Implement select study

Implement the select study UI

5 files changed, 158 insertions, 3 deletions

diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index ea47806..e506175 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -53,6 +53,23 @@ def genechips():
 
     return {}
 
+def studies_by_species_and_platform(speciesid:int, genechipid:int) -> tuple:
+    "Retrieve the studies by the related species and gene platform"
+    with database_connection() as conn:
+        with conn.cursor(cursorclass=DictCursor) as cursor:
+            query = (
+                "SELECT Species.SpeciesId, ProbeFreeze.* "
+                "FROM Species INNER JOIN InbredSet "
+                "ON Species.SpeciesId=InbredSet.SpeciesId "
+                "INNER JOIN ProbeFreeze "
+                "ON InbredSet.InbredSetId=ProbeFreeze.InbredSetId "
+                "WHERE Species.SpeciesId = %s "
+                "AND ProbeFreeze.ChipId = %s")
+            cursor.execute(query, (speciesid, genechipid))
+            return tuple(cursor.fetchall())
+
+    return tuple()
+
 @dbinsertbp.route("/platform", methods=["POST"])
 def select_platform():
     "Select the platform (GeneChipId) used for the data."
@@ -76,7 +93,24 @@ def select_platform():
 
 @dbinsertbp.route("/study", methods=["POST"])
 def select_study():
-    return "Not implemented yet"
+    "View to select/create the study (ProbeFreeze) associated with the data."
+    form = request.form
+    try:
+        assert form.get("filename"), "filename"
+        assert form.get("filetype"), "filetype"
+        assert form.get("species"), "species"
+        assert form.get("genechipid"), "platform"
+
+        speciesid = form["species"]
+        genechipid = form["genechipid"]
+
+        the_studies = studies_by_species_and_platform(speciesid, genechipid)
+        return render_template(
+            "select_study.html", filename=form["filename"],
+            filetype=form["filetype"], species=speciesid, genechipid=genechipid,
+            studies=the_studies)
+    except AssertionError as aserr:
+        return render_error(f"Missing data: {aserr.args[0]}")
 
 @dbinsertbp.route("/select-dataset", methods=["POST"])
 def select_dataset():
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
index d27952a..a42ffb0 100644
--- a/qc_app/static/css/styles.css
+++ b/qc_app/static/css/styles.css
@@ -117,10 +117,16 @@ fieldset {
 
 .form-col-2 {
     grid-column: 2 / 3;
-    width: 20%;
 }
 
 input[disabled="true"],input[disabled="disabled"] {
     border-color: #878787;
     background-color: #A9A9A9;
 }
+
+form legend {
+    padding-left: 3em;
+    text-transform: capitalize;
+    font-weight: bolder;
+    line-height: 2em;
+}
diff --git a/qc_app/static/css/two-column-with-separator.css b/qc_app/static/css/two-column-with-separator.css
new file mode 100644
index 0000000..b6efd46
--- /dev/null
+++ b/qc_app/static/css/two-column-with-separator.css
@@ -0,0 +1,27 @@
+.two-column-with-separator {
+    display: grid;
+    grid-template-columns: 9fr 1fr 9fr;
+}
+
+.two-col-sep-col1 {
+    grid-column: 1 / 2;
+}
+
+.two-col-sep-separator {
+    grid-column: 2 / 3;
+    text-align: center;
+    color: #FE3535;
+    font-weight: bolder;
+}
+
+.two-col-sep-col2 {
+    grid-column: 3 / 4;
+}
+
+.two-col-sep-col1, .two-col-sep-col2 {
+    border-style: solid;
+    border-color: #FE3535;
+    border-width: 1px;
+    border-radius: 2em;
+    padding: 2em 3em 2em 3em;
+}
diff --git a/qc_app/templates/select_platform.html b/qc_app/templates/select_platform.html
index f8db736..131003d 100644
--- a/qc_app/templates/select_platform.html
+++ b/qc_app/templates/select_platform.html
@@ -3,7 +3,7 @@
 {%block title%}Select Dataset{%endblock%}
 
 {%block contents%}
-<h1 class="heading">{{filename}}: select platform</h2>
+<h2 class="heading">{{filename}}: select platform</h2>
 
 <form method="POST" action="{{url_for('dbinsert.select_study')}}"
       id="select-platform-form" data-genechips="{{genechips_data}}">
diff --git a/qc_app/templates/select_study.html b/qc_app/templates/select_study.html
new file mode 100644
index 0000000..8d7a98b
--- /dev/null
+++ b/qc_app/templates/select_study.html
@@ -0,0 +1,88 @@
+{%extends "base.html"%}
+
+{%block title%}Select Dataset{%endblock%}
+
+{%block css%}
+<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
+{%endblock%}
+
+{%block contents%}
+<h2 class="heading">{{filename}}: select study</h2>
+
+<div class="two-column-with-separator">
+  <form method="POST" action="{{url_for('dbinsert.select_study')}}"
+	id="select-platform-form" data-genechips="{{genechips_data}}"
+	class="two-col-sep-col1">
+    <legend>Select from existing study</legend>
+    <input type="hidden" name="filename" value="{{filename}}" />
+    <input type="hidden" name="filetype" value="{{filetype}}" />
+    <input type="hidden" name="species" value="{{species}}" />
+    <input type="hidden" name="genechipid" value="{{genechipid}}" />
+
+    <fieldset>
+      <label for="study" class="form-col-1">study:</label>
+      <select id="study" name="studyid" class="form-col-2">
+	{%for study in studies:%}
+	<option value="{{study['ProbeFreezeId']}}">{{study["Name"]}}</option>
+	{%endfor%}
+      </select>
+    </fieldset>
+
+    <fieldset>
+      <input type="submit" value="submit selected study"
+	     class="btn btn-main form-col-2"
+	     {%if studies | length == 0:%}
+	     disabled="disabled"
+	     {%endif%} />
+    </fieldset>
+  </form>
+
+  <p class="two-col-sep-separator">OR</p>
+
+  <form method="POST" action="{{url_for('dbinsert.select_study')}}"
+	id="select-platform-form" data-genechips="{{genechips_data}}"
+	class="two-col-sep-col2">
+    <legend>Create new study</legend>
+    <input type="hidden" name="filename" value="{{filename}}" />
+    <input type="hidden" name="filetype" value="{{filetype}}" />
+    <input type="hidden" name="species" value="{{species}}" />
+    <input type="hidden" name="genechipid" value="{{genechipid}}" />
+
+    <fieldset>
+      <label for="studyname" class="form-col-1">name:</label>
+      <input type="text" id="studyname" name="studyname" class="form-col-2"
+	     required="required" />
+    </fieldset>
+
+    <fieldset>
+      <label for="studyfullname" class="form-col-1">full name:</label>
+      <input type="text" id="studyfullname" name="studyfullname"
+	     class="form-col-2" />
+    </fieldset>
+
+    <fieldset>
+      <label for="studyshortname" class="form-col-1">short name:</label>
+      <input type="text" id="studyshortname" name="studyshortname"
+	     class="form-col-2" />
+    </fieldset>
+
+    <fieldset>
+      <label for="group" class="form-col-1">group:</label>
+      <select id="group" name="inbredsetid" class="form-col-2">
+      </select>
+    </fieldset>
+
+    <fieldset>
+      <label for="tissue" class="form-col-1">tissue:</label>
+      <select id="tissue" name="tissueid" class="form-col-2">
+      </select>
+    </fieldset>
+
+    <fieldset>
+      <input type="submit" value="create study"
+	     class="btn btn-main form-col-2" />
+    </fieldset>
+  </form>
+</div>
+
+{%endblock%}