Some fixes for export Fasta

lib/functions.py

@@ -142,8 +142,9 @@ class Functions:
     def read_index(index_file):
         index = OrderedDict()
         with open(index_file, "r") as index_f:
-            lines = index_f.readlines()
-            for line in lines[1:]:
+            # Sample name without special chars:
+            sample_name = re.sub('[^A-Za-z0-9_\-.]+', '', index_f.readline().strip("\n").replace(" ", "_"))
+            for line in index_f:
                 if line != "":
                     parts = line.strip("\n").split("\t")
                     name = parts[0]
@@ -153,7 +154,7 @@ class Functions:
                         "length": lenght,
                         "to_reverse": to_reverse
                     }
-        return index
+        return index, sample_name
 
     @staticmethod
     @db_session
@@ -162,25 +163,26 @@ class Functions:
         return j1.email
 
     @staticmethod
-    def send_fasta_ready(mailer, job_name):
+    def send_fasta_ready(mailer, job_name, sample_name, compressed=False):
         config_reader = AppConfigReader()
         web_url = config_reader.get_web_url()
         with open(os.path.join(os.path.dirname(os.path.realpath(__file__)), "mail_templates", "dl_fasta.html")) \
                 as t_file:
             template = Template(t_file.read())
-            message_html = template.render(job_name=job_name, status="success", url_base=web_url)
+            message_html = template.render(job_name=job_name, status="success", url_base=web_url,
+                                           sample_name=sample_name, compressed=compressed)
         message = "D-Genies\n\n" \
                   "Job %s - Download fasta\n\n" % job_name
-        message += "Query fasta file for job %s is ready to download." % job_name
+        message += "Query fasta file for job %s (query: %s) is ready to download.\n" % (job_name, sample_name)
         message += "You can click on the link below to download it:\n\n"
-        message += "%s/fasta-query/%s" % (web_url, job_name)
+        message += "%s/fasta-query/%s/%s" % (web_url, job_name, sample_name + ".fasta" + (".gz" if compressed else ""))
         mailer.send_mail([Functions.get_mail_for_job(job_name)], "Job %s - Download fasta" % job_name, message,
                          message_html)
 
     @staticmethod
     def sort_fasta(job_name, fasta_file, index_file, lock_file, compress=False, mailer=None):
         print("Loading index...")
-        index = Functions.read_index(index_file)
+        index, sample_name = Functions.read_index(index_file)
         print("Starting fasta sort...")
         is_compressed = fasta_file.endswith(".gz")
         if is_compressed:
@@ -200,5 +202,13 @@ class Functions:
             Functions.compress(fasta_file_o)
         os.remove(lock_file)
         if mailer is not None:
-            Functions.send_fasta_ready(mailer, job_name)
+            Functions.send_fasta_ready(mailer, job_name, sample_name, compress)
         print("Fasta sort done!")
+
+    @staticmethod
+    def compress_and_send_mail(job_name, fasta_file, index_file, compressed, mailer):
+        print("Compress!")
+        Functions.compress(fasta_file)
+        index, sample_name = Functions.read_index(index_file)
+        Functions.send_fasta_ready(mailer, job_name, sample_name, compressed)
+        print("DONE!")
\ No newline at end of file

lib/mail_templates/dl_fasta.html

@@ -28,8 +28,8 @@
 </h3>
 <p>Hi,</p>
 {% if status == "success" %}
-    <p>Query fasta file for job {{ job_name }} is ready to download.
-        You can <a href="{{ url_base }}/fasta-query/{{ job_name }}">click here</a> to download it.</p>
+    <p>Query fasta file for job {{ job_name }} (query: {{ sample_name }}) is ready to download.<br/>
+        You can <a href="{{ url_base }}/fasta-query/{{ job_name }}/{{ sample_name }}.fasta{% if compressed %}.gz{% endif %}">click here</a> to download it.</p>
 {% else %}
     <p>Build of query fasta file for job {{ job_name }} has failed. You can try again. If the problem persists, please contact the support.</p>
 {% endif %}

srv/main.py

@@ -207,6 +207,7 @@ def build_fasta(id_res):
     res_dir = os.path.join(app_data, id_res)
     lock_query = os.path.join(res_dir, ".query-fasta-build")
     is_sorted = os.path.exists(os.path.join(res_dir, ".sorted"))
+    compressed = request.form["gzip"].lower() == "true"
     query_fasta = Functions.get_fasta_file(res_dir, "query", is_sorted)
     if query_fasta is not None:
         if is_sorted and not query_fasta.endswith(".sorted"):
@@ -217,7 +218,7 @@ def build_fasta(id_res):
                 "fasta_file": query_fasta,
                 "index_file": os.path.join(res_dir, "query.idx.sorted"),
                 "lock_file": lock_query,
-                "compress": request.form["gzip"],
+                "compress": compressed,
                 "mailer": mailer
             })
             thread.start()
@@ -227,6 +228,18 @@ def build_fasta(id_res):
             return jsonify({"success": True, "status": 1, "status_message": "In progress"})
         else:
             # No sort to do or sort done
+            if compressed and not query_fasta.endswith(".gz.fasta"):
+                # If compressed file is asked, we must compress it now if not done before...
+                Path(lock_query).touch()
+                thread = threading.Timer(1, Functions.compress_and_send_mail, kwargs={
+                    "job_name": id_res,
+                    "fasta_file": query_fasta,
+                    "index_file": os.path.join(res_dir, "query.idx.sorted"),
+                    "compressed": compressed,
+                    "mailer": mailer
+                })
+                thread.start()
+                return jsonify({"success": True, "status": 1, "status_message": "In progress"})
             return jsonify({"success": True, "status": 2, "status_message": "Done",
                             "gzip": query_fasta.endswith(".gz") or query_fasta.endswith(".gz.sorted")})
     else:
@@ -234,8 +247,9 @@ def build_fasta(id_res):
                         "message": "Unable to get fasta file for query. Please contact us to report the bug"})
 
 
-@app.route('/fasta-query/<id_res>', methods=['GET'])
-def dl_fasta(id_res):
+@app.route('/fasta-query/<id_res>', defaults={'filename': ""}, methods=['GET'])
+@app.route('/fasta-query/<id_res>/<filename>', methods=['GET'])  # Use fake URL in mail to set download file name
+def dl_fasta(id_res, filename):
     res_dir = os.path.join(app_data, id_res)
     lock_query = os.path.join(res_dir, ".query-fasta-build")
     is_sorted = os.path.exists(os.path.join(res_dir, ".sorted"))