Implement dataset selection

- Implement UI enabling selection from existing datasets
- Start implementation of UI that enables creation of new dataset

5 files changed, 98 insertions, 259 deletions

diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 4fbd0d3..523152d 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -177,6 +177,17 @@ def create_study():
         flash(f"Missing data: {aserr.args[0]}", "alert-error")
         return redirect(url_for("dbinsert.select_study"), code=307)
 
+def datasets_by_study(studyid:int) -> tuple:
+    "Retrieve datasets associated with a study with the ID `studyid`."
+    with database_connection() as conn:
+        with conn.cursor(cursorclass=DictCursor) as cursor:
+            query = "SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s"
+            print(f"QUERY: {query}\n\tPARAMS: ({studyid},)")
+            cursor.execute(query, (studyid,))
+            return tuple(cursor.fetchall())
+
+    return tuple()
+
 @dbinsertbp.route("/dataset", methods=["POST"])
 def select_dataset():
     "Select the dataset to add the file contents against"
@@ -186,15 +197,14 @@ def select_dataset():
         assert form.get("filetype"), "filetype"
         assert form.get("species"), "species"
         assert form.get("genechipid"), "platform"
-        assert (form.get("studyid") or form.get(studyname)), ""
-        assert form.get(""), ""
-        assert form.get(""), ""
-        assert form.get(""), ""
-        assert form.get(""), ""
+        assert (form.get("studyid") or request.args.get("studyid")), "study"
 
+        studyid=(form.get("studyid") or request.args.get("studyid"))
+        datasets = datasets_by_study(studyid)
         return render_template(
             "select_dataset.html", filename=form["filename"],
-            filetype=form["filetype"], species=speciesid, genechipid=genechipid)
+            filetype=form["filetype"], species=form["species"],
+            genechipid=form["genechipid"], studyid=studyid, datasets=datasets)
     except AssertionError as aserr:
         return render_error(f"Missing data: {aserr.args[0]}")
 
diff --git a/qc_app/static/js/dbinsert.js b/qc_app/static/js/dbinsert.js
deleted file mode 100644
index 63d2c86..0000000
--- a/qc_app/static/js/dbinsert.js
+++ /dev/null
@@ -1,156 +0,0 @@
-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);
-}
-
-function setup_groups(group_data) {
-    elt = document.getElementById("group");
-    remove_children(elt);
-    the_groups = group_data.reduce(
-	function(acc, row) {
-	    grouping = row[2].slice(7).trim();
-	    if(acc[grouping] === undefined) {
-		acc[grouping] = [];
-	    }
-	    acc[grouping].push([row[0], row[1]]);
-	    return acc;
-	},
-	{});
-    for(grouping in the_groups) {
-	optgrp = document.createElement("optgroup");
-	optgrp.setAttribute("label", grouping);
-	the_groups[grouping].forEach(group => {
-	    opt = document.createElement("option");
-	    opt.setAttribute("value", group[0]);
-	    opt.appendChild(document.createTextNode(group[1]));
-	    optgrp.appendChild(opt);
-	});
-	elt.appendChild(optgrp);
-    }
-    trigger_change_event(elt);
-}
-
-function setup_types(type_data) {
-    elt = document.getElementById("type");
-    remove_children(elt);
-    the_types = type_data.reduce(function(acc, row) {
-	grp = row[2];
-	if(acc[grp] === undefined) {
-	    acc[grp] = [];
-	}
-	acc[grp].push([row[0], row[1]]);
-	return acc;
-    }, {});
-    for(type_group in the_types) {
-	optgrp = document.createElement("optgroup");
-	optgrp.setAttribute("label", type_group);
-	the_types[type_group].forEach(type => {
-	    opt = document.createElement("option");
-	    opt.setAttribute("value", type[0]);
-	    opt.appendChild(document.createTextNode(type[1]));
-	    optgrp.appendChild(opt);
-	});
-	elt.appendChild(optgrp);
-    }
-    trigger_change_event(elt);
-}
-
-function setup_datasets(dataset_data) {
-    elt = document.getElementById("dataset");
-    remove_children(elt);
-    dataset_data.forEach(dataset => {
-	opt = document.createElement("option");
-	opt.setAttribute("value", dataset[0]);
-	opt.appendChild(document.createTextNode(
-	    "[" + dataset[1] + "] " + dataset[2]));
-	elt.appendChild(opt);
-    });
-    trigger_change_event(elt);
-}
-
-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-dataset-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 menu_contents() {
-    return JSON.parse(
-	document.getElementById("select-dataset-form").getAttribute(
-	    "data-menu-content"));
-}
-
-function genechips() {
-    return JSON.parse(
-	document.getElementById("select-dataset-form").getAttribute(
-	    "data-genechips"));
-}
-
-function update_menu(event) {
-    menu = menu_contents();
-    genec = genechips();
-
-    species_elt = document.getElementById("species");
-    group_elt = document.getElementById("group");
-    type_elt = document.getElementById("type");
-    dataset_elt = document.getElementById("dataset");
-
-    if(event.target == species_elt) {
-	setup_groups(menu["groups"][species_elt.value]);
-	setup_genechips(genec[species_elt.value.toLowerCase()]);
-    }
-
-    if(event.target == group_elt) {
-	setup_types(menu["types"][species_elt.value][group_elt.value]);
-    }
-
-    if(event.target == type_elt) {
-	setup_datasets(
-	    menu["datasets"][species_elt.value][group_elt.value][type_elt.value]
-	);
-    }
-}
diff --git a/qc_app/templates/dbupdate_hidden_fields.html b/qc_app/templates/dbupdate_hidden_fields.html
index ec31202..c66ebba 100644
--- a/qc_app/templates/dbupdate_hidden_fields.html
+++ b/qc_app/templates/dbupdate_hidden_fields.html
@@ -10,5 +10,14 @@
 {%if kwargs.get("genechipid"):%}
 <input type="hidden" name="genechipid" value="{{kwargs['genechipid']}}" />
 {%endif%}
+{%if kwargs.get("inbredsetid"):%}
+<input type="hidden" name="inbredsetid" value="{{kwargs['inbredsetid']}}" />
+{%endif%}
+{%if kwargs.get("tissueid"):%}
+<input type="hidden" name="tissueid" value="{{kwargs['tissueid']}}" />
+{%endif%}
+{%if kwargs.get("studyid"):%}
+<input type="hidden" name="studyid" value="{{kwargs['studyid']}}" />
+{%endif%}
 
 {%endmacro%}
diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html
index 4846f2c..59ead59 100644
--- a/qc_app/templates/select_dataset.html
+++ b/qc_app/templates/select_dataset.html
@@ -1,111 +1,87 @@
 {%extends "base.html"%}
+{%from "dbupdate_hidden_fields.html" import hidden_fields%}
 
 {%block title%}Select Dataset{%endblock%}
 
+{%block css%}
+<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
+{%endblock%}
+
 {%block contents%}
 <h1 class="heading">{{filename}}: select dataset</h2>
 
-<form method="POST" action="{{url_for('dbinsert.insert_data')}}"
-      id="select-dataset-form"
-      data-menu-content="{{menu_contents}}"
-      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[0]}}"
-	      {%if row[0] == default_species:%}
-	      selected="selected"
+<div class="two-column-with-separator">
+  <form method="POST" action="{{url_for('dbinsert.insert_data')}}"
+	id="select-dataset-form" class="two-col-sep-col1">
+    <legend>choose existing dataset</legend>
+    {{hidden_fields(
+    filename, filetype, species=species, genechipid=genechipid,
+    studyid=studyid)}}
+
+    <fieldset>
+      <label for="dataset" class="form-col-1">dataset:</label>
+      <select id="dataset" name="dataset" class="form-col-2"
+	      {%if datasets | length == 0:%}
+	      disabled="disabled"
 	      {%endif%}>
-	{{row[1]}}
-      </option>
-      {%endfor%}
-    </select>
-  </fieldset>
-
-  <fieldset>
-    <label for="group" class="form-col-1">group:</label>
-    <select id="group" name="group" class="form-col-2">
-      {%for grouping, grps in groups.items():%}
-      <optgroup label="{{grouping}}">
-	{%for group in grps:%}
-	<option value="{{group[0]}}">{{group[1]}}</option>
-	{%endfor%}
-      </optgroup>
-      {%endfor%}
-    </select>
-  </fieldset>
-
-  <fieldset>
-    <label for="type" class="form-col-1">type:</label>
-    <select id="type" name="type" class="form-col-2">
-      {%for grouping, typs in types.items():%}
-      <optgroup label="{{grouping}}">
-	{%for type in typs:%}
-	<option value="{{type[0]}}">{{type[1]}}</option>
+	{%for dataset in datasets:%}
+	<option value="{{dataset['Id']}}">
+	  [{{dataset["Name"]}}] - {{dataset["FullName"]}}
+	</option>
 	{%endfor%}
-      </optgroup>
-      {%endfor%}
-    </select>
-  </fieldset>
-
-  <fieldset>
-    <label for="dataset" class="form-col-1">dataset:</label>
-    <select id="dataset" name="dataset" class="form-col-2">
-      {%for dataset_id, name1, name2 in datasets:%}
-      <option value="{{dataset_id}}">[{{name1}}] {{name2}}</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="update database" />
-  </fieldset>
-
-</form>
+      </select>
+    </fieldset>
+
+    <fieldset>
+      <input type="submit" class="btn btn-main form-col-2"
+	     value="update database"
+	     {%if datasets | length == 0:%}
+	     disabled="disabled"
+	     {%endif%} />
+    </fieldset>
+  </form>
+
+  <p class="two-col-sep-separator">OR</p>
+
+  <form method="POST" id="create-dataset-form"
+	class="two-col-sep-col2">
+    <legend>create new dataset</legend>
+    {{hidden_fields(
+    filename, filetype, species=species, genechipid=genechipid,
+    studyid=studyid)}}
+
+    <fieldset>
+      <label for="avgid">average:</label>
+      <select id="avgid" name="avgid" required="required">
+	<option value="">Select averaging method</option>
+      </select>
+    </fieldset>
+
+    <fieldset>
+      <label for="datasetname">name:</label>
+      <input id="datasetname" name="datasetname" type="text" />
+    </fieldset>
+
+    <fieldset>
+      <label for="datasetname2">name 2:</label>
+      <input id="datasetname2" name="datasetname2" type="text" />
+    </fieldset>
+
+    <fieldset>
+      <label for="datasetfullname">full name:</label>
+      <input id="datasetfullname" name="datasetfullname" type="text" />
+    </fieldset>
+
+    <fieldset>
+      <label for="datasetshortname">full name:</label>
+      <input id="datasetshortname" name="datasetshortname" type="text" />
+    </fieldset>
+  </form>
+
+</div>
 
 {%endblock%}
 
 {%block javascript%}
 <script type="text/javascript" src="/static/js/dbinsert.js"></script>
-<script type="text/javascript">
-  document.getElementById("species").addEventListener("change", update_menu);
-  document.getElementById("group").addEventListener("change", update_menu);
-  document.getElementById("type").addEventListener("change", update_menu);
-</script>
 {%endblock%}
diff --git a/qc_app/templates/select_study.html b/qc_app/templates/select_study.html
index e4b629c..d8bdcf0 100644
--- a/qc_app/templates/select_study.html
+++ b/qc_app/templates/select_study.html
@@ -11,7 +11,7 @@
 <h2 class="heading">{{filename}}: select study</h2>
 
 <div class="two-column-with-separator">
-  <form method="POST" action="{{url_for('dbinsert.select_study')}}"
+  <form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
 	id="select-platform-form" data-genechips="{{genechips_data}}"
 	class="two-col-sep-col1">
     <legend>Select from existing study</legend>