From dbcbd0ed4f453e0a770966f34ac29f71f1989c11 Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Wed, 8 Nov 2017 16:54:52 +0100
Subject: [PATCH] export now uses temp file to overcome file size limit when
 cramming it into base64 encoded string

---
 conekt/controllers/expression_profile.py | 28 ++++++++++++++++++++----
 conekt/templates/export_condition.html   |  6 +++--
 config.template.py                       |  3 +++
 3 files changed, 31 insertions(+), 6 deletions(-)

diff --git a/conekt/controllers/expression_profile.py b/conekt/controllers/expression_profile.py
index 43eea57..bb939ce 100644
--- a/conekt/controllers/expression_profile.py
+++ b/conekt/controllers/expression_profile.py
@@ -1,10 +1,12 @@
 import json
 
-from flask import Blueprint, redirect, url_for, render_template, Response, request
+from flask import Blueprint, redirect, url_for, render_template, Response, request, current_app, send_from_directory
 from sqlalchemy.orm import undefer
 
 from statistics import mean
 import sys
+import tempfile
+import os
 
 from conekt import cache
 from conekt.helpers.chartjs import prepare_expression_profile, prepare_profile_comparison
@@ -266,7 +268,7 @@ def __generate(species_id, method_id, condition):
     :param condition: Condition to be exported
     :return: output
     """
-    yield "Sequence\tAvg.Expression\tMin.Expression\tMax.Expression\n"
+    yield "Sequence\tAliases\tDescription\tAvg.Expression\tMin.Expression\tMax.Expression\n"
 
     profiles = ExpressionProfile.query.filter(ExpressionProfile.species_id == species_id). \
         filter(ExpressionProfile.sequence_id is not None). \
@@ -289,7 +291,10 @@ def __generate(species_id, method_id, condition):
                                                                       data, use_means=True)
                 values = converted_profile["data"][condition]
 
-            yield "%s\t%f\t%f\t%f\n" % (p.sequence.name, mean(values), min(values), max(values))
+            aliases = p.sequence.aliases if p.sequence.aliases is not None else ""
+            description = p.sequence.description if p.sequence.description is not None else ""
+
+            yield "%s\t%s\t%s\t%f\t%f\t%f\n" % (p.sequence.name, aliases, description, mean(values), min(values), max(values))
 
         except Exception as e:
             print("An error occured exporting a profile with conditions %s for species %d." % (condition, species_id),
@@ -312,6 +317,21 @@ def export_expression_levels():
         method_id = int(request.form.get('methods'))
         condition = request.form.get('conditions')
 
-        return Response(__generate(species_id, method_id, condition), mimetype="text/plain")
+        _, filepath = tempfile.mkstemp(prefix='expr_', dir=current_app.config['TMP_DIR'])
+
+        filename = os.path.basename(filepath)
+        print(filepath, filename)
+
+        with open(filepath, "w") as fout:
+            for l in __generate(species_id, method_id, condition):
+                print(l, end='', file=fout)
+
+        return Response(json.dumps({"url": url_for('expression_profile.export_expression_levels_file', name=filename)}), mimetype='application/json')
     else:
         return render_template("export_condition.html", form=form)
+
+
+@expression_profile.route('/export/get_file/<name>')
+def export_expression_levels_file(name):
+    return send_from_directory(current_app.config['TMP_DIR'], name, as_attachment=True, attachment_filename='expression.tab')
+
diff --git a/conekt/templates/export_condition.html b/conekt/templates/export_condition.html
index c7e794b..6657cb2 100644
--- a/conekt/templates/export_condition.html
+++ b/conekt/templates/export_condition.html
@@ -71,15 +71,17 @@ <h1>Export expression levels</h1>
             success: function(data) {
                        $("#leafy_loader_text").html("Your Download is ready ! ");
 
+                        pdata = JSON.parse(data);
+
                         var element = document.createElement('a');
-                        element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(data));
+                        element.setAttribute('href', pdata.url);
                         element.setAttribute('download', 'expression.tab');
 
                         document.body.appendChild(element);
                         element.click();
                         document.body.removeChild(element);
 
-                       $("#leafy_loader_text").append($("<a/>").attr('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(data)).attr('download', 'expression.tab').attr('id', 'download_ready_link').text("Click here"))
+                       $("#leafy_loader_text").append($("<a/>").attr('href', pdata.url).attr('download', 'expression.tab').attr('id', 'download_ready_link').text("Click here"))
                        .append($("<span> if the download doesn't start automatically.</span>"));
                        $("#leafy_loader_close_btn").show();
                      }
diff --git a/config.template.py b/config.template.py
index 3526178..a8379b9 100644
--- a/config.template.py
+++ b/config.template.py
@@ -46,6 +46,9 @@
 WHOOSHEE_MEMORY_STORAGE = False
 WHOOSHEE_ENABLE_INDEXING = True
 
+# temp dir
+TMP_DIR = tempfile.mkdtemp()
+
 # BLAST settings
 BLAST_ENABLED = False
 BLAST_TMP_DIR = tempfile.mkdtemp()