ChangeLog

= ChangeLog
== v2.4.1 July 2015
- 07/2015 store bio-search results to json file
- 06/2015 optimized code
- 05/2015 changed method to get bio search results
- 04/2015 introduced genelist for bio-search auto-suggestion
== v2.4.0 Februar 2015
- 02/2015 updated rescue script
- 02/2015 optimized disk space handling for derived data processing
- 01/2015 optimized derived data management
- 12/2014 enable relational parameter for bio search
- 12/2014 added FC in bio search
== v2.3.1 November 2014
- 11/2014 combine characteristics (source node, sample) for single investigation dashboard 
== v2.3.0 October 2014
- 10/2014 Dashboard optimization with caching
- 10/2014 add optional license field
- 10/2014 isa2rdf update with several configuration files
- 10/2014 fixes for false input
- 10/2014 general performance optizations
== v2.2.0 July 2014
- 07/2014 add code for biosearch
- 07/2014 clean code for unformated data upload
- 07/2014 updated yard-documentation
- 07/2014 new templates: cellcount_HighContentImaging.xml and cellcount_LEAP.xml
- 07/2014 full investigation file naming support - as described in 4.1 http://isatab.sourceforge.net/docs/ISA-TAB_release-candidate-1_v1.0_24nov08.pdf
- 06/2014 fix nameing restriction for i_*.txt file
== v2.1.0 June 2014
- 05/2014 add upload of unformatted investigation data @see http://api.toxbank.net/index.php/Investigation#Create_an_investigation
- 05/2014 add SubTaskURI to process large isatab-formatted raw-datafiles => RDF::TB.hasSubTaskURI
- 05/2014 enhanced Rakefile to restore and repair SPARQL backend
- 05/2014 add methods to get a list of uploaded ftp files for user owning the token @see http://api.toxbank.net/index.php/Investigation#Get_a_list_of_uploaded_FTP_files
- 04/2014 fix missing downloaduri in template/investigation/files_by_investigation.sparql
- 03-06/2014 different fixes and improvements
== v2.0.0 March 2014
- 02/2014 yard documentation
- 02/2014 link RubyDoc.info
- 02/2014 add yard doc for sparql templates
- 02/2014 isa2rdf version 1.0.1
- 01/2014 adding FTP uploaded files to datanodes
- 01/2014 enabled zip upload with whitespaces in title
- 12/2013 link FTP files to investigation directory
- 12/2013 add SPARQL templates for routes get '/investigation/sparql/:templatename' and get '/investigation/:id/sparql/:templatename' <br>
  see also : {file:SPARQL-Templates}
- 12/2013 README overhaul
- 12/2013 extend yard documentation
- 11/2013 4store restore script in Rakefile
- 11/2013 upload of datasets only if files not empty
- 11/2013 switched to isa2rdf 1.0.0
- 11/2013 add datasets.rdf to investigation graph in backend
- 11/2013 isa2rdf version 0.0.9
- 11/2013 isa2rdf version to 0.0.8
- 10/2013 disable direct upload of xls files
- 10/2013 save flags and modified date to file in case of restore or transport backend
- 10/2013 pass java error to task
- 10/2013 remove investigation dir if rdf conversion fails
- 10/2013 fix for wrong json date format in RDF::DC.modified
- 10/2013 set heap size for isa2rdf to -Xmx2048m
- 08/2013 isa2rdf version 0.0.7
- 07/2013 remove trailing slash from graph uri
- 07/2013 isa2rdf version 0.0.6
- 07/2013 add modified configs for isa2rdf
- 06/2013 unicorn configuration added
- 05/2013 isa2rdf version 0.0.5 + add config files
- 04/2013 RDF vocabularies moved to opentox-client
- 03/2013 Task.run instead of Task.create

== v1.0.0beta March 2013
- add nt format for data processing isa2rdf => nt => 4store
- add indexing for UI (add and remove investigation URIs on $search_service[:uri]
- always return task URI on POST and PUT request
- overhaul of publication workflow
- json support for user uri list
- isa2rdf to version 0.0.4 (isa2rdf-cli-0.0.4.jar)
- remove policies if allowReadBy(Group/User) contains empty string
- update RDF::DC.modified when changing data in PUT request

== v0.0.4alpha December 2012
-Fix version number 0.0.4alpha in alpha test branch

== v0.0.4 July 2012
- Address and IDs changed
  - Service URI https://INVESTIGATIONSERVICE is now https://INVESTIGATIONSERVICE/investigation
  - IDs changed to UUIDs e.G.: https://INVESTIGATIONSERVICE/123 changed to https://INVESTIGATIONSERVICE/investigation/1f6d584a-53aa-4c59-bae3-8c7ac9cb82ff
    UUID is a v4 random UUID (Universally Unique IDentifier).
- Policy/Access management
  - allowReadByUser and allowReadByGroup parameters added to POST and PUT request (POST to service and PUT to a specific investigation).
    both values are optional and can be empty or contain single or comma separated URIs of an existing ToxBank user or group (e.G.: allowReadByUser=http://USERSERVICE/toxbank/user/U2,http://USERSERVICE/toxbank/user/U124 )
    as described here: http://api.toxbank.net/index.php/Protocol#Security.
    Every user or group get read access to the specific investigation.
  - The creator of a new investigation gets full REST access (GET/POST/PUT/DELETE). Creator is identified by its subjectid from login and should be member of the LDAP Public Investigator group (cn=PI_GROUP,ou=groups,dc=DOMAIN,dc=TLD).
- isPublished flag
  - New investigations get http://onto.toxbank.net/api/isPublished = false to its metadata RDF representation:
    e.G.:
      <rdf:Description rdf:about="https://INVESTIGATIONSERVICE/investigation/f0154c33-e27a-4683-b9cd-94473beccae3/">
        <ns0:isPublished xmlns:ns0="http://onto.toxbank.net/api/" rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</ns0:isPublished>
      </rdf:Description>
  - published parameter added to PUT request to set isPublished in metadata to true:
    curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://INVESTIGATIONSERVICE/investigation/UUID
- isSummarySearchable flag
  summarySearchable parameter added to POST and PUT request to set isSummarySearchable flag in metadata.
- Add studies, assays or data to an investigation / Updating an investigation
  - additions to or updating an investigation will be handled via PUT request

v0.0.3 May 2012
* switch from v0.0.2pre to v0.0.3