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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:48:41 UTC
[22/50] [abbrv] incubator-taverna-workbench-common-activities git
commit: taverna-localworker-activity-ui/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
deleted file mode 100644
index c82209f..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
+++ /dev/null
@@ -1,45 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=protein&retmode=xml&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-reader.close();
-outputText = writer.toString();
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>id</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>outputText</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.ncbi.ProteinINSDSeqXMLWorker.json
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
deleted file mode 100644
index 6e36120..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=protein&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker",
- "inputPorts" : [ {
- "name" : "id",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "outputText",
- "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.ncbi.ProteinTinySeqXMLWorker
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
deleted file mode 100644
index b6f9337..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
+++ /dev/null
@@ -1,45 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=xml&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-reader.close();
-outputText = writer.toString();
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>id</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>outputText</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.ncbi.ProteinTinySeqXMLWorker.json
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
deleted file mode 100644
index 471e000..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=xml&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker",
- "inputPorts" : [ {
- "name" : "id",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "outputText",
- "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.ncbi.PubMedEFetchWorker
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
deleted file mode 100644
index 71fef3c..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
+++ /dev/null
@@ -1,68 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed" +
-"&rettype=" + (((rettype == void ) || (rettype == null)) ? "full" : rettype) +
-"&retmode=" + (((retmode == void) || (retmode == null)) ? "xml" : retmode) +
-"&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-reader.close();
-outputText = writer.toString();
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>id</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>rettype</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>retmode</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>outputText</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.ncbi.PubMedEFetchWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
deleted file mode 100644
index 5e2a7df..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "if ((id == void) || (id == null) || id.equals(\"\")) {\n\tthrow new RunTimeException(\"port id must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed\" +\n\"&rettype=\" + (((rettype == void ) || (rettype == null)) ? \"full\" : rettype) +\n\"&retmode=\" + (((retmode == void) || (retmode == null)) ? \"xml\" : retmode) +\n\"&id=\" + id);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n }\nreader.close();\noutputText = writer.toString();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker",
- "inputPorts" : [ {
- "name" : "id",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "rettype",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "retmode",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "outputText",
- "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.ncbi.PubMedESearchWorker
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
deleted file mode 100644
index 37c440c..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
+++ /dev/null
@@ -1,124 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>if ((term == void) || (term == null) || term.equals("")) {
- throw new RunTimeException("port term must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed" +
-(field == void ? "" : ("&field=" + field)) +
-(retstart == void ? "" : ("&retstart=" + retstart)) +
-(retmax == void ? "" : ("&retmax=" + retmax)) +
-(mindate == void ? "" : ("&mindate=" + mindate)) +
-(maxdate == void ? "" : ("&maxdate=" + maxdate)) +
-"&rettype=" + (rettype == void ? "full" : rettype) +
-"&retmode=" + (retmode == void ? "xml" : retmode) +
-"&tool=taverna" +
-"&term=" + term);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-reader.close();
-outputText = writer.toString();
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>term</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>db</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>field</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>retstart</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>retmax</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>mindate</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>maxdate</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>rettype</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>outputText</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.ncbi.PubMedESearchWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
deleted file mode 100644
index bd29f82..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
+++ /dev/null
@@ -1,44 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "if ((term == void) || (term == null) || term.equals(\"\")) {\n\tthrow new RunTimeException(\"port term must have a non-empty value\");\n}\n\nURL url = new URL (\"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed\" +\n(field == void ? \"\" : (\"&field=\" + field)) +\n(retstart == void ? \"\" : (\"&retstart=\" + retstart)) +\n(retmax == void ? \"\" : (\"&retmax=\" + retmax)) +\n(mindate == void ? \"\" : (\"&mindate=\" + mindate)) +\n(maxdate == void ? \"\" : (\"&maxdate=\" + maxdate)) +\n\"&rettype=\" + (rettype == void ? \"full\" : rettype) +\n\"&retmode=\" + (retmode == void ? \"xml\" : retmode) +\n\"&tool=taverna\" +\n\"&term=\" + term);\n\nBufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));\nStringWriter writer = new StringWriter();\n\nchar[] buffer = new char[1024];\n while (true) {\n int r = reader.read(buffer);\n if (r <= 0) {\n break;\n }\n writer.write(buffer, 0, r);\n
}\nreader.close();\noutputText = writer.toString();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker",
- "inputPorts" : [ {
- "name" : "term",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "db",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "field",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "retstart",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "retmax",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "mindate",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "maxdate",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "rettype",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "outputText",
- "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.net.BrowseUrl
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
deleted file mode 100644
index a2317c5..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
+++ /dev/null
@@ -1,31 +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="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>url</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>import java.awt.Desktop;
-import java.net.URI;
-
-if ((url == void) || (url == null)) {
- throw new RuntimeException("Url must be specified");
-}
-
-URI uri = null;
-
-uri = new URI(url);
-
-Desktop.getDesktop().browse(uri);</script>
- <dependencies />
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></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.net.BrowseUrl.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
deleted file mode 100644
index 1a2155e..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
+++ /dev/null
@@ -1,11 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import java.awt.Desktop;\nimport java.net.URI;\n\nif ((url == void) || (url == null)) {\n\tthrow new RuntimeException(\"Url must be specified\");\n}\n\nURI uri = null;\n\nuri = new URI(url);\n\nDesktop.getDesktop().browse(uri);",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.net.BrowseUrl",
- "inputPorts" : [ {
- "name" : "url",
- "depth" : 0,
- "type" : "String"
- } ],
- "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.net.ExtractHeader
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader
deleted file mode 100644
index d3149d6..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader
+++ /dev/null
@@ -1,55 +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="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>headers</name>
- <depth>1</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>header_key</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>header_value</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>if ((headers == void) || (headers == null)) {
- throw new RuntimeException("Headers must be specified");
-}
-
-if ((header_key == void) || (header_key == null)) {
- throw new RuntimeException("Header_key must be specified");
-}
-
-String header_value = "";
-if (!header_key.endsWith(":")) {
- header_key += ":";
-}
-for (String h : headers) {
- if (h.startsWith(header_key)) {
- header_value = h.substring(header_key.length());
- header_value = header_value.trim();
- break;
- }
-}</script>
- <dependencies />
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></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.net.ExtractHeader.json
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json
deleted file mode 100644
index 0e510fa..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.net.ExtractHeader.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "if ((headers == void) || (headers == null)) {\n\tthrow new RuntimeException(\"Headers must be specified\");\n}\n\nif ((header_key == void) || (header_key == null)) {\n\tthrow new RuntimeException(\"Header_key must be specified\");\n}\n\nString header_value = \"\";\nif (!header_key.endsWith(\":\")) {\n\theader_key += \":\";\n}\nfor (String h : headers) {\n\tif (h.startsWith(header_key)) {\n\t\theader_value = h.substring(header_key.length());\n\t\theader_value = header_value.trim();\n\t\tbreak;\n\t}\n}",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.net.ExtractHeader",
- "inputPorts" : [ {
- "name" : "headers",
- "depth" : 1,
- "type" : "String"
- }, {
- "name" : "header_key",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "header_value",
- "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.ui.AskWorker
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker
deleted file mode 100644
index f094efa..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker
+++ /dev/null
@@ -1,41 +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 javax.swing.JOptionPane;
-
-answer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);
-
-
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>title</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>message</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>answer</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.ui.AskWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json
deleted file mode 100644
index c2095cc..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.AskWorker.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import javax.swing.JOptionPane;\n\nanswer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);\n\n\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.AskWorker",
- "inputPorts" : [ {
- "name" : "title",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "message",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "answer",
- "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.ui.ChooseWorker
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
deleted file mode 100644
index 5244d77..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker
+++ /dev/null
@@ -1,80 +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 javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JRadioButton;
-
-if ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {
- throw new RuntimeException("selectionValues must be specified and non-empty");
-}
-
-ButtonGroup group = new ButtonGroup();
-JPanel messagePanel = new JPanel();
-messagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));
-
-messagePanel.add(new JLabel((message == void ? null : message)));
-
-JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];
-for (int i = 0; i < buttonArray.length; i++) {
- buttonArray[i] = new JRadioButton(selectionValues.get(i));
- if (i==0) buttonArray[i].setSelected(true);
- group.add(buttonArray[i]);
- messagePanel.add(buttonArray[i]);
-}
-
-JOptionPane.showOptionDialog(null, messagePanel, (title == void ? null : title),
- JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null);
-
-String answer="";
-for (JRadioButton button : buttonArray) {
- if (button.isSelected()) {
- answer=button.getText();
- }
-}
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>title</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>message</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>selectionValues</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('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>answer</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.ui.ChooseWorker.json
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json
deleted file mode 100644
index 0410fc7..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.ChooseWorker.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import javax.swing.BoxLayout;\nimport javax.swing.ButtonGroup;\nimport javax.swing.JLabel;\nimport javax.swing.JOptionPane;\nimport javax.swing.JPanel;\nimport javax.swing.JRadioButton;\n\nif ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {\n throw new RuntimeException(\"selectionValues must be specified and non-empty\");\n}\n\nButtonGroup group = new ButtonGroup();\nJPanel messagePanel = new JPanel();\nmessagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));\n\nmessagePanel.add(new JLabel((message == void ? null : message)));\n\t\t\nJRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];\nfor (int i = 0; i < buttonArray.length; i++) {\t\t\t\n\tbuttonArray[i] = new JRadioButton(selectionValues.get(i));\n\tif (i==0) buttonArray[i].setSelected(true);\n\tgroup.add(buttonArray[i]);\n\tmessagePanel.add(buttonArray[i]);\n}\t\t\t\t\n\nJOptionPane.showOptionDialog(null, messagePanel, (title == void ? null
: title),\n\t\tJOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{\"OK\"}, null);\n\t\t\nString answer=\"\";\nfor (JRadioButton button : buttonArray) {\n\tif (button.isSelected()) {\n\t\tanswer=button.getText();\n\t}\n}\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.ChooseWorker",
- "inputPorts" : [ {
- "name" : "title",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "message",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "selectionValues",
- "depth" : 1,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "answer",
- "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.ui.SelectFileWorker
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diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker
deleted file mode 100644
index e594b7f..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker
+++ /dev/null
@@ -1,116 +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 java.awt.CardLayout;
-import java.awt.Image;
-import java.awt.Toolkit;
-import java.io.File;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.swing.ImageIcon;
-import javax.swing.JEditorPane;
-import javax.swing.JFileChooser;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.filechooser.FileFilter;
-
-class FileExtFilter extends FileFilter {
-
- public FileExtFilter(String ext, String label, boolean includeDir) {
- this.ext = ext;
- this.label = label;
- this.includeDir = includeDir;
- }
-
- public String getDescription() {
- return this.label;
- }
-
- public boolean accept(File file) {
- if (file.isDirectory() && includeDir) {
- return true;
- } else {
- return file.getName().endsWith(this.ext);
- }
- }
-
- String ext, label;
-
- boolean includeDir;
-}
-
-if (title == void) {
- title = null;
-}
-
-if ((fileExtensions == void) || (fileExtensions == null)) {
- fileExtensions = "";
-}
-
-if ((fileExtLabels == void) || (fileExtLabels == null)) {
- fileExtLabels = "";
-}
-
-JFileChooser chooser = new JFileChooser();
-chooser.setDialogTitle(title);
-
-String[] fileTypeList = fileExtensions.split(",");
-String[] filterLabelList = fileExtLabels.split(",");
-
-if (fileTypeList != null && filterLabelList != null && fileTypeList.length != filterLabelList.length) {
- throw new RuntimeException("The list of extensions and file filter labels must be the same length");
-}
-
-// create the file filters
-for (int i = 0; i < fileTypeList.length; i++) {
- FileExtFilter filter = new FileExtFilter(fileTypeList[i], filterLabelList[i], true);
- chooser.setFileFilter(filter);
-}
-
-chooser.showOpenDialog(null);
-File file = chooser.getSelectedFile();
-selectedFile = file.getAbsolutePath();
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>title</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>fileExtensions</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>fileExtLabels</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>selectedFile</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.ui.SelectFileWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json
deleted file mode 100644
index 1d71cef..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import java.awt.CardLayout;\nimport java.awt.Image;\nimport java.awt.Toolkit;\nimport java.io.File;\nimport java.util.HashMap;\nimport java.util.Map;\n\nimport javax.swing.ImageIcon;\nimport javax.swing.JEditorPane;\nimport javax.swing.JFileChooser;\nimport javax.swing.JLabel;\nimport javax.swing.JPanel;\nimport javax.swing.filechooser.FileFilter;\n\nclass FileExtFilter extends FileFilter {\n\n\tpublic FileExtFilter(String ext, String label, boolean includeDir) {\n\t\tthis.ext = ext;\n\t\tthis.label = label;\n\t\tthis.includeDir = includeDir;\n\t}\n\n\tpublic String getDescription() {\n\t\treturn this.label;\n\t}\n\n\tpublic boolean accept(File file) {\n\t\tif (file.isDirectory() && includeDir) {\n\t\t\treturn true;\n\t\t} else {\n\t\t\treturn file.getName().endsWith(this.ext);\n\t\t}\n\t}\n\n\tString ext, label;\n\n\tboolean includeDir;\n}\n\nif (title == void) {\n\ttitle = null;\n}\n\nif ((fileExtensions == void) || (fileExtensions == null)) {\n\tfileExtensions = \"\
";\n}\n\nif ((fileExtLabels == void) || (fileExtLabels == null)) {\n\tfileExtLabels = \"\";\n}\n\nJFileChooser chooser = new JFileChooser();\nchooser.setDialogTitle(title);\n\nString[] fileTypeList = fileExtensions.split(\",\");\nString[] filterLabelList = fileExtLabels.split(\",\");\n\nif (fileTypeList != null && filterLabelList != null && fileTypeList.length != filterLabelList.length) {\n\tthrow new RuntimeException(\"The list of extensions and file filter labels must be the same length\");\n}\n\n// create the file filters\nfor (int i = 0; i < fileTypeList.length; i++) {\n\tFileExtFilter filter = new FileExtFilter(fileTypeList[i], filterLabelList[i], true);\n\tchooser.setFileFilter(filter);\n}\n\nchooser.showOpenDialog(null);\nFile file = chooser.getSelectedFile();\nselectedFile = file.getAbsolutePath();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.SelectFileWorker",
- "inputPorts" : [ {
- "name" : "title",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "fileExtensions",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "fileExtLabels",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "selectedFile",
- "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.ui.SelectWorker
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker
deleted file mode 100644
index 1745844..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker
+++ /dev/null
@@ -1,53 +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 javax.swing.JOptionPane;
-
-if ((valueList == void) || (valueList == null) || (valueList.isEmpty())) {
- throw new RuntimeException("valueList must be specified and non-empty");
-}
-
-answer = (String) JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE, null, valueList.toArray(), valueList.get(0));
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>valueList</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>message</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>title</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>answer</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.ui.SelectWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json
deleted file mode 100644
index 6c287b6..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.SelectWorker.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import javax.swing.JOptionPane;\n\nif ((valueList == void) || (valueList == null) || (valueList.isEmpty())) {\n throw new RuntimeException(\"valueList must be specified and non-empty\");\n}\n\nanswer = (String) JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE, null, valueList.toArray(), valueList.get(0));\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.SelectWorker",
- "inputPorts" : [ {
- "name" : "valueList",
- "depth" : 1,
- "type" : "String"
- }, {
- "name" : "message",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "title",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "answer",
- "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.ui.TellWorker
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker
deleted file mode 100644
index 99ee6ab..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker
+++ /dev/null
@@ -1,42 +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 javax.swing.JOptionPane;
-
-JOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.INFORMATION_MESSAGE);
-
-answer = "answer";
-
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>title</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>message</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>answer</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.ui.TellWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json
deleted file mode 100644
index 8037a42..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.TellWorker.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import javax.swing.JOptionPane;\n\nJOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title),\tJOptionPane.INFORMATION_MESSAGE);\n\nanswer = \"answer\";\n\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.TellWorker",
- "inputPorts" : [ {
- "name" : "title",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "message",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "answer",
- "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.ui.WarnWorker
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker
deleted file mode 100644
index b211ba5..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker
+++ /dev/null
@@ -1,42 +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 javax.swing.JOptionPane;
-
-JOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.WARNING_MESSAGE);
-
-answer = "answer";
-
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>title</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>message</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>answer</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.ui.WarnWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json
deleted file mode 100644
index eaa8c93..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.ui.WarnWorker.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import javax.swing.JOptionPane;\n\nJOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title),\tJOptionPane.WARNING_MESSAGE);\n\nanswer = \"answer\";\n \n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.ui.WarnWorker",
- "inputPorts" : [ {
- "name" : "title",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "message",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "answer",
- "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.xml.XPathTextWorker
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
deleted file mode 100644
index 0395225..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
+++ /dev/null
@@ -1,75 +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.dom4j.Document;
-import org.dom4j.Node;
-import org.dom4j.io.SAXReader;
-
-SAXReader reader = new SAXReader(false);
-reader.setIncludeInternalDTDDeclarations(false);
-reader.setIncludeExternalDTDDeclarations(false);
-
-Document document = reader.read(new StringReader(xmltext));
-List nodelist = document.selectNodes(xpath);
-
-// Process the elements in the nodelist
-ArrayList outputList = new ArrayList();
-ArrayList outputXmlList = new ArrayList();
-
-String val = null;
-String xmlVal = null;
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
- Node element = (Node) iter.next();
- xmlVal = element.asXML();
- val = element.getStringValue();
- if (val != null && !val.equals("")) {
- outputList.add(val);
- outputXmlList.add(xmlVal);
- }
-
-}
-
-List nodelist=outputList;
-List nodelistAsXML=outputXmlList;</script>
- <dependencies>
- <string>dom4j:dom4j:1.6</string>
- </dependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>xpath</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>xml-text</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>nodelist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>nodelistAsXML</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('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.xml.XPathTextWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json
deleted file mode 100644
index 3fa2385..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import org.dom4j.Document;\nimport org.dom4j.Node;\nimport org.dom4j.io.SAXReader;\n\nSAXReader reader = new SAXReader(false);\nreader.setIncludeInternalDTDDeclarations(false);\nreader.setIncludeExternalDTDDeclarations(false);\n\nDocument document = reader.read(new StringReader(xmltext));\nList nodelist = document.selectNodes(xpath);\n\n// Process the elements in the nodelist\nArrayList outputList = new ArrayList();\nArrayList outputXmlList = new ArrayList();\n\nString val = null;\nString xmlVal = null;\nfor (Iterator iter = nodelist.iterator(); iter.hasNext();) {\n\tNode element = (Node) iter.next();\n\txmlVal = element.asXML();\n\tval = element.getStringValue();\n\tif (val != null && !val.equals(\"\")) {\n\t\toutputList.add(val);\n\t\toutputXmlList.add(xmlVal);\n\t}\n\n}\n\nList nodelist=outputList;\nList nodelistAsXML=outputXmlList;",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker",
- "inputPorts" : [ {
- "name" : "xpath",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "xml-text",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "nodelist",
- "depth" : 1,
- "granularDepth" : 1
- }, {
- "name" : "nodelistAsXML",
- "depth" : 1,
- "granularDepth" : 1
- } ],
- "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.xml.XSLTWorker
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
deleted file mode 100644
index 1532b63..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
+++ /dev/null
@@ -1,152 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="outputStr" to="outputStr" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.StringWriter;
-import java.io.Writer;
-import java.net.URL;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.xml.transform.Result;
-import javax.xml.transform.Source;
-import javax.xml.transform.SourceLocator;
-import javax.xml.transform.Templates;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.transform.stream.StreamSource;
-
-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);
- }
-
-BufferedWriter getWriter (String fileUrl) throws IOException {
- Writer writer;
- try {
- writer = new FileWriter(fileUrl);
- }
- catch (FileNotFoundException e) {
- // try a real URL instead
- URL url = new URL(fileUrl);
- writer = new OutputStreamWriter (url.openConnection().getOutputStream());
- }
- return new BufferedWriter(writer);
- }
-
-String xslFilename = xslFileURL;
-String outFilename;
-if (outFileURL != void) {
- outFilename = outFileURL;
-}
-
-String ext;
-if (outputExt != void) {
- ext = outputExt;
-}
-
-if (((outFilename == null) || outFilename.equals("")) && (ext != null)) {
- outFilename = inFileURL.substring(0, inFileURL.indexOf(".")+1) + ext;
-}
-
-// Create transformer factory
-TransformerFactory factory = TransformerFactory.newInstance();
-
-// Use the factory to create a template containing the xsl file
-Templates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));
-
-// Use the template to create a transformer
-Transformer xformer = template.newTransformer();
-
-// Prepare the input and output files
-Reader sourceReader = getReader(inFileURL);
-Source source = new StreamSource(sourceReader);
-StringWriter resultStr = new StringWriter();
-Result result = new StreamResult(resultStr);
-
-// Apply the xsl file to the source file and write the result to the
-// output file
-xformer.transform(source, result);
-
-outputStr = resultStr.toString();
-
-if ((outFilename != null) && !outFilename.equals("")) {
-
- BufferedWriter out = getWriter(outFilename);
-
- out.write(outputStr);
- out.close();
-}
-sourceReader.close();
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>xslFileURL</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>outFileURL</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>inFileURL</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>outputExt</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>outputStr</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.xml.XSLTWorker.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json
deleted file mode 100644
index 09aff0d..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorker.json
+++ /dev/null
@@ -1,28 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "import java.io.BufferedReader;\nimport java.io.BufferedWriter;\nimport java.io.FileInputStream;\nimport java.io.FileNotFoundException;\nimport java.io.FileReader;\nimport java.io.FileWriter;\nimport java.io.IOException;\nimport java.io.InputStreamReader;\nimport java.io.OutputStreamWriter;\nimport java.io.StringWriter;\nimport java.io.Writer;\nimport java.net.URL;\nimport java.util.HashMap;\nimport java.util.Map;\n\nimport javax.xml.transform.Result;\nimport javax.xml.transform.Source;\nimport javax.xml.transform.SourceLocator;\nimport javax.xml.transform.Templates;\nimport javax.xml.transform.Transformer;\nimport javax.xml.transform.TransformerConfigurationException;\nimport javax.xml.transform.TransformerException;\nimport javax.xml.transform.TransformerFactory;\nimport javax.xml.transform.stream.StreamResult;\nimport javax.xml.transform.stream.StreamSource;\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\nBufferedWriter getWriter (String fileUrl) throws IOException {\n\t\tWriter writer;\n\t\ttry {\n\t\t\twriter = new FileWriter(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\twriter = new OutputStreamWriter (url.openConnection().getOutputStream());\n\t\t}\n\t\treturn new BufferedWriter(writer);\n\t}\n\t\nString xslFilename = xslFileURL;\nString outFilename;\nif (outFileURL != void) {\n outFilename = outFileURL;\n}\n\nString ext;\nif (outputExt != void) {\n ext = outputExt;\n}\n\nif (((outFilename == null) || outFilename.equals(\"\")) && (ext != null)) {\n\t\toutFilename = inFileURL.substring(0, inFileURL.indexOf(\".\")+1) + ext;\n}\n\
n// Create transformer factory\nTransformerFactory factory = TransformerFactory.newInstance();\n\n// Use the factory to create a template containing the xsl file\nTemplates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));\n\n// Use the template to create a transformer\nTransformer xformer = template.newTransformer();\n\n// Prepare the input and output files\nReader sourceReader = getReader(inFileURL);\nSource source = new StreamSource(sourceReader);\nStringWriter resultStr = new StringWriter();\nResult result = new StreamResult(resultStr);\n\n// Apply the xsl file to the source file and write the result to the\n// output file\nxformer.transform(source, result);\n\noutputStr = resultStr.toString();\n\nif ((outFilename != null) && !outFilename.equals(\"\")) {\n\n\tBufferedWriter out = getWriter(outFilename);\n\n\tout.write(outputStr);\n\tout.close();\n}\nsourceReader.close();\n",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.xml.XSLTWorker",
- "inputPorts" : [ {
- "name" : "xslFileURL",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "outFileURL",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "inFileURL",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "outputExt",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "outputStr",
- "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.xml.XSLTWorkerWithParameters
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
deleted file mode 100644
index 768c8f9..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters
+++ /dev/null
@@ -1,100 +0,0 @@
-<activity xmlns="http://taverna.sf.net/2008/xml/t2flow">
- <class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class>
- <inputMap>
- <map from="xsltString" to="xsltString" />
- <map from="paramList" to="paramList" />
- <map from="sourceString" to="sourceString" />
- </inputMap>
- <outputMap>
- <map from="outputString" to="outputString" />
- </outputMap>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>sourceString</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>xsltString</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>paramList</name>
- <depth>1</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>outputString</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>//From a proposal by Mikolaj Rybinski
-import javax.xml.transform.Source;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.transform.stream.StreamSource;
-
-param(paramstr) {
- nameAndValue = paramstr.split("=");
- if (nameAndValue.length != 2) {
- throw new RuntimeException("Wrong parameter format: \"" + paramstr + "\".");
- }
- name = nameAndValue[0].trim();
- value = nameAndValue[1].trim();
- return this;
-}
-
-if ((sourceString == void) || (sourceString == null)) {
- throw new RuntimeException("sourceString must be specified");
-}
-
-if ((xsltString == void) || (xsltString == null)) {
- throw new RuntimeException("xsltString must be specified");
-}
-
-Source inSource = new StreamSource(new StringReader(sourceString));
-Source xslSource = new StreamSource(new StringReader(xsltString));
-
-// the factory pattern supports different XSLT processors
-// e.g. set the "javax.xml.transform.TransformerFactory" system property
-TransformerFactory tnfFact = TransformerFactory.newInstance();
-Transformer tnf = tnfFact.newTransformer(xslSource);
-
-if (paramList != void) {
- for (String paramstr : paramList) {
- p = param(paramstr);
- tnf.setParameter(p.name, p.value);
- }
-}
-
-Writer outputWriter = new StringWriter();
-tnf.transform(inSource, new StreamResult(outputWriter));
-outputString = outputWriter.toString();</script>
- <dependencies />
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/d157489f/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json
----------------------------------------------------------------------
diff --git a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json b/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json
deleted file mode 100644
index 0800c76..0000000
--- a/src/main/resources/net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "//From a proposal by Mikolaj Rybinski\nimport javax.xml.transform.Source;\nimport javax.xml.transform.Transformer;\nimport javax.xml.transform.TransformerFactory;\nimport javax.xml.transform.stream.StreamResult;\nimport javax.xml.transform.stream.StreamSource;\n\nparam(paramstr) {\n nameAndValue = paramstr.split(\"=\");\n if (nameAndValue.length != 2) {\n throw new RuntimeException(\"Wrong parameter format: \\\"\" + paramstr + \"\\\".\");\n }\n name = nameAndValue[0].trim();\n value = nameAndValue[1].trim();\n return this;\n}\n\nif ((sourceString == void) || (sourceString == null)) {\n throw new RuntimeException(\"sourceString must be specified\");\n}\n\nif ((xsltString == void) || (xsltString == null)) {\n throw new RuntimeException(\"xsltString must be specified\");\n}\n\nSource inSource = new StreamSource(new StringReader(sourceString));\nSource xslSource = new StreamSource(new StringReader(xsltString));\n\n// the factory patte
rn supports different XSLT processors\n// e.g. set the \"javax.xml.transform.TransformerFactory\" system property\nTransformerFactory tnfFact = TransformerFactory.newInstance();\nTransformer tnf = tnfFact.newTransformer(xslSource);\n\nif (paramList != void) {\n for (String paramstr : paramList) {\n p = param(paramstr);\n tnf.setParameter(p.name, p.value);\n }\n}\n\nWriter outputWriter = new StringWriter();\ntnf.transform(inSource, new StreamResult(outputWriter));\noutputString = outputWriter.toString();",
- "localworkerName" : "net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters",
- "inputPorts" : [ {
- "name" : "sourceString",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "xsltString",
- "depth" : 0,
- "type" : "String"
- }, {
- "name" : "paramList",
- "depth" : 1,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "outputString",
- "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/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
----------------------------------------------------------------------
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
deleted file mode 100644
index 35b50d0..0000000
--- a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
+++ /dev/null
@@ -1,44 +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>if ((bytes == void) || (bytes == null)) {
- throw new RuntimeException("The 'bytes' parameter must be specified");
-}
-if (encoding == void) {
- string = new String(bytes);
-} else {
- string = new String(bytes, encoding);
-}
-</script>
- <dependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>[B</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>bytes</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'application/octet-stream'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>encoding</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>string</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/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json
----------------------------------------------------------------------
diff --git a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json b/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json
deleted file mode 100644
index ae7f934..0000000
--- a/src/main/resources/org.embl.ebi.escience.scuflworkers.java.ByteArrayToString.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "classLoaderSharing" : "workflow",
- "script" : "if ((bytes == void) || (bytes == null)) {\n\tthrow new RuntimeException(\"The 'bytes' parameter must be specified\");\n}\nif (encoding == void) {\n\tstring = new String(bytes);\n} else {\n\tstring = new String(bytes, encoding);\n}\n",
- "localworkerName" : "org.embl.ebi.escience.scuflworkers.java.ByteArrayToString",
- "inputPorts" : [ {
- "name" : "bytes",
- "depth" : 0,
- "type" : "byte[]"
- }, {
- "name" : "encoding",
- "depth" : 0,
- "type" : "String"
- } ],
- "outputPorts" : [ {
- "name" : "string",
- "depth" : 0,
- "granularDepth" : 0
- } ],
- "isAltered" : false
-}
\ No newline at end of file