First commit of a functional project

Author: ggilestro

metadata_db_server.py

@@ -0,0 +1,179 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#  metadata_db_server.py
+#  
+#  Copyright 2022 Giorgio Gilestro <giorgio@gilest.ro>
+#  
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#  
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#  
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software
+#  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+#  MA 02110-1301, USA.
+#  
+#  
+
+import os
+import logging
+import optparse
+import json
+import bottle
+
+from ast import literal_eval
+from ethoscopy.metadata_db import db_organiser, metadata_handler, metadata_crawler
+
+app = bottle.Bottle()
+STATIC_DIR = "./static"
+
+@app.route('/static/<filepath:path>')
+def server_static(filepath):
+    return bottle.static_file(filepath, root=STATIC_DIR)
+
+@app.route('/')
+def index():
+    return bottle.static_file('index.html', root=STATIC_DIR)
+
+@app.route('/save', method='POST')
+def save():
+
+    # text parameters that were received
+    #for k in bottle.request.forms.keys(): print (k, bottle.request.forms.get(k)) 
+
+    #file upload
+    allowed_extensions = ['.csv', '.tsv']
+
+    upload = bottle.request.files.get('file')
+    if not upload:
+        return {'success' : False, 'message' : 'A metadata file was not specified.'}
+
+    name, ext = os.path.splitext(upload.filename)
+    if ext not in allowed_extensions:
+        return {'success' : False, 'message' : 'Extensions allowed are %s.' % " / ".join(allowed_extensions)}
+
+    try:
+        upload.save(meta_db.upload_folder, overwrite=True)
+
+    except Exception as e:
+        print (e)
+        return {'success' : False, 'message' : str(e)}
+
+    try:
+        #After saving, creates the info file
+        uploaded_metadata = metadata_handler (  filename = os.path.join (meta_db.upload_folder, upload.filename), 
+                                                project = bottle.request.forms.get('project'),
+                                                tags = literal_eval(bottle.request.forms.get('tags')),
+                                                authors = literal_eval(bottle.request.forms.get('authors')),
+                                                doi = bottle.request.forms.get('doi'),
+                                                description = bottle.request.forms.get('description')
+                                                )
+        uploaded_metadata.save()
+
+        meta_db.refresh_all_info()
+
+        return {'success' : True, 'message' : 'Metadata file successfully uploaded.' }
+
+    except Exception as e:
+        return {'success' : False, 'message' : str(e)}
+
+
+@app.route('/download', method='GET')
+def download():
+    hash_id = bottle.request.query.get('id', '')
+    dwn_type = bottle.request.query.get('type', '')
+    fullpath = meta_db.request(hash_id)['filename']
+    path, filename = os.path.split( fullpath )
+    
+    if dwn_type == 'metadata':
+        return bottle.static_file (filename, root=path,  download=filename)
+
+    elif dwn_type == 'db_found':
+        md = metadata_handler(fullpath)
+        fn = os.path.splitext(filename)[0] + '.db_found.csv'
+        md.list_dbs(notfound=False).to_csv(os.path.join ('/tmp/', fn))
+        return bottle.static_file (fn, root='/tmp/',  download=fn)
+
+    elif dwn_type == 'db_notfound':
+        md = metadata_handler(fullpath)
+        fn = os.path.splitext(filename)[0] + '.db_notfound.csv'
+        md.list_dbs(notfound=True).to_csv(os.path.join ('/tmp/', fn))
+        return bottle.static_file (fn, root='/tmp/',  download=fn)
+        
+
+@app.route('/refresh', method='GET')
+def refresh():
+    hash_id = bottle.request.query.get('id', '')
+    filename = meta_db.request(hash_id)['filename']
+    md = metadata_handler ( filename )
+    md.associate_to_db(etho_db)
+    md.save()
+    return {'success' : True, 'message' : 'Metadata succefully associated.' }
+
+
+@app.route('/info_tree', method='GET')
+def get_metadata_tree():
+    return meta_db.all_projects
+
+
+@app.route('/metadata', method='GET')
+def get_metadata():
+    hash_id = bottle.request.query.get('id', '')
+    return meta_db.request(hash_id)
+
+@app.route('/known')
+def available_options():
+    return meta_db.available_options
+
+def close(exit_status=0):
+    logging.info("Closing server")
+    os._exit(exit_status)
+    
+    
+if __name__ == '__main__':
+    logging.getLogger().setLevel(logging.INFO)
+    parser = optparse.OptionParser()
+    parser.add_option("-d", "--db_path", dest="db_path", default="/mnt/ethoscope_results", help="Path to the root of the ethoscope db files")
+    parser.add_option("-f", "--db_file", dest="db_file", default="/opt/ethoscope_db", help="Path to the saved db file")
+
+    parser.add_option("-D", "--debug", dest="debug", default=False, help="Set DEBUG mode ON", action="store_true")
+    parser.add_option("-p", "--port", dest="port", default=8081, help="port")
+
+    (options, args) = parser.parse_args()
+
+    option_dict = vars(options)
+    DB_PATH = option_dict["db_path"]
+    DB_FILE = option_dict["db_file"]
+
+    PORT = option_dict["port"]
+    DEBUG = option_dict["debug"]
+
+    if DEBUG:
+        logging.basicConfig()
+        logging.getLogger().setLevel(logging.DEBUG)
+        logging.info("Logging using DEBUG SETTINGS")
+
+
+    etho_db = db_organiser(DB_PATH, refresh=False)
+    meta_db = metadata_crawler()
+
+    try:
+        app.run(host='0.0.0.0', port=PORT, debug=DEBUG)
+
+    except KeyboardInterrupt:
+        logging.info("Stopping server cleanly")
+        pass
+
+    except socket.error as e:
+        logging.error(traceback.format_exc())
+        logging.error("Port %i is probably not accessible for you. Maybe use another one e.g.`-p 8000`" % PORT)
+
+    except Exception as e:
+        logging.error(traceback.format_exc())

static/css/dropzone.css

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+
+.dropzone {
+    width: auto;
+    height: 100px;
+    border: 2px dashed #ccc;
+    color: grey;
+    line-height: 100px;
+    text-align: center;
+}
+
+.dropzone.dragover {
+    border-color: #000;
+    color: #000;
+}

static/css/fontawesome-all.min.css

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+@font-face {
+  font-family: 'Material Icons';
+  font-style: normal;
+  font-weight: 400;
+  src: url(https://fonts.gstatic.com/s/materialicons/v139/flUhRq6tzZclQEJ-Vdg-IuiaDsNZ.ttf) format('truetype');
+}
+
+.material-icons {
+  font-family: 'Material Icons';
+  font-weight: normal;
+  font-style: normal;
+  font-size: 24px;
+  line-height: 1;
+  letter-spacing: normal;
+  text-transform: none;
+  display: inline-block;
+  white-space: nowrap;
+  word-wrap: normal;
+  direction: ltr;
+}