biovel.git
4 years agoremoving lines master root/trunk/BioVeL
Andreas Kohlbecker [Wed, 25 Feb 2015 10:05:10 +0000 (10:05 +0000)]
removing lines

4 years agoa third one
Andreas Kohlbecker [Wed, 25 Feb 2015 09:02:23 +0000 (09:02 +0000)]
a third one

4 years agoanother new line
Andreas Kohlbecker [Wed, 25 Feb 2015 09:01:41 +0000 (09:01 +0000)]
another new line

4 years agoa new line
Andreas Kohlbecker [Wed, 25 Feb 2015 09:01:22 +0000 (09:01 +0000)]
a new line

4 years agoBranch '/trunk/BioVeL' replaced from /branches/BioVeL/ottos-mops:22898
Andreas Kohlbecker [Wed, 25 Feb 2015 08:49:11 +0000 (08:49 +0000)]
Branch '/trunk/BioVeL' replaced from /branches/BioVeL/ottos-mops:22898

4 years agoresolving conficts ottos-mops root/branches/BioVeL/ottos-mops
Andreas Kohlbecker [Wed, 25 Feb 2015 08:49:11 +0000 (08:49 +0000)]
resolving conficts

4 years ago...
Andreas Kohlbecker [Wed, 25 Feb 2015 08:35:04 +0000 (08:35 +0000)]
...

4 years agoMerge branch 'master' of edit-com:/var/git/biovel attic/trunk/BioVeL/22889
Andreas Kohlbecker [Wed, 25 Feb 2015 08:35:04 +0000 (08:35 +0000)]
Merge branch 'master' of edit-com:/var/git/biovel

4 years agomore on ottos mops
Andreas Kohlbecker [Wed, 25 Feb 2015 08:35:04 +0000 (08:35 +0000)]
more on ottos mops

4 years agojandl
Andreas Kohlbecker [Wed, 25 Feb 2015 08:35:04 +0000 (08:35 +0000)]
jandl

4 years agosomething to pick branch1 root/branches/BioVeL/branch1
Andreas Kohlbecker [Wed, 25 Feb 2015 08:35:04 +0000 (08:35 +0000)]
something to pick

4 years agorenaming a file
Andreas Kohlbecker [Wed, 25 Feb 2015 08:35:04 +0000 (08:35 +0000)]
renaming a file

4 years agonew banch to try out more git features
Andreas Kohlbecker [Wed, 25 Feb 2015 08:35:04 +0000 (08:35 +0000)]
new banch to try out more git features

5 years agotesting git -> svn forsubgit
Cherian Mathew [Mon, 10 Mar 2014 12:58:36 +0000 (12:58 +0000)]
testing git -> svn forsubgit

5 years agoanotherfile root/tags/BioVeL/BioVeL-1.0.0 BioVeL-1.0.0
Andreas Kohlbecker [Wed, 5 Mar 2014 14:12:31 +0000 (14:12 +0000)]
anotherfile

5 years agotesting permissions
Cherian Mathew [Sat, 1 Mar 2014 08:04:45 +0000 (08:04 +0000)]
testing permissions

5 years agotesting root permissions
Cherian Mathew [Sat, 1 Mar 2014 07:38:00 +0000 (07:38 +0000)]
testing root permissions

5 years agoi did it again
Andreas Kohlbecker [Fri, 28 Feb 2014 16:10:49 +0000 (16:10 +0000)]
i did it again

5 years agoit was me
Andreas Kohlbecker [Fri, 28 Feb 2014 16:08:27 +0000 (16:08 +0000)]
it was me

5 years agotesting subgit
Cherian Mathew [Fri, 28 Feb 2014 16:04:20 +0000 (16:04 +0000)]
testing subgit

6 years ago- Changed merge strings to flattening to first element to avoid loading data into...
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

6 years agoadded Mac OSX fix for http post data newline when uploading data to GRefine.
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.

6 years agoadded 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.

7 years agoadded latest version of synexpansion nested workflow
Cherian Mathew [Thu, 26 Jul 2012 14:45:32 +0000 (14:45 +0000)]
added latest version of synexpansion nested workflow

7 years agocorrected name expansion info header from appearing in occurrence results
Cherian Mathew [Thu, 26 Jul 2012 14:08:15 +0000 (14:08 +0000)]
corrected name expansion info header from appearing in occurrence results

7 years agoadded corrected no-limit version of the gbif occurrence retrieval nested workflow
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

7 years agoworkflows to retrieve occurrences from GBIF Occurrence bank.
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

7 years agosynexp_xml_to_csv.xsl: sperated nameLabel elements into brackets
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

7 years agotext file containg header line for name expansion result csv
Cherian Mathew [Thu, 26 Jul 2012 08:55:28 +0000 (08:55 +0000)]
text file containg header line for name expansion result csv

7 years agoxsl file which contains utility templates
Cherian Mathew [Thu, 26 Jul 2012 08:52:11 +0000 (08:52 +0000)]
xsl file which contains utility templates

7 years agoconverts the response from the synonym expansion part of the workflow to a name relat...
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.

7 years agoadded possibility for multiple accepted names in GBIF Syn. Expansionx
Cherian Mathew [Fri, 29 Jun 2012 09:42:13 +0000 (09:42 +0000)]
added possibility for multiple accepted names in GBIF Syn. Expansionx

7 years ago- added transformation to build csv data related to names after the name expansion...
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

7 years agoadded latest version of BioSTIF nested workflow (using httpx)
Cherian Mathew [Tue, 26 Jun 2012 15:05:05 +0000 (15:05 +0000)]
added latest version of BioSTIF nested workflow (using httpx)

7 years agoupdated col web service url.
Cherian Mathew [Tue, 26 Jun 2012 12:47:36 +0000 (12:47 +0000)]
updated col web service url.

7 years agoadded seor workflow with 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

7 years agointegrated new version of syn expansion / occurrence retrieval part of the workflow
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

7 years ago- fallen back to synonym taxon id search for canonical name targetting the gbif check...
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

7 years agoadded checklist url attribute to synonymResponse tag
Cherian Mathew [Wed, 6 Jun 2012 13:38:02 +0000 (13:38 +0000)]
added checklist url attribute to synonymResponse tag

7 years agoadded 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

7 years ago- Updated GBIF Name Search to use canonnical search
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

7 years ago- fixed bugs for targetting gbif checklist banks
Cherian Mathew [Wed, 6 Jun 2012 08:20:11 +0000 (08:20 +0000)]
- fixed bugs for targetting gbif checklist banks

7 years ago- Added GBIF Data agreement for 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

7 years agojava code for the Data Cleaning workflow.
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.

7 years ago- corrected CoL copyright logic
Cherian Mathew [Fri, 1 Jun 2012 09:51:10 +0000 (09:51 +0000)]
- corrected CoL copyright logic
- added first version of GBIF Checklist Banks

7 years agochanged output to string instead of list of strings
Cherian Mathew [Wed, 11 Apr 2012 09:01:56 +0000 (09:01 +0000)]
changed output to string instead of list of strings

7 years agoAdded copyright, data use agreement for CoL, GBIF.
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

7 years agoWorkflow which handles the Synonym Expansion and Occurrence Retrieval part of the...
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

7 years agocorrected dataProviderName to SLW:recordedBy field
Cherian Mathew [Tue, 3 Apr 2012 16:10:27 +0000 (16:10 +0000)]
corrected dataProviderName to SLW:recordedBy field

7 years ago(no commit message)
Cherian Mathew [Tue, 3 Apr 2012 15:48:03 +0000 (15:48 +0000)]

7 years agoschema which defines the internal synonym request / response pair.
Cherian Mathew [Tue, 3 Apr 2012 15:46:59 +0000 (15:46 +0000)]
schema which defines the internal synonym request / response pair.

7 years agoxslt to transform internal synonym request to a CoL request
Cherian Mathew [Tue, 3 Apr 2012 15:46:23 +0000 (15:46 +0000)]
xslt to transform internal synonym request to a CoL request

7 years agoxslt for transforming CoL Response to internal synonym response format
Cherian Mathew [Tue, 3 Apr 2012 15:34:11 +0000 (15:34 +0000)]
xslt for transforming CoL Response to internal synonym response format

7 years agoxslt for transforming SLW ArtData Portal response to Data Refinement Workflow input...
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

7 years agoheader file for data refining csv input
Cherian Mathew [Tue, 3 Apr 2012 15:27:32 +0000 (15:27 +0000)]
header file for data refining csv input

7 years agoIntegration of all three parts of the workflow (BioSTIFF is not yet added) .
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) .

7 years agoTest input for main Data Cleaning Workflow.
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.

7 years agoMain Workflow for the Data Cleaning Project.
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

7 years agoupdated format options
Cherian Mathew [Wed, 14 Mar 2012 13:55:09 +0000 (13:55 +0000)]
updated format options

7 years agonested workflow which integrates google refine in Taverna
Cherian Mathew [Wed, 14 Mar 2012 13:36:28 +0000 (13:36 +0000)]
nested workflow which integrates google refine in Taverna

7 years ago-changed xsl to wrap quotes around fields 'only' when a comma is present
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

7 years agoXSLT for GBIFResponse to CSV format.
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.

7 years agocreated sub directroty structure for project
Cherian Mathew [Wed, 29 Feb 2012 13:44:26 +0000 (13:44 +0000)]
created sub  directroty structure for project

7 years agotesting updates
Cherian Mathew [Tue, 28 Feb 2012 12:47:03 +0000 (12:47 +0000)]
testing updates

7 years agoReadme file for project
Andreas Müller [Thu, 23 Feb 2012 14:45:25 +0000 (14:45 +0000)]
Readme file for project

7 years ago(no commit message)
Andreas Müller [Thu, 23 Feb 2012 14:44:50 +0000 (14:44 +0000)]

7 years agoAdding BioVeL repo
n.hoffmann [Thu, 23 Feb 2012 13:35:56 +0000 (13:35 +0000)]
Adding BioVeL repo