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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:49:38 UTC
[11/16] incubator-taverna-workbench-common-activities git commit:
Temporarily empty repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/b4725724/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
deleted file mode 100644
index 6e9adb4..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader
+++ /dev/null
@@ -1,76 +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>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/b4725724/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
deleted file mode 100644
index 1424433..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileReader.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "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/b4725724/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
deleted file mode 100644
index 88ac962..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter
+++ /dev/null
@@ -1,57 +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>
- 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/b4725724/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
deleted file mode 100644
index 5a9f368..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.io.TextFileWriter.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
- "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/b4725724/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
deleted file mode 100644
index b6263cf..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
+++ /dev/null
@@ -1,309 +0,0 @@
-<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/b4725724/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
deleted file mode 100644
index da1f005..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker.json
+++ /dev/null
@@ -1,44 +0,0 @@
-{
- "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/b4725724/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
deleted file mode 100644
index fa0748c..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
+++ /dev/null
@@ -1,229 +0,0 @@
-<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/b4725724/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
deleted file mode 100644
index 3144afd..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker.json
+++ /dev/null
@@ -1,36 +0,0 @@
-{
- "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/b4725724/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
deleted file mode 100644
index 8b7a680..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
+++ /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=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/b4725724/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
deleted file mode 100644
index feb26cc..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker.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=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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
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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
deleted file mode 100644
index 80f791a..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
+++ /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=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/b4725724/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
deleted file mode 100644
index e616f51..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker.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=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/b4725724/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
deleted file mode 100644
index 2ce601b..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker
+++ /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=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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.json
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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
deleted file mode 100644
index 8dfbdbe..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker.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=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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
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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
deleted file mode 100644
index aad694a..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker
+++ /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=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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.json
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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
deleted file mode 100644
index 3867455..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker.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=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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
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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
deleted file mode 100644
index c07b04e..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
+++ /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=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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.json
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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
deleted file mode 100644
index fc5b181..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker.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=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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
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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
deleted file mode 100644
index bf85c2b..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker
+++ /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=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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.json
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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
deleted file mode 100644
index 160ce92..0000000
--- a/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker.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=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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker
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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
deleted file mode 100644
index c82209f..0000000
--- a/taverna-localworker-activity-ui/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
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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
deleted file mode 100644
index 6e36120..0000000
--- a/taverna-localworker-activity-ui/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
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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
deleted file mode 100644
index b6f9337..0000000
--- a/taverna-localworker-activity-ui/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/b4725724/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
deleted file mode 100644
index 471e000..0000000
--- a/taverna-localworker-activity-ui/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/b4725724/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
deleted file mode 100644
index 71fef3c..0000000
--- a/taverna-localworker-activity-ui/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/b4725724/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
deleted file mode 100644
index 5e2a7df..0000000
--- a/taverna-localworker-activity-ui/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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.ncbi.PubMedESearchWorker
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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
deleted file mode 100644
index 37c440c..0000000
--- a/taverna-localworker-activity-ui/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/b4725724/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
deleted file mode 100644
index bd29f82..0000000
--- a/taverna-localworker-activity-ui/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/b4725724/taverna-localworker-activity-ui/src/main/resources/net.sourceforge.taverna.scuflworkers.net.BrowseUrl
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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
deleted file mode 100644
index a2317c5..0000000
--- a/taverna-localworker-activity-ui/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
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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
deleted file mode 100644
index 1a2155e..0000000
--- a/taverna-localworker-activity-ui/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