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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:48:43 UTC
[24/50] [abbrv] incubator-taverna-workbench-common-activities git
commit: taverna-localworker-activity-ui/
taverna-localworker-activity-ui/
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/commit/d157489f
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/tree/d157489f
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/diff/d157489f
Branch: refs/heads/master
Commit: d157489f1fff9c0d5533be199859b3d5f52a125b
Parents: b241be8
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon Feb 9 17:27:30 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon Feb 9 17:27:30 2015 +0000
----------------------------------------------------------------------
.gitignore | 24 --
.travis.yml | 1 -
README.md | 7 -
pom.xml | 142 ---------
.../LocalworkerActivityConfigurationAction.java | 117 -------
.../menu/ConfigureLocalworkerMenuAction.java | 62 ----
.../LocalworkerActivityIcon.java | 58 ----
.../LocalworkerServiceDescription.java | 105 -------
.../LocalworkerServiceProvider.java | 297 ------------------
.../views/LocalworkerActivityConfigView.java | 42 ---
.../LocalworkerActivityContextualView.java | 115 -------
.../views/LocalworkerActivityViewFactory.java | 82 -----
...rvicedescriptions.ServiceDescriptionProvider | 1 -
.../net.sf.taverna.t2.ui.menu.MenuComponent | 1 -
...a.t2.workbench.activityicons.ActivityIconSPI | 1 -
...ntextualviews.activity.ContextualViewFactory | 1 -
.../localworker-activity-ui-context-osgi.xml | 24 --
.../spring/localworker-activity-ui-context.xml | 27 --
src/main/resources/localworker.png | Bin 706 -> 0 bytes
src/main/resources/localworker_names | 67 ----
...rna.scuflworkers.biojava.GenBankParserWorker | 74 -----
...cuflworkers.biojava.GenBankParserWorker.json | 16 -
...verna.scuflworkers.biojava.ReverseCompWorker | 43 ---
....scuflworkers.biojava.ReverseCompWorker.json | 16 -
...a.scuflworkers.biojava.SwissProtParserWorker | 72 -----
...flworkers.biojava.SwissProtParserWorker.json | 16 -
...averna.scuflworkers.biojava.TranscribeWorker | 48 ---
...a.scuflworkers.biojava.TranscribeWorker.json | 16 -
...na.scuflworkers.io.ConcatenateFileListWorker | 101 ------
...uflworkers.io.ConcatenateFileListWorker.json | 24 --
...ge.taverna.scuflworkers.io.EnvVariableWorker | 33 --
...verna.scuflworkers.io.EnvVariableWorker.json | 11 -
...ge.taverna.scuflworkers.io.FileListByExtTask | 73 -----
...verna.scuflworkers.io.FileListByExtTask.json | 20 --
....taverna.scuflworkers.io.FileListByRegexTask | 71 -----
...rna.scuflworkers.io.FileListByRegexTask.json | 20 --
...ceforge.taverna.scuflworkers.io.LocalCommand | 80 -----
...ge.taverna.scuflworkers.io.LocalCommand.json | 20 --
...forge.taverna.scuflworkers.io.TextFileReader | 76 -----
....taverna.scuflworkers.io.TextFileReader.json | 20 --
...forge.taverna.scuflworkers.io.TextFileWriter | 57 ----
....taverna.scuflworkers.io.TextFileWriter.json | 24 --
...rge.taverna.scuflworkers.jdbc.SQLQueryWorker | 309 -------------------
...averna.scuflworkers.jdbc.SQLQueryWorker.json | 44 ---
...ge.taverna.scuflworkers.jdbc.SQLUpdateWorker | 229 --------------
...verna.scuflworkers.jdbc.SQLUpdateWorker.json | 36 ---
...erna.scuflworkers.ncbi.NucleotideFastaWorker | 45 ---
...scuflworkers.ncbi.NucleotideFastaWorker.json | 16 -
...erna.scuflworkers.ncbi.NucleotideGBSeqWorker | 45 ---
...scuflworkers.ncbi.NucleotideGBSeqWorker.json | 16 -
...scuflworkers.ncbi.NucleotideINSDSeqXMLWorker | 45 ---
...workers.ncbi.NucleotideINSDSeqXMLWorker.json | 16 -
...scuflworkers.ncbi.NucleotideTinySeqXMLWorker | 45 ---
...workers.ncbi.NucleotideTinySeqXMLWorker.json | 16 -
...taverna.scuflworkers.ncbi.ProteinFastaWorker | 45 ---
...na.scuflworkers.ncbi.ProteinFastaWorker.json | 16 -
...taverna.scuflworkers.ncbi.ProteinGBSeqWorker | 45 ---
...na.scuflworkers.ncbi.ProteinGBSeqWorker.json | 16 -
...na.scuflworkers.ncbi.ProteinINSDSeqXMLWorker | 45 ---
...uflworkers.ncbi.ProteinINSDSeqXMLWorker.json | 16 -
...na.scuflworkers.ncbi.ProteinTinySeqXMLWorker | 45 ---
...uflworkers.ncbi.ProteinTinySeqXMLWorker.json | 16 -
...taverna.scuflworkers.ncbi.PubMedEFetchWorker | 68 ----
...na.scuflworkers.ncbi.PubMedEFetchWorker.json | 24 --
...averna.scuflworkers.ncbi.PubMedESearchWorker | 124 --------
...a.scuflworkers.ncbi.PubMedESearchWorker.json | 44 ---
...urceforge.taverna.scuflworkers.net.BrowseUrl | 31 --
...orge.taverna.scuflworkers.net.BrowseUrl.json | 11 -
...forge.taverna.scuflworkers.net.ExtractHeader | 55 ----
....taverna.scuflworkers.net.ExtractHeader.json | 20 --
...ourceforge.taverna.scuflworkers.ui.AskWorker | 41 ---
...forge.taverna.scuflworkers.ui.AskWorker.json | 20 --
...ceforge.taverna.scuflworkers.ui.ChooseWorker | 80 -----
...ge.taverna.scuflworkers.ui.ChooseWorker.json | 24 --
...rge.taverna.scuflworkers.ui.SelectFileWorker | 116 -------
...averna.scuflworkers.ui.SelectFileWorker.json | 24 --
...ceforge.taverna.scuflworkers.ui.SelectWorker | 53 ----
...ge.taverna.scuflworkers.ui.SelectWorker.json | 24 --
...urceforge.taverna.scuflworkers.ui.TellWorker | 42 ---
...orge.taverna.scuflworkers.ui.TellWorker.json | 20 --
...urceforge.taverna.scuflworkers.ui.WarnWorker | 42 ---
...orge.taverna.scuflworkers.ui.WarnWorker.json | 20 --
...rge.taverna.scuflworkers.xml.XPathTextWorker | 75 -----
...averna.scuflworkers.xml.XPathTextWorker.json | 24 --
...rceforge.taverna.scuflworkers.xml.XSLTWorker | 152 ---------
...rge.taverna.scuflworkers.xml.XSLTWorker.json | 28 --
...na.scuflworkers.xml.XSLTWorkerWithParameters | 100 ------
...uflworkers.xml.XSLTWorkerWithParameters.json | 24 --
...escience.scuflworkers.java.ByteArrayToString | 44 ---
...nce.scuflworkers.java.ByteArrayToString.json | 20 --
....ebi.escience.scuflworkers.java.DecodeBase64 | 31 --
...escience.scuflworkers.java.DecodeBase64.json | 16 -
...embl.ebi.escience.scuflworkers.java.EchoList | 26 --
...ebi.escience.scuflworkers.java.EchoList.json | 16 -
...escience.scuflworkers.java.EmitLotsOfStrings | 19 --
...nce.scuflworkers.java.EmitLotsOfStrings.json | 11 -
....ebi.escience.scuflworkers.java.EncodeBase64 | 30 --
...escience.scuflworkers.java.EncodeBase64.json | 16 -
...escience.scuflworkers.java.ExtractImageLinks | 41 ---
...nce.scuflworkers.java.ExtractImageLinks.json | 16 -
....escience.scuflworkers.java.FilterStringList | 43 ---
...ence.scuflworkers.java.FilterStringList.json | 20 --
...l.ebi.escience.scuflworkers.java.FlattenList | 39 ---
....escience.scuflworkers.java.FlattenList.json | 16 -
...mbl.ebi.escience.scuflworkers.java.PadNumber | 44 ---
...bi.escience.scuflworkers.java.PadNumber.json | 20 --
...cuflworkers.java.RegularExpressionStringList | 60 ----
...orkers.java.RegularExpressionStringList.json | 24 --
...mbl.ebi.escience.scuflworkers.java.SendEmail | 85 -----
...bi.escience.scuflworkers.java.SendEmail.json | 27 --
....ebi.escience.scuflworkers.java.SplitByRegex | 47 ---
...escience.scuflworkers.java.SplitByRegex.json | 20 --
....ebi.escience.scuflworkers.java.StringConcat | 36 ---
...escience.scuflworkers.java.StringConcat.json | 20 --
...i.escience.scuflworkers.java.StringListMerge | 49 ---
...ience.scuflworkers.java.StringListMerge.json | 20 --
...cience.scuflworkers.java.StringSetDifference | 49 ---
...e.scuflworkers.java.StringSetDifference.json | 20 --
...ence.scuflworkers.java.StringSetIntersection | 43 ---
...scuflworkers.java.StringSetIntersection.json | 20 --
...bi.escience.scuflworkers.java.StringSetUnion | 43 ---
...cience.scuflworkers.java.StringSetUnion.json | 20 --
...ence.scuflworkers.java.StringStripDuplicates | 33 --
...scuflworkers.java.StringStripDuplicates.json | 16 -
...scuflworkers.java.TestAlwaysFailingProcessor | 36 ---
...workers.java.TestAlwaysFailingProcessor.json | 20 --
...science.scuflworkers.java.TestSometimesFails | 34 --
...ce.scuflworkers.java.TestSometimesFails.json | 16 -
...i.escience.scuflworkers.java.WebImageFetcher | 64 ----
...ience.scuflworkers.java.WebImageFetcher.json | 20 --
...bi.escience.scuflworkers.java.WebPageFetcher | 68 ----
...cience.scuflworkers.java.WebPageFetcher.json | 20 --
taverna-localworker-activity-ui/pom.xml | 142 +++++++++
.../LocalworkerActivityConfigurationAction.java | 117 +++++++
.../menu/ConfigureLocalworkerMenuAction.java | 62 ++++
.../LocalworkerActivityIcon.java | 58 ++++
.../LocalworkerServiceDescription.java | 105 +++++++
.../LocalworkerServiceProvider.java | 297 ++++++++++++++++++
.../views/LocalworkerActivityConfigView.java | 42 +++
.../LocalworkerActivityContextualView.java | 115 +++++++
.../views/LocalworkerActivityViewFactory.java | 82 +++++
...rvicedescriptions.ServiceDescriptionProvider | 1 +
.../net.sf.taverna.t2.ui.menu.MenuComponent | 1 +
...a.t2.workbench.activityicons.ActivityIconSPI | 1 +
...ntextualviews.activity.ContextualViewFactory | 1 +
.../localworker-activity-ui-context-osgi.xml | 24 ++
.../spring/localworker-activity-ui-context.xml | 27 ++
.../src/main/resources/localworker.png | Bin 0 -> 706 bytes
.../src/main/resources/localworker_names | 67 ++++
...rna.scuflworkers.biojava.GenBankParserWorker | 74 +++++
...cuflworkers.biojava.GenBankParserWorker.json | 16 +
...verna.scuflworkers.biojava.ReverseCompWorker | 43 +++
....scuflworkers.biojava.ReverseCompWorker.json | 16 +
...a.scuflworkers.biojava.SwissProtParserWorker | 72 +++++
...flworkers.biojava.SwissProtParserWorker.json | 16 +
...averna.scuflworkers.biojava.TranscribeWorker | 48 +++
...a.scuflworkers.biojava.TranscribeWorker.json | 16 +
...na.scuflworkers.io.ConcatenateFileListWorker | 101 ++++++
...uflworkers.io.ConcatenateFileListWorker.json | 24 ++
...ge.taverna.scuflworkers.io.EnvVariableWorker | 33 ++
...verna.scuflworkers.io.EnvVariableWorker.json | 11 +
...ge.taverna.scuflworkers.io.FileListByExtTask | 73 +++++
...verna.scuflworkers.io.FileListByExtTask.json | 20 ++
....taverna.scuflworkers.io.FileListByRegexTask | 71 +++++
...rna.scuflworkers.io.FileListByRegexTask.json | 20 ++
...ceforge.taverna.scuflworkers.io.LocalCommand | 80 +++++
...ge.taverna.scuflworkers.io.LocalCommand.json | 20 ++
...forge.taverna.scuflworkers.io.TextFileReader | 76 +++++
....taverna.scuflworkers.io.TextFileReader.json | 20 ++
...forge.taverna.scuflworkers.io.TextFileWriter | 57 ++++
....taverna.scuflworkers.io.TextFileWriter.json | 24 ++
...rge.taverna.scuflworkers.jdbc.SQLQueryWorker | 309 +++++++++++++++++++
...averna.scuflworkers.jdbc.SQLQueryWorker.json | 44 +++
...ge.taverna.scuflworkers.jdbc.SQLUpdateWorker | 229 ++++++++++++++
...verna.scuflworkers.jdbc.SQLUpdateWorker.json | 36 +++
...erna.scuflworkers.ncbi.NucleotideFastaWorker | 45 +++
...scuflworkers.ncbi.NucleotideFastaWorker.json | 16 +
...erna.scuflworkers.ncbi.NucleotideGBSeqWorker | 45 +++
...scuflworkers.ncbi.NucleotideGBSeqWorker.json | 16 +
...scuflworkers.ncbi.NucleotideINSDSeqXMLWorker | 45 +++
...workers.ncbi.NucleotideINSDSeqXMLWorker.json | 16 +
...scuflworkers.ncbi.NucleotideTinySeqXMLWorker | 45 +++
...workers.ncbi.NucleotideTinySeqXMLWorker.json | 16 +
...taverna.scuflworkers.ncbi.ProteinFastaWorker | 45 +++
...na.scuflworkers.ncbi.ProteinFastaWorker.json | 16 +
...taverna.scuflworkers.ncbi.ProteinGBSeqWorker | 45 +++
...na.scuflworkers.ncbi.ProteinGBSeqWorker.json | 16 +
...na.scuflworkers.ncbi.ProteinINSDSeqXMLWorker | 45 +++
...uflworkers.ncbi.ProteinINSDSeqXMLWorker.json | 16 +
...na.scuflworkers.ncbi.ProteinTinySeqXMLWorker | 45 +++
...uflworkers.ncbi.ProteinTinySeqXMLWorker.json | 16 +
...taverna.scuflworkers.ncbi.PubMedEFetchWorker | 68 ++++
...na.scuflworkers.ncbi.PubMedEFetchWorker.json | 24 ++
...averna.scuflworkers.ncbi.PubMedESearchWorker | 124 ++++++++
...a.scuflworkers.ncbi.PubMedESearchWorker.json | 44 +++
...urceforge.taverna.scuflworkers.net.BrowseUrl | 31 ++
...orge.taverna.scuflworkers.net.BrowseUrl.json | 11 +
...forge.taverna.scuflworkers.net.ExtractHeader | 55 ++++
....taverna.scuflworkers.net.ExtractHeader.json | 20 ++
...ourceforge.taverna.scuflworkers.ui.AskWorker | 41 +++
...forge.taverna.scuflworkers.ui.AskWorker.json | 20 ++
...ceforge.taverna.scuflworkers.ui.ChooseWorker | 80 +++++
...ge.taverna.scuflworkers.ui.ChooseWorker.json | 24 ++
...rge.taverna.scuflworkers.ui.SelectFileWorker | 116 +++++++
...averna.scuflworkers.ui.SelectFileWorker.json | 24 ++
...ceforge.taverna.scuflworkers.ui.SelectWorker | 53 ++++
...ge.taverna.scuflworkers.ui.SelectWorker.json | 24 ++
...urceforge.taverna.scuflworkers.ui.TellWorker | 42 +++
...orge.taverna.scuflworkers.ui.TellWorker.json | 20 ++
...urceforge.taverna.scuflworkers.ui.WarnWorker | 42 +++
...orge.taverna.scuflworkers.ui.WarnWorker.json | 20 ++
...rge.taverna.scuflworkers.xml.XPathTextWorker | 75 +++++
...averna.scuflworkers.xml.XPathTextWorker.json | 24 ++
...rceforge.taverna.scuflworkers.xml.XSLTWorker | 152 +++++++++
...rge.taverna.scuflworkers.xml.XSLTWorker.json | 28 ++
...na.scuflworkers.xml.XSLTWorkerWithParameters | 100 ++++++
...uflworkers.xml.XSLTWorkerWithParameters.json | 24 ++
...escience.scuflworkers.java.ByteArrayToString | 44 +++
...nce.scuflworkers.java.ByteArrayToString.json | 20 ++
....ebi.escience.scuflworkers.java.DecodeBase64 | 31 ++
...escience.scuflworkers.java.DecodeBase64.json | 16 +
...embl.ebi.escience.scuflworkers.java.EchoList | 26 ++
...ebi.escience.scuflworkers.java.EchoList.json | 16 +
...escience.scuflworkers.java.EmitLotsOfStrings | 19 ++
...nce.scuflworkers.java.EmitLotsOfStrings.json | 11 +
....ebi.escience.scuflworkers.java.EncodeBase64 | 30 ++
...escience.scuflworkers.java.EncodeBase64.json | 16 +
...escience.scuflworkers.java.ExtractImageLinks | 41 +++
...nce.scuflworkers.java.ExtractImageLinks.json | 16 +
....escience.scuflworkers.java.FilterStringList | 43 +++
...ence.scuflworkers.java.FilterStringList.json | 20 ++
...l.ebi.escience.scuflworkers.java.FlattenList | 39 +++
....escience.scuflworkers.java.FlattenList.json | 16 +
...mbl.ebi.escience.scuflworkers.java.PadNumber | 44 +++
...bi.escience.scuflworkers.java.PadNumber.json | 20 ++
...cuflworkers.java.RegularExpressionStringList | 60 ++++
...orkers.java.RegularExpressionStringList.json | 24 ++
...mbl.ebi.escience.scuflworkers.java.SendEmail | 85 +++++
...bi.escience.scuflworkers.java.SendEmail.json | 27 ++
....ebi.escience.scuflworkers.java.SplitByRegex | 47 +++
...escience.scuflworkers.java.SplitByRegex.json | 20 ++
....ebi.escience.scuflworkers.java.StringConcat | 36 +++
...escience.scuflworkers.java.StringConcat.json | 20 ++
...i.escience.scuflworkers.java.StringListMerge | 49 +++
...ience.scuflworkers.java.StringListMerge.json | 20 ++
...cience.scuflworkers.java.StringSetDifference | 49 +++
...e.scuflworkers.java.StringSetDifference.json | 20 ++
...ence.scuflworkers.java.StringSetIntersection | 43 +++
...scuflworkers.java.StringSetIntersection.json | 20 ++
...bi.escience.scuflworkers.java.StringSetUnion | 43 +++
...cience.scuflworkers.java.StringSetUnion.json | 20 ++
...ence.scuflworkers.java.StringStripDuplicates | 33 ++
...scuflworkers.java.StringStripDuplicates.json | 16 +
...scuflworkers.java.TestAlwaysFailingProcessor | 36 +++
...workers.java.TestAlwaysFailingProcessor.json | 20 ++
...science.scuflworkers.java.TestSometimesFails | 34 ++
...ce.scuflworkers.java.TestSometimesFails.json | 16 +
...i.escience.scuflworkers.java.WebImageFetcher | 64 ++++
...ience.scuflworkers.java.WebImageFetcher.json | 20 ++
...bi.escience.scuflworkers.java.WebPageFetcher | 68 ++++
...cience.scuflworkers.java.WebPageFetcher.json | 20 ++
261 files changed, 5843 insertions(+), 5875 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index ebe0e5b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,24 +0,0 @@
-# ignore project files #
-.classpath
-.project
-.settings/
-catalog-v001.xml
-
-# ignore target files #
-target/
-bin/
-build/
-dist/
-apidoc/
-*.swp
-
-# ignore svn files if there
-.svn
-
-# ignore log files #
-*.log
-/logs/*
-*/logs/*
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index dff5f3a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1 +0,0 @@
-language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
deleted file mode 100644
index fa84f7e..0000000
--- a/README.md
+++ /dev/null
@@ -1,7 +0,0 @@
-Taverna Workflow system Local Worker Activity: User Interface part for use in the Taverna Workbench.
-
-[](https://travis-ci.org/taverna/taverna-localworker-activity-ui)
-
-Extends https://github.com/taverna/taverna-localworker-activity
-
-This code was previously hosted at http://taverna.googlecode.com/svn/taverna/ui/net.sf.taverna.t2.ui-activities/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 556de86..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>localworker-activity-ui</artifactId>
- <version>2.0-SNAPSHOT</version>
- <packaging>bundle</packaging>
- <name>Taverna 2 Localworker Activity UI</name>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>beanshell-activity-ui</artifactId>
- <version>${t2.activities.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-icons-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-palette-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>edits-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>file-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>menu-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-app-configuration-api</artifactId>
- <version>${taverna.configuration.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>2.2.2</version>
- </dependency>
-
- <!-- category:biojava -->
- <!-- net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker -->
- <!-- net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker -->
- <!-- net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker -->
- <!-- net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker -->
- <dependency>
- <groupId>uk.org.mygrid.resources</groupId>
- <artifactId>biojava</artifactId>
- <version>1.4pre1</version>
- </dependency>
- <!-- category:xml -->
- <!-- net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker -->
- <dependency>
- <groupId>org.dom4j</groupId>
- <artifactId>com.springsource.org.dom4j</artifactId>
- <version>${dom4j.version}</version>
- </dependency>
- <!-- <dependency>
- <groupId>dom4j</groupId>
- <artifactId>dom4j</artifactId>
- <version>1.6</version>
- </dependency> -->
- <!-- category:net -->
- <!-- org.embl.ebi.escience.scuflworkers.java.SendEmail -->
- <dependency>
- <groupId>javax.mail</groupId>
- <artifactId>com.springsource.javax.mail</artifactId>
- <version>${mail.version}</version>
- </dependency>
- <!-- <dependency>
- <groupId>javax.mail</groupId>
- <artifactId>mail</artifactId>
- <version>1.4</version>
- </dependency> -->
- <dependency>
- <groupId>javax.activation</groupId>
- <artifactId>com.springsource.javax.activation</artifactId>
- <version>1.1.1</version>
- </dependency>
- <!-- <dependency>
- <groupId>javax.activation</groupId>
- <artifactId>activation</artifactId>
- <version>1.1</version>
- </dependency> -->
- <!-- category:base64 -->
- <!-- org.embl.ebi.escience.scuflworkers.java.EncodeBase64 -->
- <!-- org.embl.ebi.escience.scuflworkers.java.DecodeBase64 -->
- <dependency>
- <groupId>commons-codec</groupId>
- <artifactId>commons-codec</artifactId>
- <version>${commons.codec.version}</version>
- </dependency>
- <!-- <dependency>
- <groupId>commons-codec</groupId>
- <artifactId>commons-codec</artifactId>
- <version>1.3</version>
- </dependency> -->
- </dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository
- </url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
-</project>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java b/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
deleted file mode 100644
index 2016ad0..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/actions/LocalworkerActivityConfigurationAction.java
+++ /dev/null
@@ -1,117 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.localworker.actions;
-
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-
-import javax.swing.Action;
-import javax.swing.JOptionPane;
-
-import net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityConfigView;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-import uk.org.taverna.scufl2.api.common.Scufl2Tools;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * The {@link LocalworkerActivity}s have pre-defined scripts, ports etc in a serialised form on
- * disk. So if the user wants to change them they have to do so at own risk.
- *
- * @author Ian Dunlop
- */
-@SuppressWarnings("serial")
-public class LocalworkerActivityConfigurationAction extends ActivityConfigurationAction {
-
- public static final String EDIT_LOCALWORKER_SCRIPT = "Edit beanshell script";
-
- private final EditManager editManager;
-
- private final FileManager fileManager;
-
- private final ApplicationConfiguration applicationConfiguration;
-
- private Scufl2Tools scufl2Tools = new Scufl2Tools();
-
- public LocalworkerActivityConfigurationAction(Activity activity, Frame owner,
- EditManager editManager, FileManager fileManager,
- ActivityIconManager activityIconManager,
- ServiceDescriptionRegistry serviceDescriptionRegistry,
- ApplicationConfiguration applicationConfiguration) {
- super(activity, activityIconManager, serviceDescriptionRegistry);
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.applicationConfiguration = applicationConfiguration;
- putValue(Action.NAME, EDIT_LOCALWORKER_SCRIPT);
- }
-
- /**
- * If the localworker has not been changed it pops up a {@link JOptionPane} warning the user
- * that they change things at their own risk. Otherwise just show the config view
- */
- public void actionPerformed(ActionEvent e) {
- Object[] options = { "Continue", "Cancel" };
- Configuration configuration = scufl2Tools.configurationFor(activity, activity.getParent());
- JsonNode json = configuration.getJson();
- if (!json.get("isAltered").booleanValue()) {
- int n = JOptionPane
- .showOptionDialog(
- null,
- "Changing the properties of a Local Worker may affect its behaviour. Do you want to continue?",
- "WARNING", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE,
- null, // do not use a
- // custom Icon
- options, options[0]);
-
- if (n == 0) {
- // continue was clicked so prepare for config
- openDialog();
- } else {
- // do nothing
- }
- } else {
- openDialog();
- }
- }
-
- private void openDialog() {
- ActivityConfigurationDialog currentDialog = ActivityConfigurationAction
- .getDialog(getActivity());
- if (currentDialog != null) {
- currentDialog.toFront();
- return;
- }
- final LocalworkerActivityConfigView localworkerConfigView = new LocalworkerActivityConfigView(
- getActivity(), applicationConfiguration);
- final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(),
- localworkerConfigView, editManager);
- ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
-
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java b/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
deleted file mode 100644
index 3afed8d..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/menu/ConfigureLocalworkerMenuAction.java
+++ /dev/null
@@ -1,62 +0,0 @@
-package net.sf.taverna.t2.activities.localworker.menu;
-
-import javax.swing.Action;
-
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-
-import net.sf.taverna.t2.activities.beanshell.actions.BeanshellActivityConfigurationAction;
-import net.sf.taverna.t2.activities.localworker.actions.LocalworkerActivityConfigurationAction;
-import net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
-import net.sf.taverna.t2.ui.menu.MenuComponent;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-
-public class ConfigureLocalworkerMenuAction extends AbstractConfigureActivityMenuAction implements
- MenuComponent, ContextualMenuComponent {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
- private ApplicationConfiguration applicationConfiguration;
-
- public ConfigureLocalworkerMenuAction() {
- super(LocalworkerServiceDescription.ACTIVITY_TYPE);
- }
-
- @Override
- protected Action createAction() {
- Action result = null;
- result = new LocalworkerActivityConfigurationAction(findActivity(), getParentFrame(),
- editManager, fileManager, activityIconManager, serviceDescriptionRegistry,
- applicationConfiguration);
- result.putValue(Action.NAME, BeanshellActivityConfigurationAction.EDIT_BEANSHELL_SCRIPT);
- addMenuDots(result);
- return result;
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
- public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
- this.applicationConfiguration = applicationConfiguration;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java b/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
deleted file mode 100644
index 7d6bb5a..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerActivityIcon.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.localworker.servicedescriptions;
-
-import java.net.URI;
-
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
-
-/**
- *
- * @author Alex Nenadic
- * @author David Withers
- */
-public class LocalworkerActivityIcon implements ActivityIconSPI {
-
- private static Icon icon;
-
- public int canProvideIconScore(URI activityType) {
- if (LocalworkerServiceDescription.ACTIVITY_TYPE.equals(activityType))
- return DEFAULT_ICON + 1;
- else
- return NO_ICON;
- }
-
- public Icon getIcon(URI activityType) {
- return getLocalworkerIcon();
- }
-
- public static Icon getLocalworkerIcon() {
- if (icon == null) {
- icon = new ImageIcon(LocalworkerActivityIcon.class
- .getResource("/localworker.png"));
- }
- return icon;
- }
-}
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java b/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
deleted file mode 100644
index 38718b8..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceDescription.java
+++ /dev/null
@@ -1,105 +0,0 @@
-package net.sf.taverna.t2.activities.localworker.servicedescriptions;
-
-import java.net.URI;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-public class LocalworkerServiceDescription extends ServiceDescription {
-
- public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/localworker");
-
- private static final String LOCALWORKER = ServiceDescription.LOCAL_SERVICES;
-
- private JsonNode json;
- private String operation;
- private String category;
- private String provider;
- private String localworkerName;
-
- public JsonNode getJson() {
- return json;
- }
-
- public void setJson(JsonNode json) {
- this.json = json;
- }
-
- public String getOperation() {
- return operation;
- }
-
- public void setOperation(String operation) {
- this.operation = operation;
- }
-
- public String getCategory() {
- return category;
- }
-
- public void setCategory(String category) {
- this.category = category;
- }
-
- public String getProvider() {
- return provider;
- }
-
- public void setProvider(String provider) {
- this.provider = provider;
- }
-
- public String getLocalworkerName() {
- return localworkerName;
- }
-
- public void setLocalworkerName(String localworkerName) {
- this.localworkerName = localworkerName;
- }
-
- public String getType() {
- return "Localworker";
- }
-
- @Override
- public URI getActivityType() {
- return ACTIVITY_TYPE;
- }
-
- @Override
- public Configuration getActivityConfiguration() {
- Configuration configuration = new Configuration();
- configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
- configuration.setJson(getJson());
- return configuration;
- }
-
- @Override
- public Icon getIcon() {
- return LocalworkerActivityIcon.getLocalworkerIcon();
- }
-
- @Override
- public String getName() {
- return operation;
- }
-
- @Override
- public List<? extends Comparable<?>> getPath() {
- List<String> result =
- Arrays.asList (LOCALWORKER, category);
- return result;
- }
-
- @Override
- protected List<Object> getIdentifyingData() {
- return Arrays.<Object>asList(getJson());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java b/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
deleted file mode 100644
index 42345db..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/servicedescriptions/LocalworkerServiceProvider.java
+++ /dev/null
@@ -1,297 +0,0 @@
-package net.sf.taverna.t2.activities.localworker.servicedescriptions;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-import org.apache.log4j.Logger;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-public class LocalworkerServiceProvider implements ServiceDescriptionProvider {
-
- private static final String LOCALWORKER_NAMES = "/localworker_names";
-
- private static final String LOCALWORKER_SERVICE = "Local service";
-
- private static Logger logger = Logger.getLogger(Logger.class);
-
- private static final URI providerId = URI
- .create("http://taverna.sf.net/2010/service-provider/localworker");
-
- /** Used to deserialize the Activities stored on disk */
- private ObjectMapper objectMapper = new ObjectMapper();
-
- private static Map<String, String> localWorkerToScript = new HashMap<String, String>();
-
- static {
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.ByteArrayToString",
- "Byte Array To String");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.DecodeBase64",
- "Decode Base 64 to byte Array");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EchoList", "Echo List");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings",
- "Create Lots Of Strings");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.EncodeBase64",
- "Encode Byte Array to Base 64");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks",
- "Get image URLs from HTTP document");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.FilterStringList",
- "Filter List of Strings by regex");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.FlattenList",
- "Flatten List");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.PadNumber",
- "Pad numeral with leading 0s");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList",
- "Filter list of strings extracting match to a regex");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SendEmail",
- "Send an Email");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SliceList",
- "Extract Elements from a List");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.SplitByRegex",
- "Split string into string list by regular expression");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringConcat",
- "Concatenate two strings");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringListMerge",
- "Merge String List to a String");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetDifference",
- "String List Difference");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetIntersection",
- "String List Intersection");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringSetUnion",
- "String List Union");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates",
- "Remove String Duplicates");
- localWorkerToScript.put(
- "org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor",
- "Always Fails");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.TestSometimesFails",
- "Sometimes Fails");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.WebImageFetcher",
- "Get Image From URL");
- localWorkerToScript.put("org.embl.ebi.escience.scuflworkers.java.WebPageFetcher",
- "Get Web Page from URL");
-
- // xml:XPathText
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker",
- "XPath From Text");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.xml.XSLTWorker",
- "Transform XML");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters",
- "Transform XML with parameters");
-
- // biojava
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker",
- "Read Gen Bank File");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker",
- "Reverse Complement DNA");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker",
- "Read Swiss Prot File");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker",
- "Transcribe DNA");
-
- // io
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.TextFileReader",
- "Read Text File");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.TextFileWriter",
- "Write Text File");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.LocalCommand",
- "Execute Command Line App");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.FileListByExtTask",
- "List Files by Extension");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask",
- "List Files By Regex");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.DataRangeTask",
- "Select Data Range From File");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker",
- "Concatenate Files");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker",
- "Get Environment Variables as XML");
-
- // ui
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.AskWorker", "Ask");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.SelectWorker", "Select");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.ChooseWorker", "Choose");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.TellWorker", "Tell");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.WarnWorker", "Warn");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker",
- "Select File");
- // ncbi
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker",
- "Get Nucleotide FASTA");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker",
- "Get Nucleotide GBSeq XML");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker",
- "Get Nucleotide INSDSeq XML");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker",
- "Get Nucleotide TinySeq XML");
-
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker",
- "Get Protein FASTA");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker",
- "Get Protein INSDSeq XML");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker",
- "Get Protein GBSeq XML");
- localWorkerToScript.put(
- "net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker",
- "Get Protein TinySeq XML");
-
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker",
- "Search PubMed XML");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker",
- "Get PubMed XML By PMID");
-
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker",
- "Execute SQL Query");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker",
- "Execute SQL Update");
-
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.net.BrowseUrl",
- "Open web browser at a URL");
- localWorkerToScript.put("net.sourceforge.taverna.scuflworkers.net.ExtractHeader",
- "Extract HTTP Header");
- }
-
- public String getName() {
- return LOCALWORKER_SERVICE;
- }
-
- /**
- * Use the {@link net.sf.taverna.t2.activities.localworker.translator.LocalworkerTranslator} to
- * get a {@link Map} of all the local workers. Use the keys in this map
- * to load all the serialized activities from disk by using
- * <code> getClass().getResourceAsStream("/" + className) </code> to get
- * them and then the {@link ActivityXMLDeserializer} to get the actual {@link Activity}. Create
- * the {@link LocalworkerActivityItem} by
- * populating them with the correct ports and depths. Sets the category to
- * match the T1 version so that a query by category will split the local
- * workers in to the correct place.
- */
- public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) {
-
- List<ServiceDescription> items = new ArrayList<ServiceDescription>();
-
- InputStream inputStream = getClass().getResourceAsStream(LOCALWORKER_NAMES);
- if (inputStream == null) {
- logger.error("Could not find resource " + LOCALWORKER_NAMES);
- return;
- }
- BufferedReader inputReader = new BufferedReader(new InputStreamReader(inputStream));
- String line = "";
- String category = null;
- try {
- while ((line = inputReader.readLine()) != null) {
- if (line.startsWith("category")) {
- String[] split = line.split(":");
- category = split[1];
- } else {
- LocalworkerServiceDescription createItem;
- try {
- createItem = createItem(line);
- } catch (ItemCreationException e) {
- logger.warn("Could not create item for: " + line, e);
- continue;
- }
- createItem.setCategory(category);
- createItem.setProvider("myGrid");
- items.add(createItem);
- }
- }
- } catch (IOException e1) {
- logger.warn("Could not read local worker definitions from " + LOCALWORKER_NAMES);
- }
- callBack.partialResults(items);
- callBack.finished();
-
- }
-
- @SuppressWarnings("serial")
- public class ItemCreationException extends Exception {
-
- public ItemCreationException() {
- super();
- }
-
- public ItemCreationException(String message, Throwable cause) {
- super(message, cause);
- }
-
- public ItemCreationException(String message) {
- super(message);
- }
-
- public ItemCreationException(Throwable cause) {
- super(cause);
- }
-
- }
-
- /**
- * Loads the deserialised local worker from disk and creates a {@link LocalworkerActivityItem}
- * with the correct ports and script from it
- *
- * @param line
- * @return a LocalWorker with the appropriate Input/Output ports and script
- * @throws ItemCreationException
- */
- private LocalworkerServiceDescription createItem(String line) throws ItemCreationException {
- // get the file from disk
- String resource = "/" + line + ".json";
- InputStream resourceAsStream = getClass().getResourceAsStream(resource);
- if (resourceAsStream == null) {
- throw new ItemCreationException("Could not find resource " + resource);
- }
-
- JsonNode json;
- try {
- json = objectMapper.readTree(resourceAsStream);
- } catch (IOException e) {
- throw new ItemCreationException("Could not read resource " + resource, e);
- }
-
- LocalworkerServiceDescription item = new LocalworkerServiceDescription();
- item.setJson(json);
- item.setLocalworkerName(line);
- item.setOperation(localWorkerToScript.get(line));
- return item;
-
- }
-
- public Icon getIcon() {
- return LocalworkerActivityIcon.getLocalworkerIcon();
- }
-
- @Override
- public String toString() {
- return "Local workers provider";
- }
-
- public static String getServiceNameFromClassname(String classname) {
- return (localWorkerToScript.get(classname));
- }
-
- public String getId() {
- return providerId.toString();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java b/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
deleted file mode 100644
index 155c631..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityConfigView.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.localworker.views;
-
-import net.sf.taverna.t2.activities.beanshell.views.BeanshellConfigurationPanel;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-@SuppressWarnings("serial")
-public class LocalworkerActivityConfigView extends BeanshellConfigurationPanel {
-
- public LocalworkerActivityConfigView(Activity activity, ApplicationConfiguration applicationConfiguration) {
- super(activity, applicationConfiguration);
- }
-
- public boolean isConfigurationChanged() {
- boolean configurationChanged = super.isConfigurationChanged();
- if (configurationChanged) {
- getJson().put("isAltered", true);
- }
- return configurationChanged;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java b/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
deleted file mode 100644
index fc09d57..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityContextualView.java
+++ /dev/null
@@ -1,115 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.localworker.views;
-
-import java.awt.Frame;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.localworker.actions.LocalworkerActivityConfigurationAction;
-import net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-import uk.org.taverna.scufl2.api.port.InputActivityPort;
-import uk.org.taverna.scufl2.api.port.OutputActivityPort;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-@SuppressWarnings("serial")
-public class LocalworkerActivityContextualView extends HTMLBasedActivityContextualView {
-
- private final EditManager editManager;
- private final FileManager fileManager;
- private final ActivityIconManager activityIconManager;
- private final ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- private final ApplicationConfiguration applicationConfiguration;
-
- public LocalworkerActivityContextualView(Activity activity, EditManager editManager,
- FileManager fileManager, ColourManager colourManager,
- ActivityIconManager activityIconManager,
- ServiceDescriptionRegistry serviceDescriptionRegistry,
- ApplicationConfiguration applicationConfiguration) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.activityIconManager = activityIconManager;
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- this.applicationConfiguration = applicationConfiguration;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- StringBuilder html = new StringBuilder();
- html.append("<tr><th>Input Port Name</th><th>Depth</th></tr>");
- for (InputActivityPort inputActivityPort : getActivity().getInputPorts()) {
- html.append("<tr><td>" + inputActivityPort.getName() + "</td><td>");
- html.append(inputActivityPort.getDepth() + "</td></tr>");
- }
- html.append("<tr><th>Output Port Name</th><th>Depth</th></tr>");
- for (OutputActivityPort outputActivityPort : getActivity().getOutputPorts()) {
- html.append("<tr><td>" + outputActivityPort.getName() + "</td><td>");
- html.append(outputActivityPort.getDepth() + "</td></tr>");
- }
- return html.toString();
- }
-
- @Override
- public String getViewTitle() {
- String result = "";
- Configuration configuration = getConfigBean();
- JsonNode json = configuration.getJson();
- String workerName = LocalworkerServiceProvider.getServiceNameFromClassname(json.get(
- "localworkerName").textValue());
- if (json.get("isAltered").booleanValue()) {
- result = "Altered local worker service";
- if ((workerName != null) && !workerName.equals("")) {
- result += " - originally " + workerName;
- }
- } else {
- result = "Local worker service";
- if ((workerName != null) && !workerName.equals("")) {
- result += " - " + workerName;
- }
- }
- return result;
- }
-
- @Override
- public Action getConfigureAction(Frame owner) {
- return new LocalworkerActivityConfigurationAction(getActivity(), owner, editManager,
- fileManager, activityIconManager, serviceDescriptionRegistry,
- applicationConfiguration);
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java b/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
deleted file mode 100644
index 4fec0a2..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/localworker/views/LocalworkerActivityViewFactory.java
+++ /dev/null
@@ -1,82 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.localworker.views;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class LocalworkerActivityViewFactory implements ContextualViewFactory<Activity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ColourManager colourManager;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
- private ApplicationConfiguration applicationConfiguration;
-
- public boolean canHandle(Object object) {
- return object instanceof Activity
- && ((Activity) object).getType()
- .equals(LocalworkerServiceDescription.ACTIVITY_TYPE);
- }
-
- public List<ContextualView> getViews(Activity activity) {
- return Arrays.asList(new ContextualView[] { new LocalworkerActivityContextualView(activity,
- editManager, fileManager, colourManager, activityIconManager,
- serviceDescriptionRegistry, applicationConfiguration) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
- public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
- this.applicationConfiguration = applicationConfiguration;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
----------------------------------------------------------------------
diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
deleted file mode 100644
index c3c01e0..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
----------------------------------------------------------------------
diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
deleted file mode 100644
index 5911ddf..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.localworker.menu.ConfigureLocalworkerMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
deleted file mode 100644
index 720a022..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
----------------------------------------------------------------------
diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
deleted file mode 100644
index f1d2c0d..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
----------------------------------------------------------------------
diff --git a/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml b/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
deleted file mode 100644
index dd4c7a8..0000000
--- a/src/main/resources/META-INF/spring/localworker-activity-ui-context-osgi.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="LocalworkerActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
-
- <service ref="LocalworkerServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
-
- <service ref="ConfigureLocalworkerMenuAction" auto-export="interfaces" />
-
- <service ref="LocalworkerActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
-
- <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
- <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
- <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
- <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
- <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
- <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
----------------------------------------------------------------------
diff --git a/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml b/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
deleted file mode 100644
index edcd6be..0000000
--- a/src/main/resources/META-INF/spring/localworker-activity-ui-context.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="LocalworkerActivityIcon" class="net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerActivityIcon" />
-
- <bean id="LocalworkerServiceProvider" class="net.sf.taverna.t2.activities.localworker.servicedescriptions.LocalworkerServiceProvider" />
-
- <bean id="ConfigureLocalworkerMenuAction" class="net.sf.taverna.t2.activities.localworker.menu.ConfigureLocalworkerMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- <property name="applicationConfiguration" ref="applicationConfiguration" />
- </bean>
-
- <bean id="LocalworkerActivityViewFactory" class="net.sf.taverna.t2.activities.localworker.views.LocalworkerActivityViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="colourManager" ref="colourManager" />
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- <property name="applicationConfiguration" ref="applicationConfiguration" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/localworker.png
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diff --git a/src/main/resources/localworker.png b/src/main/resources/localworker.png
deleted file mode 100644
index 758a457..0000000
Binary files a/src/main/resources/localworker.png and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/localworker_names
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diff --git a/src/main/resources/localworker_names b/src/main/resources/localworker_names
deleted file mode 100644
index 3df452c..0000000
--- a/src/main/resources/localworker_names
+++ /dev/null
@@ -1,67 +0,0 @@
-category:biojava
-net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
-net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
-net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
-net.sourceforge.taverna.scuflworkers.biojava.TranscribeWorker
-category:io
-net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker
-net.sourceforge.taverna.scuflworkers.io.FileListByExtTask
-net.sourceforge.taverna.scuflworkers.io.FileListByRegexTask
-net.sourceforge.taverna.scuflworkers.io.EnvVariableWorker
-net.sourceforge.taverna.scuflworkers.io.LocalCommand
-net.sourceforge.taverna.scuflworkers.io.TextFileReader
-net.sourceforge.taverna.scuflworkers.io.TextFileWriter
-category:ui
-net.sourceforge.taverna.scuflworkers.ui.AskWorker
-net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
-net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker
-net.sourceforge.taverna.scuflworkers.ui.SelectWorker
-net.sourceforge.taverna.scuflworkers.ui.TellWorker
-net.sourceforge.taverna.scuflworkers.ui.WarnWorker
-category:xml
-net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
-net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
-net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
-category:list
-org.embl.ebi.escience.scuflworkers.java.EchoList
-org.embl.ebi.escience.scuflworkers.java.FlattenList
-org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
-org.embl.ebi.escience.scuflworkers.java.StringListMerge
-category:test
-org.embl.ebi.escience.scuflworkers.java.TestAlwaysFailingProcessor
-org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings
-org.embl.ebi.escience.scuflworkers.java.TestSometimesFails
-category:text
-org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
-org.embl.ebi.escience.scuflworkers.java.StringSetDifference
-org.embl.ebi.escience.scuflworkers.java.StringSetIntersection
-org.embl.ebi.escience.scuflworkers.java.StringSetUnion
-org.embl.ebi.escience.scuflworkers.java.PadNumber
-org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
-org.embl.ebi.escience.scuflworkers.java.SplitByRegex
-org.embl.ebi.escience.scuflworkers.java.StringConcat
-org.embl.ebi.escience.scuflworkers.java.FilterStringList
-category:net
-org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
-org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
-org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks
-org.embl.ebi.escience.scuflworkers.java.SendEmail
-net.sourceforge.taverna.scuflworkers.net.BrowseUrl
-net.sourceforge.taverna.scuflworkers.net.ExtractHeader
-category:base64
-org.embl.ebi.escience.scuflworkers.java.EncodeBase64
-org.embl.ebi.escience.scuflworkers.java.DecodeBase64
-category:ncbi
-net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
-net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
-net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
-net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
-net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
-net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
-net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
-net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
-net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
-net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
-category:jdbc
-net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
-net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
deleted file mode 100644
index d6c62b2..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker
+++ /dev/null
@@ -1,74 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow">
-
-
-<class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import org.biojava.bio.seq.Sequence;
-import org.biojava.bio.seq.SequenceIterator;
-import org.biojava.bio.seq.io.SeqIOTools;
-import org.biojava.bio.seq.io.agave.AgaveWriter;
-
-BufferedReader getReader (String fileUrl) throws IOException {
- InputStreamReader reader;
- try {
- reader = new FileReader(fileUrl);
- }
- catch (FileNotFoundException e) {
- // try a real URL instead
- URL url = new URL(fileUrl);
- reader = new InputStreamReader (url.openStream());
- }
- return new BufferedReader(reader);
- }
-
-if ((fileUrl == void) || (fileUrl == null)) {
- throw new RuntimeException("The fileUrl must be specified");
-}
-
-BufferedReader br = getReader(fileUrl);
-
-// read the GenBank File
-SequenceIterator sequences = SeqIOTools.readGenbank(br);
-
-// iterate through the sequences
-ByteArrayOutputStream os = new ByteArrayOutputStream();
-StringBuffer sb = new StringBuffer();
-AgaveWriter writer = new AgaveWriter();
-PrintStream ps = new PrintStream(os);
-
-while (sequences.hasNext()) {
- Sequence seq = sequences.nextSequence();
- writer.writeSequence(seq, ps);
- sb.append(os.toString());
-}
-
-genbankdata = sb.toString();
-br.close();
-ps.close();
-
-</script>
- <dependencies class="java.util.Collections$SingletonList">
- <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
- </dependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>fileUrl</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>genbankdata</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
deleted file mode 100644
index 452850f..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import org.biojava.bio.seq.Sequence;\nimport org.biojava.bio.seq.SequenceIterator;\nimport org.biojava.bio.seq.io.SeqIOTools;\nimport org.biojava.bio.seq.io.agave.AgaveWriter;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\nif ((fileUrl == void) || (fileUrl == null)) {\n throw new RuntimeException(\"The fileUrl must be specified\");\n}\n\nBufferedReader br = getReader(fileUrl);\n\n// read the GenBank File\nSequenceIterator sequences = SeqIOTools.readGenbank(br);\n\n// iterate through the sequences\nByteArrayOutputStream os = new ByteArrayOutputStream();\nStringBuffer sb = new StringBuffer();\nAgaveWriter writer = new AgaveWriter();\nPrintStrea
m ps = new PrintStream(os);\n\nwhile (sequences.hasNext()) {\n\tSequence seq = sequences.nextSequence();\n\twriter.writeSequence(seq, ps);\n\tsb.append(os.toString());\n}\n\ngenbankdata = sb.toString();\nbr.close();\nps.close();\n \n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.GenBankParserWorker",
- "inputPorts" : [ {
- "name" : "fileUrl",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "genbankdata",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
deleted file mode 100644
index 0044c82..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker
+++ /dev/null
@@ -1,43 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import org.biojava.bio.seq.DNATools;
-import org.biojava.bio.symbol.SymbolList;
-
-if ((rawSeq == void) || (rawSeq == null)) {
- throw new RuntimeException("The rawSeq must be specified");
-}
-
-// make a DNA SymbolListbena
-SymbolList symL = DNATools.createDNA(rawSeq);
-
-// reverse complement it
-symL = DNATools.reverseComplement(symL);
-
-// prove that it worked
-revSeq = symL.seqString();
-</script>
- <dependencies class="java.util.Collections$SingletonList">
- <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
- </dependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>rawSeq</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>revSeq</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
deleted file mode 100644
index c214819..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import org.biojava.bio.seq.DNATools;\nimport org.biojava.bio.symbol.SymbolList;\n\nif ((rawSeq == void) || (rawSeq == null)) {\n throw new RuntimeException(\"The rawSeq must be specified\");\n}\n\n// make a DNA SymbolListbena\nSymbolList symL = DNATools.createDNA(rawSeq);\n\n// reverse complement it\nsymL = DNATools.reverseComplement(symL);\n\n// prove that it worked\nrevSeq = symL.seqString();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.ReverseCompWorker",
- "inputPorts" : [ {
- "name" : "rawSeq",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "revSeq",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
deleted file mode 100644
index 7f64778..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker
+++ /dev/null
@@ -1,72 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import org.biojava.bio.seq.Sequence;
-import org.biojava.bio.seq.SequenceIterator;
-import org.biojava.bio.seq.io.SeqIOTools;
-import org.biojava.bio.seq.io.agave.AgaveWriter;
-
-BufferedReader getReader (String fileUrl) throws IOException {
- InputStreamReader reader;
- try {
- reader = new FileReader(fileUrl);
- }
- catch (FileNotFoundException e) {
- // try a real URL instead
- URL url = new URL(fileUrl);
- reader = new InputStreamReader (url.openStream());
- }
- return new BufferedReader(reader);
- }
-
-if ((fileUrl == void) || (fileUrl == null)) {
- throw new RuntimeException("The fileUrl must be specified");
-}
-
-BufferedReader br = getReader(fileUrl);
-
-// read the EMBL File
-SequenceIterator sequences = SeqIOTools.readSwissprot(br);
-
-// Prepare the writer
-AgaveWriter writer = new AgaveWriter();
-ByteArrayOutputStream os = new ByteArrayOutputStream();
-StringBuffer sb = new StringBuffer();
-PrintStream ps = new PrintStream(os);
-
-// iterate through the sequences
-while (sequences.hasNext()) {
- Sequence seq = sequences.nextSequence();
- writer.writeSequence(seq, ps);
- sb.append(os.toString());
-}
-results = sb.toString();
-
-br.close();
-ps.close();
-
-</script>
- <dependencies class="java.util.Collections$SingletonList">
- <element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element>
- </dependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>fileUrl</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>results</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
deleted file mode 100644
index 929c316..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import org.biojava.bio.seq.Sequence;\nimport org.biojava.bio.seq.SequenceIterator;\nimport org.biojava.bio.seq.io.SeqIOTools;\nimport org.biojava.bio.seq.io.agave.AgaveWriter;\n\nBufferedReader getReader (String fileUrl) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\treader = new FileReader(fileUrl);\n\t\t}\n\t\tcatch (FileNotFoundException e) {\n\t\t\t// try a real URL instead\n\t\t\tURL url = new URL(fileUrl);\n\t\t\treader = new InputStreamReader (url.openStream());\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\t\nif ((fileUrl == void) || (fileUrl == null)) {\n throw new RuntimeException(\"The fileUrl must be specified\");\n}\n\t\nBufferedReader br = getReader(fileUrl);\n\n// read the EMBL File\nSequenceIterator sequences = SeqIOTools.readSwissprot(br);\n\n// Prepare the writer\nAgaveWriter writer = new AgaveWriter();\nByteArrayOutputStream os = new ByteArrayOutputStream();\nStringBuffer sb = new StringBuffer();\nPrintStream ps = ne
w PrintStream(os);\n\n// iterate through the sequences\nwhile (sequences.hasNext()) {\n\tSequence seq = sequences.nextSequence();\n\twriter.writeSequence(seq, ps);\n\tsb.append(os.toString());\n}\nresults = sb.toString();\n\nbr.close();\nps.close();\n \n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker",
- "inputPorts" : [ {
- "name" : "fileUrl",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "results",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file