Compute pcorrs with selected target traits

Modify the code to request computation of partial correlations with
selected traits rather than a complete dataset.

3 files changed, 182 insertions, 18 deletions

diff --git a/wqflask/wqflask/partial_correlations_views.py b/wqflask/wqflask/partial_correlations_views.py
index 41bbe7d7..40c5132b 100644
--- a/wqflask/wqflask/partial_correlations_views.py
+++ b/wqflask/wqflask/partial_correlations_views.py
@@ -116,8 +116,20 @@ def controls_error(args):
                   "of three control traits"),))}
     return args
 
-def target_db_error(args):
-    if not args["target_db"]:
+def target_traits_error(args, with_target_traits):
+    target_traits_present = (
+        (args.get("target_traits") is not None) and
+        (len(args["target_traits"]) > 0))
+    if with_target_traits and not target_traits_present:
+        return {
+            **args,
+            "errors": (
+                args.get("errors", tuple()) +
+                (("You must provide at least one target trait"),))}
+    return args
+
+def target_db_error(args, with_target_db: bool):
+    if with_target_db and not args["target_db"]:
         return {
             **args,
             "errors": (
@@ -151,17 +163,24 @@ def criteria_error(args):
                 args.get("errors", tuple()) +
                 ("Invalid return number provided",))}
 
-def errors(args):
-    return criteria_error(method_error(target_db_error(controls_error(
-        primary_error(args)))))
+def errors(args, with_target_db: bool):
+    return criteria_error(
+        method_error(
+            target_traits_error(
+                target_db_error(
+                    controls_error(primary_error(args)),
+                    with_target_db),
+                not with_target_db)))
 
 def __classify_args(acc, item):
     if item[1].startswith("primary_"):
         return {
             **acc,
-            "primary_trait": (acc.get("primary_trait", tuple()) + (item,))} 
+            "primary_trait": (acc.get("primary_trait", tuple()) + (item,))}
     if item[1].startswith("controls_"):
         return {**acc, "control_traits": (acc.get("control_traits", tuple()) + (item,))}
+    if item[1].startswith("targets_"):
+        return {**acc, "target_traits": (acc.get("target_traits", tuple()) + (item,))}
     if item[0] == "target_db":
         return {**acc, "target_db": item[1]}
     if item[0] == "method":
@@ -179,7 +198,10 @@ def __build_args(raw_form, traits):
             (name[1][8:] for name in args["primary_trait"])],
         "control_traits": [
             item for item in traits if item["trait_name"] in
-            (name[1][9:] for name in args["control_traits"])]
+            (name[1][9:] for name in args["control_traits"])],
+        "target_traits": [
+            item for item in traits if item["trait_name"] in
+            (name[1][8:] for name in args["target_traits"])]
     }
 
 def parse_trait(trait_str):
@@ -204,13 +226,31 @@ def render_error(error_message):
         "partial_correlations/pcorrs_error.html",
         message = error_message)
 
+def __format_number(num):
+    if num is None or math.isnan(num):
+        return ""
+    if abs(num) <= 1.04E-4:
+        return f"{num:.2e}"
+    return f"{num:.5f}"
+
 def handle_200_response(response):
-    if response["status"] == "success":
+    if response["status"] == "queued":
         return redirect(
             url_for(
                 "poll_partial_correlation_results",
                 command_id=response["results"]),
             code=303)
+    if response["status"] == "success":
+        return render_template(
+            "partial_correlations/pcorrs_results_with_target_traits.html",
+            primary = response["results"]["results"]["primary_trait"],
+            controls = response["results"]["results"]["control_traits"],
+            pcorrs = sorted(
+                response["results"]["results"]["correlations"],
+                key = lambda item: item["partial_corr_p_value"]),
+            method = response["results"]["results"]["method"],
+            enumerate = enumerate,
+            format_number = __format_number)
     return render_error(response["results"])
 
 def handle_response(response):
@@ -227,12 +267,34 @@ def partial_correlations():
         parse_trait(trait) for trait in
         form.get("trait_list").split(";;;"))
 
-    if form.get("submit") == "Run Partial Correlations":
-        args = errors(__build_args(form, traits))
+    submit = form.get("submit")
+
+    if submit in ("with_target_pearsons", "with_target_spearmans"):
+        method = "pearsons" if "pearsons" in submit else "spearmans"
+        args = {
+            **errors(__build_args(form, traits), with_target_db=False),
+            "method": method
+        }
+        if len(args.get("errors", [])) == 0:
+            post_data = {
+                **args,
+                "primary_trait": args["primary_trait"][0],
+                "with_target_db": False
+            }
+            return handle_response(requests.post(
+                url=f"{GN_SERVER_URL}api/correlation/partial",
+                json=post_data))
+
+        for error in args["errors"]:
+            flash(error, "alert-danger")
+
+    if submit == "Run Partial Correlations":
+        args = errors(__build_args(form, traits), with_target_db=True)
         if len(args.get("errors", [])) == 0:
             post_data = {
                 **args,
-                "primary_trait": args["primary_trait"][0]
+                "primary_trait": args["primary_trait"][0],
+                "with_target_db": False
             }
             return handle_response(requests.post(
                 url=f"{GN_SERVER_URL}api/correlation/partial",
@@ -251,12 +313,6 @@ def partial_correlations():
 
 def process_pcorrs_command_output(result):
     if result["status"] == "success":
-        def __format_number(num):
-            if num is None or math.isnan(num):
-                return ""
-            if abs(num) <= 1.04E-4:
-                return f"{num:.2e}"
-            return f"{num:.5f}"
 
         return render_template(
             "partial_correlations/pcorrs_results_presentation.html",
diff --git a/wqflask/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html b/wqflask/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html
new file mode 100644
index 00000000..acea8f60
--- /dev/null
+++ b/wqflask/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html
@@ -0,0 +1,108 @@
+{%extends "base.html"%}
+
+{%block title%}Partial Correlations:{%endblock%}
+
+{%block css%}
+<link rel="stylesheet" type="text/css"
+      href="{{url_for('css', filename='DataTables/css/jquery.dataTables.css')}}" />
+<link rel="stylesheet" type="text/css"
+      href="{{url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css')}}">
+<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
+<link rel="stylesheet" type="text/css"
+      href="/static/new/css/partial_correlations.css" />
+{%endblock%}
+
+{%block content%}
+<div class="container">
+  <p>
+    <strong>Primary Trait</strong><br /><br />
+    <a href="{{url_for(
+	     'show_trait_page',
+	     trait_id=primary['trait_name'],
+	     dataset=primary['dataset_name'])}}"
+       title="Link to trait data for trait {{primary['trait_name']}}">
+      {{primary["dataset_type"]}}/{{primary["trait_name"]}}
+      [{{primary["symbol"] }} on Chr {{primary["chr"]}} @ {{primary["mb"]}}]:
+      {{primary["description"]}}
+    </a> --- FROM: {{primary["dataset_name"]}}
+  </p>
+  <p><strong>Control Traits</strong><br /><br />
+    {%for trait in controls:%}
+    <a href="{{url_for(
+	     'show_trait_page',
+	     trait_id=trait['trait_name'],
+	     dataset=trait['dataset_name'])}}"
+       title="Link to trait data for trait {{trait['trait_name']}}">
+      {{trait["dataset_type"]}}/{{trait["trait_name"]}}
+      [{{trait["symbol"] }} on Chr {{trait["chr"]}} @ {{trait["mb"]}}]:
+      {{trait["description"]}}
+    </a> --- FROM: {{trait["dataset_name"]}}<br />
+    {%endfor%}
+  </p>
+
+  <table id="part-corr-results-publish"
+	 class="table-hover table-striped cell-border dataTable">
+    <thead>
+      <tr>
+	<th>_</th>
+	<th>Index</th>
+	<th>Database</th>
+	<th>Record</th>
+	<th>Symbol</th>
+	<th>Description</th>
+	<th>N</th>
+	{%if method == "spearmans":%}
+	<th>Partial rho</th>
+	<th>p(partial rho)</th>
+	<th>rho</th>
+	<th>p(rho)</th>
+	<th>delta rho</th>
+	{%else:%}
+	<th>Partial r</th>
+	<th>p(partial r)</th>
+	<th>r</th>
+	<th>p(r)</th>
+	<th>delta r</th>
+	{%endif%}
+      </tr>
+    </thead>
+
+    <tbody>
+      {%for idx, trait in enumerate(pcorrs, start=1):%}
+      <tr>
+	<td>
+	  <input type="checkbox" name="chk_{{trait['trait_name']}}"
+		 value="{{trait['trait_fullname']}}">
+	</td>
+	<td>{{idx}}</td>
+	<td>{{trait["dataset_name"]}}</td>
+	<td>{{trait["trait_name"]}}</td>
+	<td>{{trait["symbol"]}}</td>
+	<td>{{trait["description"]}}</td>
+	<td>{{trait["noverlap"]}}</td>
+	<td>{{format_number(trait["partial_corr"])}}</td>
+	<td>{{format_number(trait["partial_corr_p_value"])}}</td>
+	<td>{{format_number(trait["corr"])}}</td>
+	<td>{{format_number(trait["corr_p_value"])}}</td>
+	<td>{{format_number(trait["delta"])}}</td>
+      </tr>
+      {%else:%}
+      <tr>
+	<td colspan="12">
+	  No correlations were computed
+	</td>
+      </tr>
+      {%endfor%}
+    </tbody>
+  </table>
+
+</div>
+{%endblock%}
+
+{%block js%}
+<!--
+  <script type="text/javascript"
+	  src="/static/new/javascript/partial_correlations.js"></script>
+-->
+{%endblock%}
diff --git a/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html b/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html
index e1e392c6..fc60aa3e 100644
--- a/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html
+++ b/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html
@@ -66,7 +66,7 @@
 	  <td>
 	    <input type="radio" name="trait_{{trait['trait_name']}}"
 		   id="trait_{{trait['trait_name']}}"
-		   value="target_{{trait['trait_name']}}" checked="checked" />
+		   value="targets_{{trait['trait_name']}}" checked="checked" />
 	  </td>
 	  <td>
 	    <input type="radio" name="trait_{{trait['trait_name']}}"