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Cherian Mathew [Sat, 1 Mar 2014 07:38:00 +0000 (07:38 +0000)]
testing root permissions
Andreas Kohlbecker [Fri, 28 Feb 2014 16:10:49 +0000 (16:10 +0000)]
i did it again
Andreas Kohlbecker [Fri, 28 Feb 2014 16:08:27 +0000 (16:08 +0000)]
it was me
Cherian Mathew [Fri, 28 Feb 2014 16:04:20 +0000 (16:04 +0000)]
testing subgit
Cherian Mathew [Thu, 1 Nov 2012 09:05:50 +0000 (09:05 +0000)]
- Changed merge strings to flattening to first element to avoid loading data into memory.
- Added annotation
Cherian Mathew [Fri, 28 Sep 2012 13:52:32 +0000 (13:52 +0000)]
added Mac OSX fix for http post data newline when uploading data to GRefine.
Cherian Mathew [Fri, 28 Sep 2012 13:48:28 +0000 (13:48 +0000)]
added Mac OSX fix for http post data newline when uploading data to GRefine.
Cherian Mathew [Thu, 26 Jul 2012 14:45:32 +0000 (14:45 +0000)]
added latest version of synexpansion nested workflow
Cherian Mathew [Thu, 26 Jul 2012 14:08:15 +0000 (14:08 +0000)]
corrected name expansion info header from appearing in occurrence results
Cherian Mathew [Thu, 26 Jul 2012 13:26:32 +0000 (13:26 +0000)]
added corrected no-limit version of the gbif occurrence retrieval nested workflow
Cherian Mathew [Thu, 26 Jul 2012 12:49:04 +0000 (12:49 +0000)]
workflows to retrieve occurrences from GBIF Occurrence bank.
allows to retrive all occurrences with no limit
Cherian Mathew [Thu, 26 Jul 2012 09:00:02 +0000 (09:00 +0000)]
synexp_xml_to_csv.xsl: sperated nameLabel elements into brackets
synonymcheckmsg.xsd: now includes nameLabel and nameCanonical in request
colres_to_synres.xsl: updated to extract name with authorship
Cherian Mathew [Thu, 26 Jul 2012 08:55:28 +0000 (08:55 +0000)]
text file containg header line for name expansion result csv
Cherian Mathew [Thu, 26 Jul 2012 08:52:11 +0000 (08:52 +0000)]
xsl file which contains utility templates
Cherian Mathew [Wed, 11 Jul 2012 11:03:09 +0000 (11:03 +0000)]
converts the response from the synonym expansion part of the workflow to a name related output information.
Cherian Mathew [Fri, 29 Jun 2012 09:42:13 +0000 (09:42 +0000)]
added possibility for multiple accepted names in GBIF Syn. Expansionx
Cherian Mathew [Thu, 28 Jun 2012 16:20:39 +0000 (16:20 +0000)]
- added transformation to build csv data related to names after the name expansion step
- added possibility to save name information
Cherian Mathew [Tue, 26 Jun 2012 15:05:05 +0000 (15:05 +0000)]
added latest version of BioSTIF nested workflow (using httpx)
Cherian Mathew [Tue, 26 Jun 2012 12:47:36 +0000 (12:47 +0000)]
updated col web service url.
Cherian Mathew [Tue, 26 Jun 2012 12:46:51 +0000 (12:46 +0000)]
added seor workflow with updated col web service url
Cherian Mathew [Wed, 13 Jun 2012 10:33:23 +0000 (10:33 +0000)]
integrated new version of syn expansion / occurrence retrieval part of the workflow
Cherian Mathew [Thu, 7 Jun 2012 10:57:44 +0000 (10:57 +0000)]
- fallen back to synonym taxon id search for canonical name targetting the gbif checklist bank
- added source url for gbif checklist responses
- added workaround for CoL synonym source url
Cherian Mathew [Wed, 6 Jun 2012 13:38:02 +0000 (13:38 +0000)]
added checklist url attribute to synonymResponse tag
Cherian Mathew [Wed, 6 Jun 2012 13:34:34 +0000 (13:34 +0000)]
added checklist url attribute to synonymResponse tag
Cherian Mathew [Wed, 6 Jun 2012 12:45:14 +0000 (12:45 +0000)]
- Updated GBIF Name Search to use canonnical search
- Added checklist url to tabs in Synonym Expansion Input Dialog
- Allow Synonym Expansion Input Dialog to be expandable
Cherian Mathew [Wed, 6 Jun 2012 08:20:11 +0000 (08:20 +0000)]
- fixed bugs for targetting gbif checklist banks
Cherian Mathew [Fri, 1 Jun 2012 15:41:02 +0000 (15:41 +0000)]
- Added GBIF Data agreement for checklist banks
- Corrected merging of data from multiple checklists
Cherian Mathew [Fri, 1 Jun 2012 10:07:12 +0000 (10:07 +0000)]
java code for the Data Cleaning workflow.
contains all gui elements which are called from beanshells in the workflow.
Cherian Mathew [Fri, 1 Jun 2012 09:51:10 +0000 (09:51 +0000)]
- corrected CoL copyright logic
- added first version of GBIF Checklist Banks
Cherian Mathew [Wed, 11 Apr 2012 09:01:56 +0000 (09:01 +0000)]
changed output to string instead of list of strings
Cherian Mathew [Wed, 11 Apr 2012 08:57:49 +0000 (08:57 +0000)]
Added copyright, data use agreement for CoL, GBIF.
Integrated all three parts of the workflow together
Cherian Mathew [Thu, 5 Apr 2012 15:25:59 +0000 (15:25 +0000)]
Workflow which handles the Synonym Expansion and Occurrence Retrieval part of the Data Refinement Workflow
Cherian Mathew [Tue, 3 Apr 2012 16:10:27 +0000 (16:10 +0000)]
corrected dataProviderName to SLW:recordedBy field
Cherian Mathew [Tue, 3 Apr 2012 15:48:03 +0000 (15:48 +0000)]
Cherian Mathew [Tue, 3 Apr 2012 15:46:59 +0000 (15:46 +0000)]
schema which defines the internal synonym request / response pair.
Cherian Mathew [Tue, 3 Apr 2012 15:46:23 +0000 (15:46 +0000)]
xslt to transform internal synonym request to a CoL request
Cherian Mathew [Tue, 3 Apr 2012 15:34:11 +0000 (15:34 +0000)]
xslt for transforming CoL Response to internal synonym response format
Cherian Mathew [Tue, 3 Apr 2012 15:29:06 +0000 (15:29 +0000)]
xslt for transforming SLW ArtData Portal response to Data Refinement Workflow input Elements
Cherian Mathew [Tue, 3 Apr 2012 15:27:32 +0000 (15:27 +0000)]
header file for data refining csv input
Cherian Mathew [Tue, 3 Apr 2012 15:22:59 +0000 (15:22 +0000)]
Integration of all three parts of the workflow (BioSTIFF is not yet added) .
Cherian Mathew [Fri, 30 Mar 2012 13:41:00 +0000 (13:41 +0000)]
Test input for main Data Cleaning Workflow.
Part of the potentially invasive species for the MS6 (May 2012) Workshop.
Cherian Mathew [Fri, 30 Mar 2012 13:37:26 +0000 (13:37 +0000)]
Main Workflow for the Data Cleaning Project.
Contains all three subparts,
- Synonym Expansion / Occurrence Retrieval
- BioSTIFF (currently passthrough)
- GRefine
Cherian Mathew [Wed, 14 Mar 2012 13:55:09 +0000 (13:55 +0000)]
updated format options
Cherian Mathew [Wed, 14 Mar 2012 13:36:28 +0000 (13:36 +0000)]
nested workflow which integrates google refine in Taverna
Cherian Mathew [Fri, 2 Mar 2012 15:13:15 +0000 (15:13 +0000)]
-changed xsl to wrap quotes around fields 'only' when a comma is present
-changed occurrence id path to taxon occurrence id
Cherian Mathew [Thu, 1 Mar 2012 15:10:45 +0000 (15:10 +0000)]
XSLT for GBIFResponse to CSV format.
To be used to generate input test cases for the Taxonomy Data Cleaning Workflow (based on https://wiki.biovel.eu/display/BioVeL/Data+Cleaning+Workflow+Elements ). Also used in the Data Cleaning workflow to convert GBIF response to csv format.
Includes handling of commas within strings (by wrapping strings in double quotes) and escaping double quotes with double quotes.
Cherian Mathew [Wed, 29 Feb 2012 13:44:26 +0000 (13:44 +0000)]
created sub directroty structure for project
Cherian Mathew [Tue, 28 Feb 2012 12:47:03 +0000 (12:47 +0000)]
testing updates
Andreas Müller [Thu, 23 Feb 2012 14:45:25 +0000 (14:45 +0000)]
Readme file for project
Andreas Müller [Thu, 23 Feb 2012 14:44:50 +0000 (14:44 +0000)]
n.hoffmann [Thu, 23 Feb 2012 13:35:56 +0000 (13:35 +0000)]
Adding BioVeL repo