Merged code with Dataflow tag 0.3rc1

README.txt

@@ -8,7 +8,7 @@ RDF-enhanced storage API, pairtree-backed.
 Installation and dependancies
 =============================
 
-The dependancies are listed in the file docs/Dependancies.pdf
+The dependancies are listed in the file docs/Dependancies.txt
 The installation instructions are available at docs/Databank_VM_Installation.txt
 
 For further infromation visit http://www.dataflow.ox.ac.uk/

debian/README

@@ -3,4 +3,4 @@ The Debian Package databank
 
 Comments regarding the Package
 
- -- Anusha Ranganathan <[email protected]>  Fri, 09 Mar 2012 17:08:50 +0000
+ -- Anusha Ranganathan <[email protected]>  Mon, 09 Apr 2012 17:08:50 +0000

debian/changelog

@@ -1,3 +1,14 @@
+databank (0.3rc1) unstable; urgency=low
+
+  * Basic support for sword deposit 
+  * Databank search interface enhanced
+  * Added function to PUT a zipfile and unpack it
+  * content negotiation also on error messages
+  * Added message workers for data indexing 
+
+ -- Anusha Ranganathan <[email protected]>  Mon, 09 Apr 2012 17:08:50 +0000
+
+
 databank (0.2) unstable; urgency=low
 
   * Added message workers

debian/config

@@ -28,10 +28,10 @@ db_go
 #db_go
 
 # Password?
-#db_input critical databank/password || true
-#db_go
+db_input critical databank/password || true
+db_go
 
 # Note on Password
-db_input critical databank/passwdnote || true
-db_go
+#db_input critical databank/passwdnote || true
+#db_go
 

debian/control

@@ -29,8 +29,8 @@ Depends: python,
          libapache2-mod-wsgi,
          redis-server,
          supervisor,
-         debconf,
-         openjdk-6-jre
+         openjdk-6-jre,
+         debconf
 Recommends: solr-tomcat
 Description: RDF-enhanced, pairtree-backed storage API
  Databank is a simple, RDF-enhanced storage API which is backed by pairtree,

debian/copyright

@@ -1,6 +1,6 @@
 This work was packaged for Debian by:
 
-    Anusha Ranganathan  <[email protected]> on Fri, 09 Mar 2012 17:08:50 +0000
+    Anusha Ranganathan  <[email protected]> on Mon, 09 Apr 2012 17:08:50 +0000
 
 It was downloaded from:
 

debian/databank.install

@@ -10,3 +10,6 @@ rdfdatabank/ /var/lib/databank/
 rdfdatabank.egg-info/ /var/lib/databank
 test.ini /var/lib/databank/
 who.ini /var/lib/databank/
+sss.conf.json /var/lib/databank/
+add_user.py /var/lib/databank/
+persisted_state.json /var/lib/databank/

debian/docs

@@ -3,5 +3,5 @@ README.txt
 requirements.txt
 docs/assigning_dois
 docs/Databank_VM_Installation.txt
-docs/Dependencies.pdf
+docs/Dependencies.txt
 docs/using_databank_api

debian/postinst

@@ -22,8 +22,8 @@ local dbstore="$RET"
 db_get databank/uri
 local dburi="$RET"
 
-#db_get databank/password
-#local dbpasswd="$RET"
+db_get databank/password
+local dbpasswd="$RET"
 
 #Modify the ini files
 CONFIG_FILE1=/etc/default/databank/production.ini
@@ -51,9 +51,15 @@ TARGET_KEY=granary.uri_root
 sed -i "s,\($TARGET_KEY *= *\).*,\1$dburi," $CONFIG_FILE1
 sed -i "s,\($TARGET_KEY *= *\).*,\1$dburi," $CONFIG_FILE2
 
-#Copy htpasswd file
+#Add the user password
 #htpasswd -b -c /var/lib/databank/passwd admin $dbpasswd
-cp /var/lib/databank/passwd-default /var/lib/databank/passwd
+#cp /var/lib/databank/passwd-default /var/lib/databank/passwd
+cd /var/lib/databank
+if ! [ -f /var/lib/databank/passwd ]
+then
+touch /var/lib/databank/passwd
+fi
+python add_user.py admin $dbpasswd
 
 #Link config files
 ln -sf /etc/default/databank/production.ini /var/lib/databank/production.ini
@@ -132,4 +138,17 @@ a2ensite databank_wsgi
 invoke-rc.d apache2 reload
 invoke-rc.d apache2 start
 
+echo ===========================================================
+echo Databank has been successfully installed
+echo
+echo Your Databank instance is available at http://localhost
+echo Databank\'s home directory is /var/lib/databank
+echo Data is stored under $dbstore
+echo
+echo To get started, visit the Databank homepage at http://localhost
+echo
+echo This paackage is brought to you by the Dataflow Team
+echo http://dataflow.ox.ac.uk
+echo ===========================================================
+
 db_stop

development.ini

@@ -1,3 +1,23 @@
+# Copyright (c) 2012 University of Oxford
+# 
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+# 
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+# 
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, --INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 #
 # rdfdatabank - Pylons development environment configuration
 #
@@ -8,7 +28,7 @@ debug = true
 # Uncomment and replace with the address which should receive any error reports
 #email_to = [email protected]
 smtp_server = localhost
-error_email_from = paste@localhost
+error_email_from = paste@databank
 
 [server:main]
 use = egg:Paste#http
@@ -28,14 +48,13 @@ sqlalchemy.url = mysql://databanksqladmin:d6sqL4dm;n@localhost:3306/databankauth
 sqlalchemy.pool_recycle = 3600
 
 cache_dir = /var/cache/databank
-beaker.session.key = localdatabank
+beaker.session.key = rdfdatabank
 beaker.session.secret = somesecret
 
-who.config_file = %(here)s/who.ini
+who.config_file = /var/lib/databank/who.ini
 who.log_level = info
-#who.log_file = /var/log/databank/who.log
 who.log_file = stdout
-#who.log_file = %(here)s/logs/who.log
+#who.log_file = /var/log/databank/who.log
 
 redis.host = localhost
 
@@ -54,14 +73,19 @@ doi.count = /var/lib/databank/rdfdatabank/config/doi_count
 broadcast.to = redis
 broadcast.queue = silochanges
 
+metadata.embargoed = False
+
 solr.host = http://localhost:8080/solr
 naming_rule = [^0-9a-zA-Z_\-\:]
+naming_rule_humanized = Numbers, alphabets and -:
 formats_served = text/html,text/xhtml,text/plain,application/json,application/rdf+xml,text/xml,text/rdf+n3,application/x-turtle,text/rdf+ntriples,text/rdf+nt
 publisher = Bodleian Libraries, University of Oxford
 rights = http://ora.ouls.ox.ac.uk/objects/uuid%3A1d00eebb-8fed-46ad-8e38-45dbdb4b224c
 license = CC0 1.0 Universal (CC0 1.0). See http://creativecommons.org/publicdomain/zero/1.0/legalcode
 #license = Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. See http://creativecommons.org/licenses/by-nc-sa/3.0/
 
+api.version = 0.3
+
 # If you'd like to fine-tune the individual locations of the cache data dirs
 # for the Cache data, or the Session saves, un-comment the desired settings
 # here:
@@ -109,8 +133,6 @@ class = FileHandler
 level = INFO
 formatter = generic
 args = ('/var/log/databank/databank.log', 'w')
-#args = ('/opt/RDFDatabank/logs/databank.log', 'w')
-#args = ('%(here)s/logs/databank.log', 'w')
 
 [formatter_generic]
 format = %(asctime)s,%(msecs)03d %(levelname)-5.5s [%(name)s] %(message)s

docs/Dependencies.txt

@@ -0,0 +1,49 @@
+Databank is a web-based application for storing, curating and publishing data-packages, and is written using python and the pylons web framework. Its default deployment includes a message queue providing databank notifications to listener services. This message queue is handled using `Redis <http://redis.io/>`_ and `Supervisor <http://supervisord.org/>`_ to maintain the listener services. The search interface in Databank is powered by `Apache SOLR <http://lucene.apache.org/solr/>`_. 
+
++--------------------------------+-----------+
+| Package name                   | Version   |
++================================+===========+
+| python                         | >=2.6     |
++--------------------------------+-----------+
+| python-pylons                  | >=0.9.7   |
++--------------------------------+-----------+                                                         
+| python-repoze.who              | =2.0a4    |
++--------------------------------+-----------+
+| python-repoze.who-friendlyform | =1.0.8    |
++--------------------------------+-----------+
+| python-rdflib                  | =2.4.2    |
++--------------------------------+-----------+
+| python-dateutil                | >=1.4.1-4 |
++--------------------------------+-----------+
+| python-libxml2                 | >=2.7.8   |
++--------------------------------+-----------+
+| python-libxslt1                | >=1.1.26-7|
++--------------------------------+-----------+
+| python-pairtree                | >=0.7.1   |
++--------------------------------+-----------+
+| python-recordsilo              | >=0.4.14  |
++--------------------------------+-----------+
+| python-solrpy                  | >=0.9.5   |
++--------------------------------+-----------+
+| python-redis                   | >=2.4.5-1 |
++--------------------------------+-----------+
+| unzip                          | >=6.0     |
++--------------------------------+-----------+
+| apache2                        | >=2.2.20  |
++--------------------------------+-----------+
+| apache2-utils                  | >=2.2.20  |
++--------------------------------+-----------+
+| libapache2-mod-wsgi            | >=3.3     |
++--------------------------------+-----------+
+| redis-server                   | >=2.2.11  |
++--------------------------------+-----------+
+| supervisor                     | >=3.0     |
++--------------------------------+-----------+
+| openjdk-6-jre                  | >=6b23    |
++--------------------------------+-----------+
+| solr-tomcat                    | >=1.4.1   |
++--------------------------------+-----------+
+| Simple Sword Server *          | 2.0       |
++--------------------------------+-----------+
+
+\* Availabale from http://sword-app.svn.sourceforge.net/viewvc/sword-app/sss/branches/sss-2/