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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 11:24:58 UTC
[11/16] incubator-taverna-workbench-common-activities git commit:
Revert "Temporarily empty repository"
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
new file mode 100644
index 0000000..6e9adb4
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
@@ -0,0 +1,76 @@
+<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>BufferedReader getReader (String fileUrl, String encoding) throws IOException {
+ InputStreamReader reader;
+ try {
+ if (encoding == null) {
+ reader = new FileReader(fileUrl);
+ } else {
+ reader = new InputStreamReader(new FileInputStream(fileUrl),encoding);
+ }
+ }
+ catch (FileNotFoundException e) {
+ // try a real URL instead
+ URL url = new URL(fileUrl);
+ if (encoding == null) {
+ reader = new InputStreamReader (url.openStream());
+ } else {
+ reader = new InputStreamReader (url.openStream(), encoding);
+ }
+ }
+ return new BufferedReader(reader);
+ }
+
+
+
+StringBuffer sb = new StringBuffer(4000);
+
+if (encoding == void) {
+ encoding = null;
+}
+
+BufferedReader in = getReader(fileurl, encoding);
+String str;
+String lineEnding = System.getProperty("line.separator");
+
+while ((str = in.readLine()) != null) {
+ sb.append(str);
+ sb.append(lineEnding);
+}
+in.close();
+filecontents = sb.toString();
+
+</script>
+ <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>
+ <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>filecontents</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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json
new file mode 100644
index 0000000..1424433
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json
@@ -0,0 +1,20 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "BufferedReader getReader (String fileUrl, String encoding) throws IOException {\n\t\tInputStreamReader reader;\n\t\ttry {\n\t\t\tif (encoding == null) {\n\t\t\t\treader = new FileReader(fileUrl);\n\t\t\t} else {\n\t\t\t\treader = new InputStreamReader(new FileInputStream(fileUrl),encoding); \n\t\t\t}\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\tif (encoding == null) {\n\t\t\t\treader = new InputStreamReader (url.openStream());\n\t\t\t} else {\n\t\t\t\treader = new InputStreamReader (url.openStream(), encoding);\n\t\t\t}\n\t\t}\n\t\treturn new BufferedReader(reader);\n\t}\n\n\n\nStringBuffer sb = new StringBuffer(4000);\n\nif (encoding == void) {\n\tencoding = null;\n}\n\nBufferedReader in = getReader(fileurl, encoding);\nString str;\nString lineEnding = System.getProperty(\"line.separator\");\n\nwhile ((str = in.readLine()) != null) {\n\tsb.append(str);\n\tsb.append(lineEnding);\n}\nin.close();
\nfilecontents = sb.toString();\n \n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.TextFileReader",
+ "inputPorts" : [ {
+ "name" : "fileurl",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "encoding",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "filecontents",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
new file mode 100644
index 0000000..88ac962
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
@@ -0,0 +1,57 @@
+<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>
+ BufferedWriter out;
+ if (encoding == void) {
+ out = new BufferedWriter(new FileWriter(outputFile));
+ }
+ else {
+ out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), encoding));
+ }
+out.write(filecontents);
+out.flush();
+out.close();
+outputFile = filecontents;
+</script>
+ <dependencies />
+ <inputs>
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+ <handledReferenceSchemes />
+ <translatedElementType>java.lang.String</translatedElementType>
+ <allowsLiteralValues>true</allowsLiteralValues>
+ <name>outputFile</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>filecontents</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>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>outputFile</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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json
new file mode 100644
index 0000000..5a9f368
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json
@@ -0,0 +1,24 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "\n BufferedWriter out;\n if (encoding == void) {\n \tout = new BufferedWriter(new FileWriter(outputFile));\n }\n else {\n \tout = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), encoding)); \n }\nout.write(filecontents);\nout.flush();\nout.close();\noutputFile = filecontents;\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.io.TextFileWriter",
+ "inputPorts" : [ {
+ "name" : "outputFile",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "filecontents",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "encoding",
+ "depth" : 0,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "outputFile",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
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diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
new file mode 100644
index 0000000..b6263cf
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
@@ -0,0 +1,309 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="password" to="password" /><map from="userid" to="userid" /><map from="params" to="params" /><map from="url" to="url" /><map from="provideXml" to="provideXml" /><map from="driver" to="driver" /><map from="sql" to="sql" /></inputMap><outputMap><map from="resultList" to="resultList" /><map from="xmlresults" to="xmlresults" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+
+ <script>
+ import java.sql.Driver;
+import java.sql.DriverManager;
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.ResultSetMetaData;
+import java.sql.SQLException;
+
+import javax.sql.rowset.WebRowSet;
+
+import com.sun.rowset.WebRowSetImpl;
+
+
+
+if ((driver == void) || (driver == null) || driver.equals("")) {
+ throw new RuntimeException("The driver must be specified");
+}
+
+if ((url == void) || (url == null) || url.equals("")) {
+ throw new RuntimeException("The url must be specified");
+}
+
+boolean provideXmlBoolean = ((provideXml != void) && (provideXml != null) && Boolean.valueOf(provideXml));
+
+if ((params == void) || (params == null)) {
+ params = new ArrayList();
+}
+
+if ((sql == void) || (sql == null) || sql.equals("")) {
+ throw new RuntimeException("The sql must be specified");
+}
+
+Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
+
+if (c == null) {
+ throw new RuntimeException("Class " + driver + " not found");
+}
+
+Driver d = c.newInstance();
+if (d == null) {
+ throw new RuntimeException("Could not create instance of driver");
+}
+
+Properties p = new Properties();
+
+if ((userid == void) || (userid == null)) {
+ userid = "";
+}
+
+p.setProperty("user", userid);
+
+if ((password == void) || (password == null)) {
+ password = "";
+}
+
+p.setProperty("password", password);
+
+Connection con = null;
+PreparedStatement ps = null;
+ResultSet rs = null;
+try {
+
+ con = d.connect(url, p);
+ ps = con.prepareStatement(sql);
+
+ int paramSize = params.size();
+ for (int i = 0; i < paramSize; i++) {
+ ps.setObject(i + 1, params.get(i));
+ }
+
+ rs = ps.executeQuery();
+
+ if (provideXmlBoolean) {
+ WebRowSet webrs = new WebRowSetImpl();
+ StringWriter sw = new StringWriter();
+ webrs.writeXml(rs, sw);
+ xmlresults = sw.toString();
+ } else {
+ xmlresults = "";
+ }
+
+ try {
+ rs.beforeFirst();
+ } catch (SQLException e) {
+ // redo the query
+ rs = ps.executeQuery();
+ }
+
+ ResultSetMetaData rsmd = rs.getMetaData();
+ int numCols = rsmd.getColumnCount();
+ resultList = new ArrayList();
+
+ // put the results into the results list.
+ while (rs.next()) {
+ List row = new ArrayList(numCols);
+ for (int i = 0; i < numCols; i++) {
+ String str = rs.getString(i + 1);
+ row.add(str == null ? "null" : str);
+ }
+ resultList.add(row);
+ }
+}
+finally {
+ if (rs != null) {
+ rs.close();
+ }
+ if (ps != null) {
+ ps.close();
+ }
+ if (con != null) {
+ con.close();
+ }
+}
+
+
+ </script>
+
+ <dependencies />
+
+ <classLoaderSharing>system</classLoaderSharing>
+
+ <localDependencies />
+
+ <artifactDependencies />
+
+ <inputs>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>driver</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>password</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>userid</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>url</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>provideXml</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>sql</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>params</name>
+
+ <depth>1</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>2</granularDepth>
+
+ <name>resultList</name>
+
+ <depth>2</depth>
+
+ <mimeTypes>
+
+ <string>text/plain</string>
+
+ </mimeTypes>
+
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+
+ <granularDepth>0</granularDepth>
+
+ <name>xmlresults</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><annotations /></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json
new file mode 100644
index 0000000..da1f005
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json
@@ -0,0 +1,44 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "\n import java.sql.Driver;\nimport java.sql.DriverManager;\nimport java.sql.Connection;\nimport java.sql.PreparedStatement;\nimport java.sql.ResultSet;\nimport java.sql.ResultSetMetaData;\nimport java.sql.SQLException;\n\nimport javax.sql.rowset.WebRowSet;\n\nimport com.sun.rowset.WebRowSetImpl;\n\n\n\nif ((driver == void) || (driver == null) || driver.equals(\"\")) {\n\tthrow new RuntimeException(\"The driver must be specified\");\n}\n\nif ((url == void) || (url == null) || url.equals(\"\")) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nboolean provideXmlBoolean = ((provideXml != void) && (provideXml != null) && Boolean.valueOf(provideXml));\n\nif ((params == void) || (params == null)) {\n params = new ArrayList();\n}\n\nif ((sql == void) || (sql == null) || sql.equals(\"\")) {\n\tthrow new RuntimeException(\"The sql must be specified\");\n}\n\nClass c = Thread.currentThread().getContextClassLoader().loadClass(driver);\n\nif (c == null) {\n\t
throw new RuntimeException(\"Class \" + driver + \" not found\");\n}\n\nDriver d = c.newInstance();\nif (d == null) {\n\tthrow new RuntimeException(\"Could not create instance of driver\");\n}\n\nProperties p = new Properties();\n\nif ((userid == void) || (userid == null)) {\n\tuserid = \"\";\n}\n\np.setProperty(\"user\", userid);\n\nif ((password == void) || (password == null)) {\n\tpassword = \"\";\n}\n\np.setProperty(\"password\", password);\n\nConnection con = null;\nPreparedStatement ps = null;\nResultSet rs = null;\ntry {\n\n\tcon = d.connect(url, p);\n\tps = con.prepareStatement(sql);\n\n\tint paramSize = params.size();\n\tfor (int i = 0; i < paramSize; i++) {\n\t\tps.setObject(i + 1, params.get(i));\n\t}\n\n\trs = ps.executeQuery();\n\n\tif (provideXmlBoolean) {\n\t\tWebRowSet webrs = new WebRowSetImpl();\n\t\tStringWriter sw = new StringWriter();\n\t\twebrs.writeXml(rs, sw);\n\t\txmlresults = sw.toString();\n\t} else {\n\t\txmlresults = \"\";\n\t}\n\n\ttry {\n\t\trs.beforeF
irst();\n\t} catch (SQLException e) {\n\t\t// redo the query\n\t\trs = ps.executeQuery();\n\t}\n\n\tResultSetMetaData rsmd = rs.getMetaData();\n\tint numCols = rsmd.getColumnCount();\n\tresultList = new ArrayList();\n\t\n\t// put the results into the results list.\n\twhile (rs.next()) {\n\t\tList row = new ArrayList(numCols);\n\t\tfor (int i = 0; i < numCols; i++) {\n\t\t\tString str = rs.getString(i + 1); \n\t\t\trow.add(str == null ? \"null\" : str); \n\t\t}\n\t\tresultList.add(row);\n\t}\n}\nfinally {\n\tif (rs != null) {\n\t\trs.close();\n\t}\n\tif (ps != null) {\n\t\tps.close();\n\t}\n\tif (con != null) {\n\t\tcon.close();\n\t}\n}\n \n\n ",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker",
+ "inputPorts" : [ {
+ "name" : "driver",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "password",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "userid",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "provideXml",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "sql",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "params",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "resultList",
+ "depth" : 2,
+ "granularDepth" : 2
+ }, {
+ "name" : "xmlresults",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
new file mode 100644
index 0000000..fa0748c
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
@@ -0,0 +1,229 @@
+<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="password" to="password" /><map from="userid" to="userid" /><map from="params" to="params" /><map from="url" to="url" /><map from="provideXml" to="provideXml" /><map from="driver" to="driver" /><map from="sql" to="sql" /></inputMap><outputMap><map from="resultList" to="resultList" /><map from="xmlresults" to="xmlresults" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+
+ <script>import java.sql.Driver;
+import java.sql.DriverManager;
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+
+if ((driver == void) || (driver == null) || driver.equals("")) {
+ throw new RuntimeException("The driver must be specified");
+}
+
+if ((url == void) || (url == null) || url.equals("")) {
+ throw new RuntimeException("The url must be specified");
+}
+
+if ((params == void) || (params == null)) {
+ params = new ArrayList();
+}
+
+if ((sql == void) || (sql == null) || sql.equals("")) {
+ throw new RuntimeException("The sql must be specified");
+}
+
+Class c = Thread.currentThread().getContextClassLoader().loadClass(driver);
+
+if (c == null) {
+ throw new RuntimeException("Class " + driver + " not found");
+}
+
+Driver d = c.newInstance();
+if (d == null) {
+ throw new RuntimeException("Could not create instance of driver");
+}
+
+Properties p = new Properties();
+
+if ((userid == void) || (userid == null)) {
+ userid = "";
+}
+
+p.setProperty("user", userid);
+
+if ((password == void) || (password == null)) {
+ password = "";
+}
+
+p.setProperty("password", password);
+
+Connection con = null;
+PreparedStatement ps = null;
+
+try {
+ con = d.connect(url, p);
+ ps = con.prepareStatement(sql);
+
+ int paramsSize = params.size();
+ for (int i = 0; i < paramsSize; i++) {
+ ps.setObject(i + 1, params.get(i));
+ }
+
+ ps.executeUpdate();
+
+ resultList = "update successful";
+}
+finally {
+ if (ps != null) {
+ ps.close();
+ }
+ if (con != null) {
+ con.close();
+ }
+}
+
+</script>
+
+ <dependencies />
+
+ <classLoaderSharing>system</classLoaderSharing>
+ <localDependencies />
+
+ <artifactDependencies />
+
+ <inputs>
+
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+
+ <handledReferenceSchemes />
+
+ <translatedElementType>java.lang.String</translatedElementType>
+
+ <allowsLiteralValues>true</allowsLiteralValues>
+
+ <name>driver</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>password</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>userid</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>url</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>sql</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>params</name>
+
+ <depth>1</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>resultList</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><annotations /></activity>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json
new file mode 100644
index 0000000..3144afd
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json
@@ -0,0 +1,36 @@
+{
+ "classLoaderSharing" : "workflow",
+ "script" : "import java.sql.Driver;\nimport java.sql.DriverManager;\nimport java.sql.Connection;\nimport java.sql.PreparedStatement;\n\nif ((driver == void) || (driver == null) || driver.equals(\"\")) {\n\tthrow new RuntimeException(\"The driver must be specified\");\n}\n\nif ((url == void) || (url == null) || url.equals(\"\")) {\n\tthrow new RuntimeException(\"The url must be specified\");\n}\n\nif ((params == void) || (params == null)) {\n params = new ArrayList();\n}\n\nif ((sql == void) || (sql == null) || sql.equals(\"\")) {\n\tthrow new RuntimeException(\"The sql must be specified\");\n}\n\nClass c = Thread.currentThread().getContextClassLoader().loadClass(driver);\n\nif (c == null) {\n\tthrow new RuntimeException(\"Class \" + driver + \" not found\");\n}\n\nDriver d = c.newInstance();\nif (d == null) {\n\tthrow new RuntimeException(\"Could not create instance of driver\");\n}\n\nProperties p = new Properties();\n\nif ((userid == void) || (userid == null)) {\n\tuserid = \"
\";\n}\n\np.setProperty(\"user\", userid);\n\nif ((password == void) || (password == null)) {\n\tpassword = \"\";\n}\n\np.setProperty(\"password\", password);\n\nConnection con = null;\nPreparedStatement ps = null;\n\ntry {\n\tcon = d.connect(url, p);\n\tps = con.prepareStatement(sql);\n\n\tint paramsSize = params.size();\n\tfor (int i = 0; i < paramsSize; i++) {\n\t\tps.setObject(i + 1, params.get(i));\n\t}\n\n\tps.executeUpdate();\n\n\tresultList = \"update successful\";\n}\nfinally {\n\tif (ps != null) {\n\t\tps.close();\n\t}\n\tif (con != null) {\n\t\tcon.close();\n\t}\n}\n\n",
+ "localworkerName" : "net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker",
+ "inputPorts" : [ {
+ "name" : "driver",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "password",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "userid",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "url",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "sql",
+ "depth" : 0,
+ "type" : "String"
+ }, {
+ "name" : "params",
+ "depth" : 1,
+ "type" : "String"
+ } ],
+ "outputPorts" : [ {
+ "name" : "resultList",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
new file mode 100644
index 0000000..8b7a680
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
@@ -0,0 +1,45 @@
+<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=nucleotide&retmode=text&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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json
new file mode 100644
index 0000000..feb26cc
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.json
@@ -0,0 +1,16 @@
+{
+ "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=nucleotide&retmode=text&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.NucleotideFastaWorker",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
new file mode 100644
index 0000000..80f791a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
@@ -0,0 +1,45 @@
+<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=gb&db=nucleotide&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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json
new file mode 100644
index 0000000..e616f51
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.json
@@ -0,0 +1,16 @@
+{
+ "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=gb&db=nucleotide&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.NucleotideGBSeqWorker",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
new file mode 100644
index 0000000..2ce601b
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
@@ -0,0 +1,45 @@
+<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=nucleotide&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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json
new file mode 100644
index 0000000..8dfbdbe
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "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=nucleotide&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.NucleotideINSDSeqXMLWorker",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
new file mode 100644
index 0000000..aad694a
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
@@ -0,0 +1,45 @@
+<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=nucleotide&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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json
new file mode 100644
index 0000000..3867455
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "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=nucleotide&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.NucleotideTinySeqXMLWorker",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
new file mode 100644
index 0000000..c07b04e
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
@@ -0,0 +1,45 @@
+<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=text&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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json
new file mode 100644
index 0000000..fc5b181
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json
@@ -0,0 +1,16 @@
+{
+ "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=text&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.ProteinFastaWorker",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
new file mode 100644
index 0000000..bf85c2b
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
@@ -0,0 +1,45 @@
+<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=gb&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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json
new file mode 100644
index 0000000..160ce92
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json
@@ -0,0 +1,16 @@
+{
+ "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=gb&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.ProteinGBSeqWorker",
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
new file mode 100644
index 0000000..c82209f
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
@@ -0,0 +1,45 @@
+<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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
new file mode 100644
index 0000000..6e36120
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
new file mode 100644
index 0000000..b6f9337
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker
@@ -0,0 +1,45 @@
+<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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
new file mode 100644
index 0000000..471e000
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker.json
@@ -0,0 +1,16 @@
+{
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
new file mode 100644
index 0000000..71fef3c
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker
@@ -0,0 +1,68 @@
+<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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
new file mode 100644
index 0000000..5e2a7df
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedEFetchWorker.json
@@ -0,0 +1,24 @@
+{
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
new file mode 100644
index 0000000..37c440c
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
@@ -0,0 +1,124 @@
+<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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
new file mode 100644
index 0000000..bd29f82
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker.json
@@ -0,0 +1,44 @@
+{
+ "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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
new file mode 100644
index 0000000..a2317c5
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
@@ -0,0 +1,31 @@
+<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/54050685/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
----------------------------------------------------------------------
diff --git a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
new file mode 100644
index 0000000..1a2155e
--- /dev/null
+++ b/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl.json
@@ -0,0 +1,11 @@
+{
+ "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