Merge pull request #225 from ofilangi/master

GraphDB prod + Fix bug

askomics/libaskomics/source_file/SourceFileGff.py

@@ -156,7 +156,7 @@ def get_turtle(self):
                 listSliceRef = []
                 listSlice = []
                 for sliceb in range(block_idxstart,block_idxend+1):
-                        listSliceRef.append(self.encodeToRDFURI(str(rec.id))+"_"+str(sliceb))
+                        listSliceRef.append(":"+self.encodeToRDFURI(str(rec.id))+"_"+str(sliceb))
                         listSlice.append(str(sliceb))
 
                 attribute_dict = {

configs/development.graphdb.ini

@@ -83,7 +83,7 @@ keys = console
 keys = generic
 
 [logger_root]
-level = INFO
+level = DEBUG
 handlers = console
 
 [logger_askomics]

configs/production.graphdb.ini

@@ -0,0 +1,101 @@
+###
+# app configuration
+# http://docs.pylonsproject.org/projects/pyramid/en/1.5-branch/narr/environment.html
+###
+
+[app:main]
+use = egg:Askomics
+
+# Pyramid debug mode
+pyramid.reload_templates = false
+pyramid.debug_authorization = false
+pyramid.debug_notfound = false
+pyramid.debug_routematch = false
+pyramid.default_locale_name = en
+pyramid.includes = pyramid_debugtoolbar
+askomics.debug = false
+# debugtoolbar.hosts = 127.0.0.1 ::1
+
+# Triplestore configuration
+askomics.endpoint    = http://localhost:7200/repositories/SYSTEM
+askomics.updatepoint = http://localhost:7200/repositories/SYSTEM/statements
+askomics.hack_virtuoso = false
+askomics.upload_user_data_method=load
+askomics.max_content_size_to_update_database = 20000
+askomics.graph = urn:sparql:askomics
+askomics.users_graph = urn:sparql:askomics:users
+askomics.prefix = http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#
+askomics.display_setting = http://www.irisa.fr/dyliss/rdfVisualization/display
+askomics.delete_method = DELETE
+#can be POST or DELETE
+
+# AskOmics configuration
+askomics.overview_lines_limit = 200
+askomics.allowed_file_types = 'text/plain','text/csv','text/tab-separated-values','text/fasta'
+askomics.upload_min_size = 1
+askomics.upload_max_size = 200000000
+askomics.files_dir = /tmp/askomics
+
+# Authentication
+askomics.salt = AskOmics
+askomics.secret = seppfmhcag
+
+# Proxy setting
+# Set askomics.proxy to:
+#   - auto to use the system proxy (default)
+#   - custom to use specified http, https, username and password information
+#   - noproxy to use AskOmics with no proxies defined
+askomics.proxy = auto
+# These parameters are used only if askomics.proxy = custom
+askomics.proxy_http = http://www.example.com:3128/
+askomics.proxy_https = https://www.example.com:3129/
+askomics.proxy_username = username
+askomics.proxy_password = password
+
+# SMTP Server
+#askomics.smtp_host=
+#askomics.smtp_port=
+#askomics.smtp_login=
+#askomics.smtp_password=
+#askomics.smtp_starttls=
+
+###
+# wsgi server configuration
+###
+
+[server:main]
+use = egg:waitress#main
+; host = localhost
+port = 6543
+
+###
+# logging configuration
+# http://docs.pylonsproject.org/projects/pyramid/en/1.5-branch/narr/logging.html
+###
+
+[loggers]
+keys = root, askomics
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = INFO
+handlers = console
+
+[logger_askomics]
+level = INFO
+handlers =
+qualname = askomics
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s