Add gallery, Implements #87

src/bin/dgenies

@@ -9,9 +9,13 @@ import time
 from dgenies.lib.crons import Crons
 from dgenies.config_reader import AppConfigReader
 from dgenies.bin.clean_jobs import parse_data_folders, parse_database, parse_upload_folders
+from dgenies.database import Gallery, Job
+from peewee import DoesNotExist
 
 runned = False
 
+config = AppConfigReader()
+
 
 def parse_args():
     parser = argparse.ArgumentParser(description="Manage dgenies application")
@@ -42,6 +46,28 @@ def parse_args():
     clear.add_argument("-m", "--max-age", help="Max age for job to delete (0 for all)", type=int, required=False,
                        default=0)
 
+    # Gallery:
+    gallery = subparsers.add_parser("gallery", help="Manage gallery")
+    subparsers_gallery = gallery.add_subparsers()
+
+    # Gallery add:
+    gallery_add = subparsers_gallery.add_parser("add", help="Add new job to the gallery")
+    gallery_add.set_defaults(which="add")
+    gallery_add.add_argument("-i", "--id-job", type=str, required=True,
+                             help="Id (name) of the job to add to the gallery")
+    gallery_add.add_argument("-n", "--name", type=str, required=True, help="Name to show in the gallery for the job")
+    gallery_add.add_argument("-p", "--pict", type=str, required=True, help="Name of the file that illustrate the job")
+
+    # Gallery del:
+    gallery_del = subparsers_gallery.add_parser("del", help="Delete a job from the gallery")
+    gallery_del.set_defaults(which="del")
+    gallery_del.add_argument("-i", "--id-job", type=str, required=False,
+                             help="Id (name) of the job to delete from the gallery")
+    gallery_del.add_argument("-n", "--name", type=str, required=False,
+                             help="Name of the job shown in the gallery")
+    gallery_del.add_argument("--remove-pict", help="Clear crons", type=bool, const=True, nargs="?", required=False,
+                       default=False)
+
     args = parser.parse_args()
 
     if args.subparser_name == "run":
@@ -51,6 +77,8 @@ def parse_args():
             print("Nothing to do.")
             return "clear", None
         return "clear", args
+    if args.subparser_name == "gallery":
+        return "gallery_" + args.which, args
 
 
 def start_browser(host, port):
@@ -79,8 +107,6 @@ def clear_crons():
 
 
 def clear_logs():
-    config = AppConfigReader()
-
     if hasattr(config, "log_dir"):
         log_files = glob(os.path.join(config.log_dir, "*.log"))
         for file in log_files:
@@ -91,10 +117,9 @@ def clear_logs():
 
 
 def clear_jobs(max_data_age=7):
-    config_reader = AppConfigReader()
 
-    upload_folder = config_reader.upload_folder
-    app_data = config_reader.app_data
+    upload_folder = config.upload_folder
+    app_data = config.app_data
     now = time.time()
 
     max_age = {
@@ -119,7 +144,7 @@ def clear_jobs(max_data_age=7):
     print("# Parsing Jobs in DB #")
     print("######################")
     print("")
-    parse_database(
+    gallery_jobs = parse_database(
         app_data=app_data,
         max_age=max_age
     )
@@ -132,11 +157,44 @@ def clear_jobs(max_data_age=7):
     parse_data_folders(
         app_data=app_data,
         now=now,
-        max_age=max_age
+        max_age=max_age,
+        gallery_jobs=gallery_jobs
     )
     print("")
 
 
+def add_to_gallery(id_job, name, picture):
+    try:
+        job = Job.get(id_job=id_job)
+    except DoesNotExist:
+        print("Error: job \"%s\" does not exists!" % id_job)
+        exit(1)
+    pict_file = os.path.join(config.app_data, "gallery", picture)
+    if not os.path.exists(pict_file):
+        print("Error: file \"%s\" does not exists!" % pict_file)
+        exit(1)
+    item = Gallery.create(job=job, name=name, picture=picture)
+    item.save()
+
+
+def del_from_gallery_by_id(id_job):
+    items = Gallery.select().join(Job).where(Job.id_job == id_job)
+    list_pictures = []
+    for item in items:
+        list_pictures.append(item.picture)
+        item.delete_instance()
+    return list_pictures
+
+
+def del_from_gallery_by_name(name):
+    items = Gallery.select().where(Gallery.name == name)
+    list_pictures = []
+    for item in items:
+        list_pictures.append(item.picture)
+        item.delete_instance()
+    return list_pictures
+
+
 if __name__ == "__main__":
     command, args = parse_args()
     if command == "run":
@@ -151,3 +209,19 @@ if __name__ == "__main__":
         if args.jobs:
             print("Cleaning jobs...")
             clear_jobs(args.max_age)
+    elif command == "gallery_add":
+        add_to_gallery(args.id_job, args.name, args.pict)
+    elif command == "gallery_del":
+        if args.id_job is None and args.name is None:
+            print("Error: please give an id or a name for the job!")
+            exit(1)
+        if args.id_job is not None:
+            pictures = del_from_gallery_by_id(args.id_job)
+        else:
+            pictures = del_from_gallery_by_name(args.name)
+        if args.remove_pict:
+            for picture in pictures:
+                try:
+                    os.remove(os.path.join(config.app_data, "gallery", picture))
+                except FileNotFoundError:
+                    pass

src/dgenies/bin/clean_jobs.py

@@ -10,7 +10,7 @@ import argparse
 
 from dgenies.config_reader import AppConfigReader
 from dgenies.lib.functions import Functions
-from dgenies.database import Job
+from dgenies.database import Job, Gallery
 
 config_reader = AppConfigReader()
 
@@ -35,6 +35,7 @@ def parse_upload_folders(upload_folder, now, max_age, fake=False):
 
 
 def parse_database(app_data, max_age, fake=False):
+    gallery_jobs = []
     with Job.connect():
         old_jobs = Job.select().where(
                       ((Job.status == "success") & (Job.date_created < datetime.now() - timedelta(days=max_age["data"])))
@@ -43,6 +44,9 @@ def parse_database(app_data, max_age, fake=False):
                   )
         for job in old_jobs:
             id_job = job.id_job
+            is_gallery = len(Gallery.select().join(Job).where(Job.id_job == id_job)) > 0
+            if is_gallery:
+                gallery_jobs.append(id_job)
             print("Removing job %s..." % id_job)
             data_dir = os.path.join(app_data, id_job)
             if os.path.exists(data_dir) and os.path.isdir(data_dir):
@@ -52,39 +56,41 @@ def parse_database(app_data, max_age, fake=False):
                 print("Job %s has no data folder!" % id_job)
             if not fake:
                 job.delete_instance()
+    return gallery_jobs
 
 
-def parse_data_folders(app_data, now, max_age, fake=False):
+def parse_data_folders(app_data, now, max_age, gallery_jobs, fake=False):
     for file in os.listdir(app_data):
-        file = os.path.join(app_data, file)
-        create_date = os.path.getctime(file)
-        age = (now - create_date) / 86400  # Age in days
-        if age > max_age["data"]:
-            try:
-                if os.path.isdir(file):
-                    print("Removing folder %s..." % file)
-                    if not fake:
-                        shutil.rmtree(file)
-                else:
-                    print("Removing file %s..." % file)
-                    if not fake:
-                        os.remove(file)
-            except OSError:
-                print(traceback.print_exc())
-        elif os.path.isdir(file):
-            query_name_file = os.path.join(file, ".query")
-            if os.path.exists(query_name_file):
-                with open(query_name_file) as query_file:
-                    sorted_file = Functions.get_fasta_file(file, "query", True)
-                    if not sorted_file.endswith(".sorted"):
-                        sorted_file = None
-                    if sorted_file is not None:
-                        create_date = os.path.getctime(sorted_file)
-                        age = (now - create_date) / 86400  # Age in days
-                        if age > max_age["fasta_sorted"]:
-                            print("Removing fasta file %s..." % sorted_file)
-                            if not fake:
-                                os.remove(sorted_file)
+        if file not in gallery_jobs:
+            file = os.path.join(app_data, file)
+            create_date = os.path.getctime(file)
+            age = (now - create_date) / 86400  # Age in days
+            if age > max_age["data"]:
+                try:
+                    if os.path.isdir(file):
+                        print("Removing folder %s..." % file)
+                        if not fake:
+                            shutil.rmtree(file)
+                    else:
+                        print("Removing file %s..." % file)
+                        if not fake:
+                            os.remove(file)
+                except OSError:
+                    print(traceback.print_exc())
+            elif os.path.isdir(file):
+                query_name_file = os.path.join(file, ".query")
+                if os.path.exists(query_name_file):
+                    with open(query_name_file) as query_file:
+                        sorted_file = Functions.get_fasta_file(file, "query", True)
+                        if not sorted_file.endswith(".sorted"):
+                            sorted_file = None
+                        if sorted_file is not None:
+                            create_date = os.path.getctime(sorted_file)
+                            age = (now - create_date) / 86400  # Age in days
+                            if age > max_age["fasta_sorted"]:
+                                print("Removing fasta file %s..." % sorted_file)
+                                if not fake:
+                                    os.remove(sorted_file)
 
 
 if __name__ == '__main__':
@@ -122,7 +128,7 @@ if __name__ == '__main__':
     print("# Parsing Jobs in DB #")
     print("######################")
     print("")
-    parse_database(
+    gallery_jobs = parse_database(
         app_data=app_data,
         max_age=max_age,
         fake=fake
@@ -137,6 +143,7 @@ if __name__ == '__main__':
         app_data=app_data,
         now=now,
         max_age=max_age,
-        fake=fake
+        fake=fake,
+        gallery_jobs=gallery_jobs
     )
     print("")

src/dgenies/database.py

 import os
 from dgenies.config_reader import AppConfigReader
-from peewee import SqliteDatabase, Model, CharField, IntegerField, DateTimeField, BooleanField, MySQLDatabase, OperationalError
+from peewee import SqliteDatabase, Model, CharField, IntegerField, DateTimeField, BooleanField, MySQLDatabase, \
+    OperationalError, ForeignKeyField
 from playhouse.shortcuts import RetryOperationalError
 from datetime import datetime
 
@@ -64,6 +65,12 @@ class Job(BaseModel):
     time_elapsed = IntegerField(null=True)
 
 
+class Gallery(BaseModel):
+    job = ForeignKeyField(Job)
+    name = CharField()
+    picture = CharField()
+
+
 class Session(BaseModel):
     s_id = CharField(max_length=20, unique=True)
     date_created = DateTimeField()
@@ -113,5 +120,8 @@ class Session(BaseModel):
 if not Job.table_exists():
     Job.create_table()
 
+if not Gallery.table_exists():
+    Gallery.create_table()
+
 if not Session.table_exists():
     Session.create_table()

src/dgenies/lib/functions.py

@@ -10,7 +10,7 @@ from collections import OrderedDict
 from Bio import SeqIO
 from jinja2 import Template
 from dgenies.config_reader import AppConfigReader
-from dgenies.database import Job
+from dgenies.database import Job, Gallery
 
 ALLOWED_EXTENSIONS = ['fa', 'fasta', 'fna', 'fa.gz', 'fasta.gz', 'fna.gz']
 
@@ -190,3 +190,15 @@ class Functions:
         os.remove(lock_file)
         index, sample_name = Functions.read_index(index_file)
         Functions.send_fasta_ready(mailer, job_name, sample_name, compressed)
+
+    @staticmethod
+    def get_gallery_items():
+        items = []
+        for item in Gallery.select():
+            items.append({
+                "name": item.name,
+                "id_job": item.job.id_job,
+                "picture": item.picture
+            })
+        return items
+

src/dgenies/templates/base.html

@@ -59,6 +59,7 @@
                                 {% endblock %}
                             </ul>
                         </li>
+                        <li class="{% if(menu == 'gallery') %}active{% endif %}"><a href="/gallery">Gallery</a></li>
                         <li class="dropdown">
                             <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span
                                     class="caret"></span></a>

src/dgenies/templates/gallery.html

+{% extends 'base.html' %}
+{% block scripts %}
+    <style>
+        .item-gallery {
+            display: inline-block;
+            width: 350px;
+            margin-right: 15px;
+            margin-bottom: 15px;
+            margin-top: 15px;
+        }
+        .item-gallery p {
+            text-align: center;
+        }
+        a:hover {
+            text-decoration: none !important;
+        }
+        p.empty {
+            margin-top: 15px;
+        }
+    </style>
+{% endblock %}
+{% block content %}
+    {% if items|length > 0 %}
+        {% for item in items %}
+            <a href="/result/{{ item.id_job }}">
+                <div class="item-gallery">
+                    <p>{{ item.name }}</p>
+                    <img src="/gallery/{{ item.picture }}" alt="illustration" width="100%"/>
+                </div>
+            </a>
+        {% endfor %}
+    {% else %}
+        <p class="empty">Gallery is empty!</p>
+    {% endif %}
+{% endblock %}
\ No newline at end of file

src/dgenies/views.py

@@ -6,7 +6,7 @@ import datetime
 import shutil
 import re
 import threading
-from flask import render_template, request, url_for, jsonify, Response, abort
+from flask import render_template, request, url_for, jsonify, Response, abort, send_file
 from pathlib import Path
 from dgenies.lib.paf import Paf
 from dgenies.lib.job_manager import JobManager
@@ -168,6 +168,19 @@ def result(id_res):
     return response
 
 
+@app.route("/gallery", methods=['GET'])
+def gallery():
+    return render_template("gallery.html", items=Functions.get_gallery_items(), menu="gallery")
+
+
+@app.route("/gallery/<filename>", methods=['GET'])
+def gallery_file(filename):
+    try:
+        return send_file(os.path.join(config_reader.app_data, "gallery", filename))
+    except FileNotFoundError:
+        abort(404)
+
+
 def get_file(file, gzip=False):  # pragma: no cover
     try:
         # Figure out how flask returns static files