute(
+                "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
+                "FROM Species")
+            return tuple(cursor.fetchall())
+
+    return tuple()
+
 def genechips():
     "Retrieve the genechip information from the database"
     def __organise_by_species__(acc, chip):
-        species = chip["species_name"]
-        if acc.get(species) is None:
-            return {**acc, species: (chip,)}
-        return {**acc, species: acc[species] + (chip,)}
+        speciesid = chip["SpeciesId"]
+        if acc.get(speciesid) is None:
+            return {**acc, speciesid: (chip,)}
+        return {**acc, species: acc[speciesid] + (chip,)}
 
     with database_connection() as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
-            cursor.execute(
-                "SELECT GeneChip.*, LOWER(Species.Name) AS species_name "
-                "FROM GeneChip INNER JOIN Species "
-                "ON GeneChip.SpeciesId=Species.SpeciesId")
+            cursor.execute("SELECT * FROM GeneChip ORDER BY GeneChipName ASC")
             return reduce(__organise_by_species__, cursor.fetchall(), {})
 
     return {}
 
+@dbinsertbp.route("/platform", methods=["POST"])
+def select_platform():
+    "Select the platform (GeneChipId) used for the data."
+    job_id = request.form["job_id"]
+    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+        job = jobs.job(rconn, job_id)
+        if job:
+            filename = job["filename"]
+            filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
+            if os.path.exists(filepath):
+                default_species = 1
+                gchips = genechips()
+                return render_template(
+                    "select_platform.html", filename=filename,
+                    filetype=job["filetype"], default_species=default_species,
+                    species=species(), genechips=gchips[default_species],
+                    genechips_data=json.dumps(gchips))
+            return render_error(f"File '{filename}' no longer exists.")
+        return render_error(f"Job '{job_id}' no longer exists.")
+    return render_error("Unknown error")
+
+@dbinsertbp.route("/study", methods=["POST"])
+def select_study():
+    return "Not implemented yet"
+
 @dbinsertbp.route("/select-dataset", methods=["POST"])
 def select_dataset():
     "Select the dataset to add the file contents against"
diff --git a/qc_app/static/js/select_platform.js b/qc_app/static/js/select_platform.js
new file mode 100644
index 0000000..d7541fa
--- /dev/null
+++ b/qc_app/static/js/select_platform.js
@@ -0,0 +1,59 @@
+function radio_column(chip) {
+    col = document.createElement("td");
+    radio = document.createElement("input");
+    radio.setAttribute("type", "radio");
+    radio.setAttribute("name", "genechipid");
+    radio.setAttribute("value", chip["GeneChipId"]);
+    radio.setAttribute("required", "required");
+    col.appendChild(radio);
+    return col;
+}
+
+function setup_genechips(genechip_data) {
+    columns = ["GeneChipName", "Name", "GeoPlatform", "GO_tree_value"]
+    submit_button = document.querySelector(
+	"#select-platform-form input[type='submit']");
+    elt = document.getElementById(
+	"genechips-table").getElementsByTagName("tbody")[0];
+    remove_children(elt);
+    if((genechip_data === undefined) || genechip_data.length === 0) {
+	row = document.createElement("tr");
+	col = document.createElement("td");
+	col.setAttribute("colspan", "5");
+	text = document.createTextNode("No chips found for selected species");
+	col.appendChild(text);
+	row.appendChild(col);
+	elt.appendChild(row);
+	submit_button.setAttribute("disabled", true);
+	return false;
+    }
+
+    submit_button.removeAttribute("disabled")
+    genechip_data.forEach(chip => {
+	row = document.createElement("tr");
+	row.appendChild(radio_column(chip));
+	columns.forEach(column => {
+	    col = document.createElement("td");
+	    content = document.createTextNode(chip[column]);
+	    col.appendChild(content);
+	    row.appendChild(col);
+	});
+	elt.appendChild(row);
+    });
+}
+
+function genechips() {
+    return JSON.parse(
+	document.getElementById("select-platform-form").getAttribute(
+	    "data-genechips"));
+}
+
+function update_genechips(event) {
+    genec = genechips();
+
+    species_elt = document.getElementById("species");
+
+    if(event.target == species_elt) {
+	setup_genechips(genec[species_elt.value.toLowerCase()]);
+    }
+}
diff --git a/qc_app/static/js/utils.js b/qc_app/static/js/utils.js
new file mode 100644
index 0000000..045dd47
--- /dev/null
+++ b/qc_app/static/js/utils.js
@@ -0,0 +1,10 @@
+function remove_children(element) {
+    Array.from(element.children).forEach(child => {
+	element.removeChild(child);
+    });
+}
+
+function trigger_change_event(element) {
+    evt = new Event("change");
+    element.dispatchEvent(evt);
+}
diff --git a/qc_app/templates/parse_results.html b/qc_app/templates/parse_results.html
index 1a224e8..80d6a2d 100644
--- a/qc_app/templates/parse_results.html
+++ b/qc_app/templates/parse_results.html
@@ -13,7 +13,7 @@
 {{errors_display(errors, "No errors found in the file", "We found the following errors")}}
 
 {%if errors | length == 0 %}
-<form method="post" action="{{url_for('dbinsert.select_dataset')}}">
+<form method="post" action="{{url_for('dbinsert.select_platform')}}">
   <input type="hidden" name="job_id" value="{{job_id}}" />
   <input type="submit" value="update database" class="btn btn-main" />
 </form>
diff --git a/qc_app/templates/select_platform.html b/qc_app/templates/select_platform.html
new file mode 100644
index 0000000..f8db736
--- /dev/null
+++ b/qc_app/templates/select_platform.html
@@ -0,0 +1,72 @@
+{%extends "base.html"%}
+
+{%block title%}Select Dataset{%endblock%}
+
+{%block contents%}
+<h1 class="heading">{{filename}}: select platform</h2>
+
+<form method="POST" action="{{url_for('dbinsert.select_study')}}"
+      id="select-platform-form" data-genechips="{{genechips_data}}">
+  <input type="hidden" name="filename" value="{{filename}}" />
+  <input type="hidden" name="filetype" value="{{filetype}}" />
+
+  <fieldset>
+    <label for="species" class="form-col-1">species</label>
+    <select id="species" name="species" class="form-col-2">
+      {%for row in species:%}
+      <option value="{{row['SpeciesId']}}"
+	      {%if row["Name"] == default_species:%}
+	      selected="selected"
+	      {%endif%}>
+	{{row["MenuName"]}}
+      </option>
+      {%endfor%}
+    </select>
+  </fieldset>
+
+  <table id="genechips-table">
+    <thead>
+      <tr>
+	<th>Select</th>
+	<th>GeneChip Name</th>
+	<th>Name</th>
+	<th>GeoPlatform</th>
+	<th>GO Tree Value</th>
+      </tr>
+    </thead>
+
+    <tbody>
+      {%for chip in genechips:%}
+      <tr>
+	<td>
+	  <input type="radio" name="genechipid" value="{{chip['GeneChipId']}}"
+		 required="required" />
+	</td>
+	<td>{{chip["GeneChipName"]}}</td>
+	<td>{{chip["Name"]}}</td>
+	<td>{{chip["GeoPlatform"]}}</td>
+	<td>{{chip["GO_tree_value"]}}</td>
+      </tr>
+      {%else%}
+      <tr>
+	<td colspan="5">No chips found for selected species</td>
+      </tr>
+      {%endfor%}
+    </tbody>
+  </table>
+
+  <fieldset>
+    <input type="submit" class="btn btn-main form-col-2"
+	   value="submit platform" />
+  </fieldset>
+</form>
+{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/utils.js"></script>
+<script type="text/javascript" src="/static/js/select_platform.js"></script>
+<script type="text/javascript">
+  document.getElementById(
+      "species").addEventListener("change", update_genechips);
+</script>
+{%endblock%}