You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:40:41 UTC
[50/51] [partial] incubator-taverna-language git commit: temporarily
empty repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-baclava-language/src/main/resources/xsd/xscufl.xsd
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/src/main/resources/xsd/xscufl.xsd b/taverna-baclava-language/src/main/resources/xsd/xscufl.xsd
deleted file mode 100644
index 75d51b3..0000000
--- a/taverna-baclava-language/src/main/resources/xsd/xscufl.xsd
+++ /dev/null
@@ -1,41 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-Licensed to the Apache Software Foundation (ASF) under one
-or more contributor license agreements. See the NOTICE file
-distributed with this work for additional information
-regarding copyright ownership. The ASF licenses this file
-to you under the Apache License, Version 2.0 (the
-"License"); you may not use this file except in compliance
-with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing,
-software distributed under the License is distributed on an
-"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-KIND, either express or implied. See the License for the
-specific language governing permissions and limitations
-under the License.
--->
-<schema xmlns="http://www.w3.org/2001/XMLSchema" targetNamespace="http://org.embl.ebi.escience/xscufl/0.1alpha" xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" elementFormDefault="qualified">
-
- <complexType name="MimeTypesType">
- <sequence>
- <element ref="s:mimeType" minOccurs="0" maxOccurs="unbounded"></element>
- </sequence>
- </complexType>
-
- <element name="metadata" type="s:MetadataType"></element>
-
- <complexType name="MetadataType">
- <sequence>
- <element ref="s:mimeTypes" minOccurs="1" maxOccurs="1"></element>
- </sequence>
- </complexType>
-
- <element name="mimeTypes" type="s:MimeTypesType"></element>
-
-
- <element name="mimeType" type="string"></element>
-
-</schema>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-baclava-language/src/test/java/org/apache/taverna/baclava/TestExample1.java
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/src/test/java/org/apache/taverna/baclava/TestExample1.java b/taverna-baclava-language/src/test/java/org/apache/taverna/baclava/TestExample1.java
deleted file mode 100644
index c27dea1..0000000
--- a/taverna-baclava-language/src/test/java/org/apache/taverna/baclava/TestExample1.java
+++ /dev/null
@@ -1,96 +0,0 @@
-package org.apache.taverna.baclava;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.util.List;
-
-import javax.xml.bind.JAXBException;
-
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
-
-public class TestExample1 {
-
- private static DataThingMapType dt;
-
- private static String[] expectedKeys = new String[] {"status", "proteinIDs", "output"};
-
- private static String[] expectedMimeTypes = new String[] {"text/plain", "text/plain", "application/octet-stream"};
-
- @BeforeClass
- public static void setUpClass() throws FileNotFoundException, JAXBException {
- ClassLoader classLoader = TestExample1.class.getClassLoader();
- File file = new File(classLoader.getResource("example1.xml").getFile());
- dt = BaclavaReader.readBaclava(new FileReader(file));
- }
-
- @Test
- public void checkRead() {
- Assert.assertNotNull("Unable to parse example1.xml", dt);
- }
-
- @Test
- public void checkNumberOfDataThings() {
- Assert.assertEquals("There should be three data things", 3, dt.getDataThing().size());
- }
-
- @Test
- public void checkDataThingKeys() {
- for (String k : expectedKeys) {
- Assert.assertNotNull(k + " should be there", getDataThingTypeByKey(k));
- }
- }
-
- @Test
- public void checkDataThingMimeTypes() {
- for (int i = 0; i < expectedKeys.length; i++) {
- String k = expectedKeys[i];
- DataThingType d = getDataThingTypeByKey(k);
- MyGridDataDocumentType doc = d.getMyGridDataDocument();
- Assert.assertNotNull("myGridDataDocument of " + k + " is missing", doc);
- MetadataType meta = doc.getMetadata();
- Assert.assertNotNull("metadata of " + k + " is missing", meta);
- MimeTypesType types = meta.getMimeTypes();
- Assert.assertNotNull("mimetypes of " + k + " is missing", types);
- List<String> mimeTypes = types.getMimeType();
- Assert.assertNotNull("mimetypes of " + k + " is null", mimeTypes);
- Assert.assertNotEquals("mimetypes of " + k + " is empty", 0, mimeTypes);
- String firstMimeType = mimeTypes.get(0);
- Assert.assertEquals("mimetype of " + k + " is wrong", expectedMimeTypes[i], firstMimeType);
- }
- }
-
- private DataThingType getDataThingTypeByKey(String key) {
- DataThingType result = null;
- for (DataThingType d : dt.getDataThing()) {
- if (d.getKey().equals(key)) {
- result = d;
- break;
- }
- }
- return result;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-baclava-language/src/test/java/org/apache/taverna/baclava/TestRoundTrip.java
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/src/test/java/org/apache/taverna/baclava/TestRoundTrip.java b/taverna-baclava-language/src/test/java/org/apache/taverna/baclava/TestRoundTrip.java
deleted file mode 100644
index 613a252..0000000
--- a/taverna-baclava-language/src/test/java/org/apache/taverna/baclava/TestRoundTrip.java
+++ /dev/null
@@ -1,59 +0,0 @@
-package org.apache.taverna.baclava;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.StringReader;
-import java.io.StringWriter;
-
-import javax.xml.bind.JAXBException;
-
-import org.junit.Assert;
-import org.junit.Test;
-
-public class TestRoundTrip {
-
- private static String[] fileNames = new String[] {"example1.xml", "example2.xml"};
-
- @Test
- public void testRoundTrips() throws JAXBException, FileNotFoundException {
- for (String fileName : fileNames) {
- ClassLoader classLoader = getClass().getClassLoader();
- File file = new File(classLoader.getResource(fileName).getFile());
- DataThingMapType o = BaclavaReader.readBaclava(new FileReader(file));
-
- StringWriter initialWriter = new StringWriter();
- BaclavaWriter.writeBaclava(o, initialWriter);
- String initialString = initialWriter.toString();
-
- DataThingMapType reread = BaclavaReader.readBaclava(new StringReader(initialString));
- StringWriter rewriteWriter = new StringWriter();
- BaclavaWriter.writeBaclava(reread, rewriteWriter);
- String rewrittenString = rewriteWriter.toString();
- Assert.assertEquals(initialString, rewrittenString);
- }
-
- }
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-baclava-language/src/test/resources/example1.xml
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/src/test/resources/example1.xml b/taverna-baclava-language/src/test/resources/example1.xml
deleted file mode 100644
index c39e73c..0000000
--- a/taverna-baclava-language/src/test/resources/example1.xml
+++ /dev/null
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!--
-Licensed to the Apache Software Foundation (ASF) under one
-or more contributor license agreements. See the NOTICE file
-distributed with this work for additional information
-regarding copyright ownership. The ASF licenses this file
-to you under the Apache License, Version 2.0 (the
-"License"); you may not use this file except in compliance
-with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing,
-software distributed under the License is distributed on an
-"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-KIND, either express or implied. See the License for the
-specific language governing permissions and limitations
-under the License.
--->
-
-<b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
- <b:dataThing key="status">
- <b:myGridDataDocument lsid="" syntactictype="l('text/plain')">
- <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha">
- <s:mimeTypes>
- <s:mimeType>text/plain</s:mimeType>
- </s:mimeTypes>
- </s:metadata>
- <b:partialOrder lsid="" type="list">
- <b:relationList />
- <b:itemList>
- <b:dataElement lsid="" index="0">
- <b:dataElementData>RklOSVNIRUQ=</b:dataElementData>
- </b:dataElement>
- </b:itemList>
- </b:partialOrder>
- </b:myGridDataDocument>
- </b:dataThing>
- <b:dataThing key="proteinIDs">
- <b:myGridDataDocument lsid="" syntactictype="'text/plain'">
- <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha">
- <s:mimeTypes>
- <s:mimeType>text/plain</s:mimeType>
- </s:mimeTypes>
- </s:metadata>
- <b:dataElement lsid="">
- <b:dataElementData>UDE1MDE4</b:dataElementData>
- </b:dataElement>
- </b:myGridDataDocument>
- </b:dataThing>
- <b:dataThing key="output">
- <b:myGridDataDocument lsid="" syntactictype="l('application/octet-stream')">
- <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha">
- <s:mimeTypes>
- <s:mimeType>application/octet-stream</s:mimeType>
- </s:mimeTypes>
- </s:metadata>
- <b:partialOrder lsid="" type="list">
- <b:relationList />
- <b:itemList>
- <b:dataElement lsid="" index="0">
- <b:dataElementData>SUQgICBnaXwxMjYyNzl8c3B8UDE1MDE4LjF8TElGX0hVTUFOCkZUICAgU0lHTkFMICAgICAgICAx
-ICAgICAzMiAgICAgICAKRlQgICBET01BSU4gICAgICAgIDEgICAgICAyICAgICAgIE4tUkVHSU9O
-LgpGVCAgIERPTUFJTiAgICAgICAgMyAgICAgMTQgICAgICAgSC1SRUdJT04uCkZUICAgRE9NQUlO
-ICAgICAgIDE1ICAgICAzMiAgICAgICBDLVJFR0lPTi4KRlQgICBET01BSU4gICAgICAgMzMgICAg
-MjAyICAgICAgIE5PTiBDWVRPUExBU01JQy4KLy8K</b:dataElementData>
- </b:dataElement>
- </b:itemList>
- </b:partialOrder>
- </b:myGridDataDocument>
- </b:dataThing>
-</b:dataThingMap>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-baclava-language/src/test/resources/example2.xml
----------------------------------------------------------------------
diff --git a/taverna-baclava-language/src/test/resources/example2.xml b/taverna-baclava-language/src/test/resources/example2.xml
deleted file mode 100644
index ff05414..0000000
--- a/taverna-baclava-language/src/test/resources/example2.xml
+++ /dev/null
@@ -1,370 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!--
-Licensed to the Apache Software Foundation (ASF) under one
-or more contributor license agreements. See the NOTICE file
-distributed with this work for additional information
-regarding copyright ownership. The ASF licenses this file
-to you under the Apache License, Version 2.0 (the
-"License"); you may not use this file except in compliance
-with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing,
-software distributed under the License is distributed on an
-"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-KIND, either express or implied. See the License for the
-specific language governing permissions and limitations
-under the License.
--->
-
-<b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
- <b:dataThing key="strings">
- <b:myGridDataDocument lsid="" syntactictype="l(l('text/plain'))">
- <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha">
- <s:mimeTypes>
- <s:mimeType>text/plain</s:mimeType>
- </s:mimeTypes>
- </s:metadata>
- <b:partialOrder lsid="" type="list">
- <b:relationList>
- <b:relation parent="0" child="1" />
- </b:relationList>
- <b:itemList>
- <b:partialOrder lsid="" type="list" index="0">
- <b:relationList>
- <b:relation parent="0" child="1" />
- <b:relation parent="1" child="2" />
- <b:relation parent="2" child="3" />
- <b:relation parent="3" child="4" />
- <b:relation parent="4" child="5" />
- <b:relation parent="5" child="6" />
- <b:relation parent="6" child="7" />
- <b:relation parent="7" child="8" />
- <b:relation parent="8" child="9" />
- <b:relation parent="9" child="10" />
- <b:relation parent="10" child="11" />
- <b:relation parent="11" child="12" />
- <b:relation parent="12" child="13" />
- <b:relation parent="13" child="14" />
- <b:relation parent="14" child="15" />
- <b:relation parent="15" child="16" />
- <b:relation parent="16" child="17" />
- <b:relation parent="17" child="18" />
- <b:relation parent="18" child="19" />
- <b:relation parent="19" child="20" />
- <b:relation parent="20" child="21" />
- <b:relation parent="21" child="22" />
- <b:relation parent="22" child="23" />
- <b:relation parent="23" child="24" />
- <b:relation parent="24" child="25" />
- <b:relation parent="25" child="26" />
- <b:relation parent="26" child="27" />
- <b:relation parent="27" child="28" />
- <b:relation parent="28" child="29" />
- <b:relation parent="29" child="30" />
- <b:relation parent="30" child="31" />
- <b:relation parent="31" child="32" />
- <b:relation parent="32" child="33" />
- <b:relation parent="33" child="34" />
- <b:relation parent="34" child="35" />
- <b:relation parent="35" child="36" />
- <b:relation parent="36" child="37" />
- <b:relation parent="37" child="38" />
- <b:relation parent="38" child="39" />
- </b:relationList>
- <b:itemList>
- <b:dataElement lsid="" index="0">
- <b:dataElementData>U3RyaW5nMA==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="1">
- <b:dataElementData>U3RyaW5nMQ==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="2">
- <b:dataElementData>U3RyaW5nMg==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="3">
- <b:dataElementData>U3RyaW5nMw==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="4">
- <b:dataElementData>U3RyaW5nNA==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="5">
- <b:dataElementData>U3RyaW5nNQ==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="6">
- <b:dataElementData>U3RyaW5nNg==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="7">
- <b:dataElementData>U3RyaW5nNw==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="8">
- <b:dataElementData>U3RyaW5nOA==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="9">
- <b:dataElementData>U3RyaW5nOQ==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="10">
- <b:dataElementData>U3RyaW5nMTA=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="11">
- <b:dataElementData>U3RyaW5nMTE=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="12">
- <b:dataElementData>U3RyaW5nMTI=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="13">
- <b:dataElementData>U3RyaW5nMTM=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="14">
- <b:dataElementData>U3RyaW5nMTQ=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="15">
- <b:dataElementData>U3RyaW5nMTU=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="16">
- <b:dataElementData>U3RyaW5nMTY=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="17">
- <b:dataElementData>U3RyaW5nMTc=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="18">
- <b:dataElementData>U3RyaW5nMTg=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="19">
- <b:dataElementData>U3RyaW5nMTk=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="20">
- <b:dataElementData>U3RyaW5nMjA=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="21">
- <b:dataElementData>U3RyaW5nMjE=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="22">
- <b:dataElementData>U3RyaW5nMjI=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="23">
- <b:dataElementData>U3RyaW5nMjM=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="24">
- <b:dataElementData>U3RyaW5nMjQ=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="25">
- <b:dataElementData>U3RyaW5nMjU=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="26">
- <b:dataElementData>U3RyaW5nMjY=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="27">
- <b:dataElementData>U3RyaW5nMjc=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="28">
- <b:dataElementData>U3RyaW5nMjg=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="29">
- <b:dataElementData>U3RyaW5nMjk=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="30">
- <b:dataElementData>U3RyaW5nMzA=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="31">
- <b:dataElementData>U3RyaW5nMzE=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="32">
- <b:dataElementData>U3RyaW5nMzI=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="33">
- <b:dataElementData>U3RyaW5nMzM=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="34">
- <b:dataElementData>U3RyaW5nMzQ=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="35">
- <b:dataElementData>U3RyaW5nMzU=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="36">
- <b:dataElementData>U3RyaW5nMzY=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="37">
- <b:dataElementData>U3RyaW5nMzc=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="38">
- <b:dataElementData>U3RyaW5nMzg=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="39">
- <b:dataElementData>U3RyaW5nMzk=</b:dataElementData>
- </b:dataElement>
- </b:itemList>
- </b:partialOrder>
- <b:partialOrder lsid="" type="list" index="1">
- <b:relationList>
- <b:relation parent="0" child="1" />
- <b:relation parent="1" child="2" />
- <b:relation parent="2" child="3" />
- <b:relation parent="3" child="4" />
- <b:relation parent="4" child="5" />
- <b:relation parent="5" child="6" />
- <b:relation parent="6" child="7" />
- <b:relation parent="7" child="8" />
- <b:relation parent="8" child="9" />
- <b:relation parent="9" child="10" />
- <b:relation parent="10" child="11" />
- <b:relation parent="11" child="12" />
- <b:relation parent="12" child="13" />
- <b:relation parent="13" child="14" />
- <b:relation parent="14" child="15" />
- <b:relation parent="15" child="16" />
- <b:relation parent="16" child="17" />
- <b:relation parent="17" child="18" />
- <b:relation parent="18" child="19" />
- <b:relation parent="19" child="20" />
- <b:relation parent="20" child="21" />
- <b:relation parent="21" child="22" />
- <b:relation parent="22" child="23" />
- <b:relation parent="23" child="24" />
- <b:relation parent="24" child="25" />
- <b:relation parent="25" child="26" />
- <b:relation parent="26" child="27" />
- <b:relation parent="27" child="28" />
- <b:relation parent="28" child="29" />
- <b:relation parent="29" child="30" />
- <b:relation parent="30" child="31" />
- <b:relation parent="31" child="32" />
- <b:relation parent="32" child="33" />
- <b:relation parent="33" child="34" />
- <b:relation parent="34" child="35" />
- <b:relation parent="35" child="36" />
- <b:relation parent="36" child="37" />
- <b:relation parent="37" child="38" />
- <b:relation parent="38" child="39" />
- </b:relationList>
- <b:itemList>
- <b:dataElement lsid="" index="0">
- <b:dataElementData>U3RyaW5nMA==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="1">
- <b:dataElementData>U3RyaW5nMQ==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="2">
- <b:dataElementData>U3RyaW5nMg==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="3">
- <b:dataElementData>U3RyaW5nMw==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="4">
- <b:dataElementData>U3RyaW5nNA==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="5">
- <b:dataElementData>U3RyaW5nNQ==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="6">
- <b:dataElementData>U3RyaW5nNg==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="7">
- <b:dataElementData>U3RyaW5nNw==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="8">
- <b:dataElementData>U3RyaW5nOA==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="9">
- <b:dataElementData>U3RyaW5nOQ==</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="10">
- <b:dataElementData>U3RyaW5nMTA=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="11">
- <b:dataElementData>U3RyaW5nMTE=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="12">
- <b:dataElementData>U3RyaW5nMTI=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="13">
- <b:dataElementData>U3RyaW5nMTM=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="14">
- <b:dataElementData>U3RyaW5nMTQ=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="15">
- <b:dataElementData>U3RyaW5nMTU=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="16">
- <b:dataElementData>U3RyaW5nMTY=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="17">
- <b:dataElementData>U3RyaW5nMTc=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="18">
- <b:dataElementData>U3RyaW5nMTg=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="19">
- <b:dataElementData>U3RyaW5nMTk=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="20">
- <b:dataElementData>U3RyaW5nMjA=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="21">
- <b:dataElementData>U3RyaW5nMjE=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="22">
- <b:dataElementData>U3RyaW5nMjI=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="23">
- <b:dataElementData>U3RyaW5nMjM=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="24">
- <b:dataElementData>U3RyaW5nMjQ=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="25">
- <b:dataElementData>U3RyaW5nMjU=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="26">
- <b:dataElementData>U3RyaW5nMjY=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="27">
- <b:dataElementData>U3RyaW5nMjc=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="28">
- <b:dataElementData>U3RyaW5nMjg=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="29">
- <b:dataElementData>U3RyaW5nMjk=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="30">
- <b:dataElementData>U3RyaW5nMzA=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="31">
- <b:dataElementData>U3RyaW5nMzE=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="32">
- <b:dataElementData>U3RyaW5nMzI=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="33">
- <b:dataElementData>U3RyaW5nMzM=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="34">
- <b:dataElementData>U3RyaW5nMzQ=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="35">
- <b:dataElementData>U3RyaW5nMzU=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="36">
- <b:dataElementData>U3RyaW5nMzY=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="37">
- <b:dataElementData>U3RyaW5nMzc=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="38">
- <b:dataElementData>U3RyaW5nMzg=</b:dataElementData>
- </b:dataElement>
- <b:dataElement lsid="" index="39">
- <b:dataElementData>U3RyaW5nMzk=</b:dataElementData>
- </b:dataElement>
- </b:itemList>
- </b:partialOrder>
- </b:itemList>
- </b:partialOrder>
- </b:myGridDataDocument>
- </b:dataThing>
-</b:dataThingMap>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-databundle/README.md
----------------------------------------------------------------------
diff --git a/taverna-databundle/README.md b/taverna-databundle/README.md
deleted file mode 100644
index dab38b6..0000000
--- a/taverna-databundle/README.md
+++ /dev/null
@@ -1,172 +0,0 @@
-Data bundles API
-================
-
-API for Taverna Data Bundles
-
-[](https://travis-ci.org/taverna/taverna-databundle)
-
-See [Data bundle requirements](http://dev.mygrid.org.uk/wiki/display/TAVOSGI/2013-02+Data+bundle+requirements)
-and [TestDataBundles.java](src/test/java/uk/org/taverna/databundle/TestDataBundles.java)
-
-This API is built on the Java 7 NIO Files and the [RO Bundle API](https://github.com/wf4ever/robundle), which
-uses the [Java 7 ZIP file provider](http://docs.oracle.com/javase/7/docs/technotes/guides/io/fsp/zipfilesystemprovider.html) to generate the Data Bundle.
-
-
-The class [org.apache.taverna.databundle.DataBundles](src/main/java/uk/org/taverna/databundle/DataBundles.java)
-complements the Java 7 [java.nio.Files](http://docs.oracle.com/javase/7/docs/api/java/nio/file/Files.html)
-API with more specific helper methods to work with Data Bundles.
-
-
-Building
---------
-```mvn clean install```
-
-should normally work, given a recent version of [Maven 3](http://maven.apache.org/download.cgi) and
-[Java 7 SDK](http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html).
-
-[myGrid's Jenkins installation](http://build.mygrid.org.uk/ci/) has automated
-builds of both [databundles](http://build.mygrid.org.uk/ci/job/databundles/)
-and [robundle](http://build.mygrid.org.uk/ci/job/robundle/), which snapshots are deployed to
-[myGrid's snapshot repository](http://build.mygrid.org.uk/maven/snapshot-repository/uk/org/taverna/databundle/databundle/).
-
-Maven should download the latest snapshot of [robundle](https://github.com/wf4ever/robundle)
-from [myGrid's snapshot repository](http://build.mygrid.org.uk/maven/snapshot-repository/org/purl/wf4ever/robundle/robundle/),
-but in some cases you might have to build robundle locally before building this project.
-
-
-Example of use
---------------
-
-Example in full is at [org.apache.taverna.databundle.TestExample](src/test/java/uk/org/taverna/databundle/TestExample.java)
-
-
-Create a new (temporary) data bundle:
-```java
- Bundle dataBundle = DataBundles.createBundle();
-```
-
-Get the input ports and the port "in1":
-```java
- Path inputs = DataBundles.getInputs(dataBundle);
- Path portIn1 = DataBundles.getPort(inputs, "in1");
-```
-
-Setting a string value for the input port:
-```java
- DataBundles.setStringValue(portIn1, "Hello");
-```
-
-And retrieving it:
-```java
- if (DataBundles.isValue(portIn1)) {
- System.out.println(DataBundles.getStringValue(portIn1));
- }
-```
-```
-Hello
-```
-
-
-Alternatively, use the regular Files methods:
-```java
- for (String line : Files
- .readAllLines(portIn1, Charset.forName("UTF-8"))) {
- System.out.println(line);
- }
-```
-
-
-Binaries and large files are done through the Files API
-```java
- try (OutputStream out = Files.newOutputStream(portIn1,
- StandardOpenOption.APPEND)) {
- out.write(32);
- }
-```
-
-Or Java 7 style:
-```java
- Path localFile = Files.createTempFile("", ".txt");
- Files.copy(portIn1, localFile, StandardCopyOption.REPLACE_EXISTING);
- System.out.println("Written to: " + localFile);
-```
-```
-Written to: C:\Users\stain\AppData\Local\Temp\2009921746200670789.txt
-```
-
-Either direction of copy works, of course:
-```java
- Files.copy(localFile,
- DataBundles.getPort(DataBundles.getOutputs(dataBundle), "out1"));
-```
-
-
-When you get a port, it can become either a value or a list:
-```java
- Path port2 = DataBundles.getPort(inputs, "port2");
- DataBundles.createList(port2); // empty list
- List<Path> list = DataBundles.getList(port2);
- assertTrue(list.isEmpty());
-```
-
-Adding items sequentially:
-```java
- Path item0 = DataBundles.newListItem(port2);
- DataBundles.setStringValue(item0, "item 0");
- DataBundles.setStringValue(DataBundles.newListItem(port2), "item 1");
- DataBundles.setStringValue(DataBundles.newListItem(port2), "item 2");
-```
-
-Set and get by explicit position:
-```java
- DataBundles.setStringValue(DataBundles.getListItem(port2, 12), "item 12");
- System.out.println(DataBundles.getStringValue(DataBundles.getListItem(port2, 2)));
-```
-```
-item 2
-```
-
-The list is sorted numerically (e.g. 2, 5, 10) and will contain nulls for empty slots:
-```java
- System.out.println(DataBundles.getList(port2));
-```
-```
-[/inputs/port2/0, /inputs/port2/1, /inputs/port2/2, null, null, null, null, null,
- null, null, null, null, /inputs/port2/12]
-```
-
-Ports can be browsed as a map by port name:
-```java
- NavigableMap<String, Path> ports = DataBundles.getPorts(inputs);
- System.out.println(ports.keySet());
-```
-```
-[in1, port2]
-```
-
-Saving a data bundle:
-```java
- Path zip = Files.createTempFile("databundle", ".zip");
- DataBundles.closeAndSaveBundle(dataBundle, zip);
- // NOTE: From now dataBundle and its Path's are CLOSED
- // and can no longer be accessed
- System.out.println("Saved to " + zip);
-```
-```
-Saved to C:\Users\stain\AppData\Local\Temp\databundle6905894602121718151.zip
-```
-
-Inspecting the zip:
-```java
- if (Desktop.isDesktopSupported()) {
- // Open ZIP file for browsing
- Desktop.getDesktop().open(zip.toFile());
- }
-```
-
-Loading a data bundle back from disk:
-```java
- try (Bundle dataBundle2 = DataBundles.openBundle(zip)) {
- // Any modifications here will be saved on (here automatic) close
- }
-```
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-databundle/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-databundle/pom.xml b/taverna-databundle/pom.xml
deleted file mode 100644
index e7ff46e..0000000
--- a/taverna-databundle/pom.xml
+++ /dev/null
@@ -1,109 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- Licensed to the Apache Software Foundation (ASF) under one or more
- contributor license agreements. See the NOTICE file distributed with
- this work for additional information regarding copyright ownership.
- The ASF licenses this file to You under the Apache License, Version 2.0
- (the "License"); you may not use this file except in compliance with
- the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-language</artifactId>
- <version>0.16.1-incubating-SNAPSHOT</version>
- </parent>
- <artifactId>taverna-databundle</artifactId>
- <name>Apache Taverna Databundle API</name>
- <description>API for dealing with Data Bundles</description>
- <dependencies>
- <dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>jena-arq</artifactId>
- <version>${jena.version}</version>
- </dependency>
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>taverna-scufl2-rdfxml</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>taverna-scufl2-t2flow</artifactId>
- <version>${project.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>taverna-scufl2-wfdesc</artifactId>
- <version>${project.version}</version>
- <optional>true</optional>
- </dependency>
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>taverna-robundle</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>${commons.io.version}</version>
- <scope>test</scope>
- </dependency>
-
-
- <dependency>
- <groupId>commons-configuration</groupId>
- <artifactId>commons-configuration</artifactId>
- <version>${commons.configuration.version}</version>
- </dependency>
- </dependencies>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <version>2.3.2</version>
- <configuration>
- <source>1.7</source>
- <target>1.7</target>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <extensions>true</extensions>
- </plugin>
- <plugin>
- <groupId>org.apache.rat</groupId>
- <artifactId>apache-rat-plugin</artifactId>
- </plugin>
- </plugins>
- <pluginManagement>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <version>2.3.7</version>
- </plugin>
- </plugins>
- </pluginManagement>
- </build>
-
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-databundle/src/main/java/org/apache/taverna/databundle/DataBundles.java
----------------------------------------------------------------------
diff --git a/taverna-databundle/src/main/java/org/apache/taverna/databundle/DataBundles.java b/taverna-databundle/src/main/java/org/apache/taverna/databundle/DataBundles.java
deleted file mode 100644
index 750a23e..0000000
--- a/taverna-databundle/src/main/java/org/apache/taverna/databundle/DataBundles.java
+++ /dev/null
@@ -1,454 +0,0 @@
-package org.apache.taverna.databundle;
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-
-import static java.nio.file.Files.createDirectories;
-import static java.nio.file.Files.delete;
-import static java.nio.file.Files.isDirectory;
-import static java.nio.file.Files.isRegularFile;
-import static java.nio.file.Files.newDirectoryStream;
-import static java.nio.file.Files.newInputStream;
-import static java.nio.file.Files.newOutputStream;
-import static java.nio.file.Files.readAllLines;
-import static java.nio.file.Files.write;
-import static java.nio.file.StandardOpenOption.CREATE;
-import static java.nio.file.StandardOpenOption.TRUNCATE_EXISTING;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.net.URI;
-import java.nio.charset.Charset;
-import java.nio.file.DirectoryIteratorException;
-import java.nio.file.DirectoryStream;
-import java.nio.file.DirectoryStream.Filter;
-import java.nio.file.FileAlreadyExistsException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.NavigableMap;
-import java.util.TreeMap;
-import java.util.UUID;
-
-import org.apache.log4j.Logger;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.scufl2.api.io.ReaderException;
-import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
-import org.apache.taverna.scufl2.api.io.WriterException;
-import org.apache.taverna.robundle.Bundle;
-import org.apache.taverna.robundle.Bundles;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-/**
- * Utility functions for dealing with data bundles.
- * <p>
- * The style of using this class is similar to that of {@link Files}. In fact, a
- * data bundle is implemented as a set of {@link Path}s.
- *
- * @author Stian Soiland-Reyes
- */
-public class DataBundles extends Bundles {
- private static final class OBJECT_MAPPER {
- // Lazy initialization of singleton
- private static final ObjectMapper instance = new ObjectMapper();
- }
-
- protected static final class ExtensionIgnoringFilter implements
- Filter<Path> {
- private final String fname;
-
- private ExtensionIgnoringFilter(Path file) {
- this.fname = filenameWithoutExtension(file);
- }
-
- @Override
- public boolean accept(Path entry) throws IOException {
- return fname.equals(filenameWithoutExtension(entry));
- }
- }
-
- private static WorkflowBundleIO wfBundleIO;
-
- private static Logger logger = Logger.getLogger(DataBundles.class);
-
- private static final String WFBUNDLE_CONTENT_TYPE = "application/vnd.taverna.scufl2.workflow-bundle";
- private static final String WFDESC_TURTLE = "text/vnd.wf4ever.wfdesc+turtle";
- private static final String WORKFLOW = "workflow";
- private static final String DOT_WFDESC_TTL = ".wfdesc.ttl";
- private static final String DOT_WFBUNDLE = ".wfbundle";
- private static final String WORKFLOWRUN_PROV_TTL = "workflowrun.prov.ttl";
- private static final String WORKFLOWRUN_JSON = "workflowrun.json";
- private static final String DOT_ERR = ".err";
- private static final String INPUTS = "inputs";
- private static final String INTERMEDIATES = "intermediates";
- private static final String OUTPUTS = "outputs";
- private static final Charset UTF8 = Charset.forName("UTF-8");
-
- private static Path anyExtension(Path path) throws IOException {
- return anyExtension(path.getParent(), path.getFileName().toString());
- }
-
- private static Path anyExtension(Path directory, String fileName)
- throws IOException {
- Path path = directory.resolve(fileName);
-
- // Prefer the fileName as it is
- if (Files.exists(path))
- return path;
- // Strip any existing extension
- String fileNameNoExt = filenameWithoutExtension(path);
- Path withoutExt = path.resolveSibling(fileNameNoExt);
- if (Files.exists(withoutExt))
- return withoutExt;
-
- // Check directory for path.*
- for (Path p : newDirectoryStream(directory, fileNameNoExt + ".*"))
- /*
- * We'll just return the first one
- *
- * TODO: Should we fail if there's more than one?
- */
- return p;
-
- /*
- * Nothing? Then let's give the existing one; perhaps it is to be
- * created.
- */
- return path;
- }
-
- private static void checkExistingAnyExtension(Path path)
- throws IOException, FileAlreadyExistsException {
- Path existing = anyExtension(path);
- if (!path.equals(existing))
- throw new FileAlreadyExistsException(existing.toString());
- }
-
- public static void createList(Path path) throws IOException {
- checkExistingAnyExtension(path);
- Files.createDirectories(path);
- }
-
- public static void deleteAllExtensions(final Path file) throws IOException {
- Filter<Path> filter = new ExtensionIgnoringFilter(file);
- try (DirectoryStream<Path> ds = newDirectoryStream(file.getParent(),
- filter)) {
- for (Path p : ds)
- deleteRecursively(p);
- }
- }
-
- protected static String filenameWithoutExtension(Path entry) {
- String fileName = entry.getFileName().toString();
- int lastDot = fileName.lastIndexOf(".");
- if (lastDot < 0)
- return fileName.replace("/", "");
- return fileName.substring(0, lastDot);
- }
-
- public static ErrorDocument getError(Path path) throws IOException {
- if (path == null)
- return null;
-
- Path errorPath = withExtension(path, DOT_ERR);
- List<String> errorList = readAllLines(errorPath, UTF8);
- int split = errorList.indexOf("");
- if (split == -1 || errorList.size() <= split)
- throw new IOException("Invalid error document: " + errorPath);
-
- ErrorDocument errorDoc = new ErrorDocument();
-
- for (String cause : errorList.subList(0, split))
- errorDoc.getCausedBy().add(path.resolveSibling(cause));
-
- errorDoc.setMessage(errorList.get(split + 1));
-
- StringBuilder errorTrace = new StringBuilder();
- for (String line : errorList.subList(split + 2, errorList.size())) {
- errorTrace.append(line);
- errorTrace.append("\n");
- }
- if (errorTrace.length() > 0)
- // Delete last \n
- errorTrace.deleteCharAt(errorTrace.length() - 1);
- errorDoc.setTrace(errorTrace.toString());
- return errorDoc;
- }
-
- public static Path getInputs(Bundle dataBundle) throws IOException {
- Path inputs = dataBundle.getRoot().resolve(INPUTS);
- createDirectories(inputs);
- return inputs;
- }
-
- private static long getEntryNumber(Path entry) throws NumberFormatException {
- String name = filenameWithoutExtension(entry);
- return Long.parseLong(name);
- }
-
- public static List<Path> getList(Path list) throws IOException {
- if (list == null)
- return null;
- List<Path> paths = new ArrayList<>();
- try (DirectoryStream<Path> ds = newDirectoryStream(list)) {
- for (Path entry : ds)
- try {
- long entryNum = getEntryNumber(entry);
- while (paths.size() <= entryNum)
- // Fill any gaps
- paths.add(null);
- // NOTE: Don't use add() as these could come in any order!
- paths.set((int) entryNum, entry);
- } catch (NumberFormatException ex) {
- }
- } catch (DirectoryIteratorException ex) {
- throw ex.getCause();
- }
- return paths;
- }
-
- public static Path getListItem(Path list, long position) throws IOException {
- if (position < 0)
- throw new IllegalArgumentException(
- "Position must be 0 or more, not: " + position);
- return anyExtension(list, Long.toString(position));
- }
-
- public static Path getOutputs(Bundle dataBundle) throws IOException {
- Path inputs = dataBundle.getRoot().resolve(OUTPUTS);
- createDirectories(inputs);
- return inputs;
- }
-
- public static Path getPort(Path map, String portName) throws IOException {
- Files.createDirectories(map);
- return anyExtension(map, portName);
- }
-
- public static NavigableMap<String, Path> getPorts(Path path)
- throws IOException {
- NavigableMap<String, Path> ports = new TreeMap<>();
- try (DirectoryStream<Path> ds = newDirectoryStream(path)) {
- for (Path p : ds)
- ports.put(filenameWithoutExtension(p), p);
- }
- return ports;
- }
-
- public static boolean hasInputs(Bundle dataBundle) {
- Path inputs = dataBundle.getRoot().resolve(INPUTS);
- return isDirectory(inputs);
- }
-
- public static boolean hasOutputs(Bundle dataBundle) {
- Path outputs = dataBundle.getRoot().resolve(OUTPUTS);
- return isDirectory(outputs);
- }
-
- public static boolean isError(Path path) {
- return isRegularFile(withExtension(path, DOT_ERR));
- }
-
- public static boolean isList(Path path) {
- return isDirectory(path);
- }
-
- public static boolean isMissing(Path item) {
- return Bundles.isMissing(item) && !isError(item);
- }
-
- public static boolean isValue(Path item) {
- return !isError(item) && Bundles.isValue(item);
- }
-
- public static Path newListItem(Path list) throws IOException {
- createList(list);
- return list.resolve(Long.toString(getListSize(list)));
- }
-
- public static Path setError(Path path, ErrorDocument error)
- throws IOException {
- return setError(path, error.getMessage(), error.getTrace(), error
- .getCausedBy().toArray(new Path[error.getCausedBy().size()]));
- }
-
- public static Path setError(Path errorPath, String message, String trace,
- Path... causedBy) throws IOException {
- errorPath = withExtension(errorPath, DOT_ERR);
- // Silly \n-based format
- List<String> errorDoc = new ArrayList<>();
- for (Path cause : causedBy) {
- Path relCause = errorPath.getParent().relativize(cause);
- errorDoc.add(relCause.toString());
- }
- errorDoc.add(""); // Our magic separator
- errorDoc.add(message);
- errorDoc.add(trace);
- checkExistingAnyExtension(errorPath);
- write(errorPath, errorDoc, UTF8, TRUNCATE_EXISTING, CREATE);
- return errorPath;
- }
-
- public static Path setReference(Path path, URI reference)
- throws IOException {
- path = withExtension(path, DOT_URL);
- checkExistingAnyExtension(path);
- return Bundles.setReference(path, reference);
- }
-
- public static void setStringValue(Path path, String string)
- throws IOException {
- checkExistingAnyExtension(path);
- Bundles.setStringValue(path, string);
- }
-
- protected static Path withExtension(Path path, String extension) {
- String filename = path.getFileName().toString();
- return path.resolveSibling(withExtensionFilename(filename, extension));
- }
-
- protected static String withExtensionFilename(String filename,
- String extension) {
- if (!extension.isEmpty() && !extension.startsWith("."))
- throw new IllegalArgumentException(
- "Extension must be empty or start with .");
- if (!extension.isEmpty()
- && filename.toLowerCase().endsWith(extension.toLowerCase()))
- return filename;
- // Everything after the last . - or just the end
- return filename.replaceFirst("(\\.[^.]*)?$", extension);
- }
-
- public static Path getWorkflowRunProvenance(Bundle dataBundle) {
- return dataBundle.getRoot().resolve(WORKFLOWRUN_PROV_TTL);
- }
-
- public static Path getWorkflowRunReport(Bundle dataBundle) {
- return dataBundle.getRoot().resolve(WORKFLOWRUN_JSON);
- }
-
- public static JsonNode getWorkflowRunReportAsJson(Bundle dataBundle)
- throws IOException {
- Path path = getWorkflowRunReport(dataBundle);
- try (InputStream jsonIn = newInputStream(path)) {
- return OBJECT_MAPPER.instance.readTree(jsonIn);
- }
- }
-
- public static void setWorkflowRunReport(Bundle dataBundle,
- JsonNode workflowRunReport) throws IOException {
- Path path = getWorkflowRunReport(dataBundle);
- try (OutputStream out = newOutputStream(path)) {
- OBJECT_MAPPER.instance.writeValue(out, workflowRunReport);
- }
- }
-
- public static Path getWorkflow(Bundle dataBundle) throws IOException {
- return anyExtension(dataBundle.getRoot(), WORKFLOW);
- }
-
- public static Path getWorkflowDescription(Bundle dataBundle)
- throws IOException {
- Path annotations = getAnnotations(dataBundle);
- return annotations.resolve(WORKFLOW + DOT_WFDESC_TTL);
- }
-
- public static void setWorkflowBundle(Bundle dataBundle,
- WorkflowBundle wfBundle) throws IOException {
- Path bundlePath = withExtension(getWorkflow(dataBundle), DOT_WFBUNDLE);
- checkExistingAnyExtension(bundlePath);
-
- // TODO: Save as nested folder?
- try (OutputStream outputStream = newOutputStream(bundlePath)) {
- getWfBundleIO().writeBundle(wfBundle, outputStream,
- WFBUNDLE_CONTENT_TYPE);
- } catch (WriterException e) {
- throw new IOException("Can't write workflow bundle to: "
- + bundlePath, e);
- }
-
- // wfdesc
- Path wfdescPath = getWorkflowDescription(dataBundle);
- try (OutputStream outputStream = newOutputStream(wfdescPath)) {
- getWfBundleIO().writeBundle(wfBundle, outputStream, WFDESC_TURTLE);
- } catch (IllegalArgumentException | WriterException e) {
- logger.warn("Can't write wfdesc to: " + bundlePath, e);
- delete(wfdescPath);
- // throw new IOException("Can't write wfdesc to: " + bundlePath, e);
- }
- }
-
- public static WorkflowBundle getWorkflowBundle(Bundle dataBundle)
- throws ReaderException, IOException {
- Path wf = getWorkflow(dataBundle);
- // String type = Files.probeContentType(wf);
- return wfBundleIO.readBundle(newInputStream(wf), null);
- }
-
- public static Path getIntermediates(Bundle dataBundle) throws IOException {
- Path intermediates = dataBundle.getRoot().resolve(INTERMEDIATES);
- createDirectories(intermediates);
- return intermediates;
- }
-
- public static Path getIntermediate(Bundle dataBundle, UUID uuid)
- throws IOException {
- String fileName = uuid.toString();
- Path intermediates = getIntermediates(dataBundle);
- // Folder is named after first 2 characters of UUID
- Path folder = intermediates.resolve(fileName.substring(0, 2));
- createDirectories(folder);
- return anyExtension(folder, fileName);
- }
-
- public static long getListSize(Path list) throws IOException {
- // Should fail if list is not a directory
- try (DirectoryStream<Path> ds = newDirectoryStream(list)) {
- long max = -1L;
- for (Path entry : ds)
- try {
- long entryNum = getEntryNumber(entry);
- if (entryNum > max)
- max = entryNum;
- } catch (NumberFormatException ex) {
- }
- return max + 1;
- } catch (DirectoryIteratorException ex) {
- throw ex.getCause();
- }
- }
-
- public static WorkflowBundleIO getWfBundleIO() {
- if (wfBundleIO == null)
- wfBundleIO = new WorkflowBundleIO();
- return wfBundleIO;
- }
-
- public static void setWfBundleIO(WorkflowBundleIO wfBundleIO) {
- if (wfBundleIO == null)
- throw new NullPointerException();
- DataBundles.wfBundleIO = wfBundleIO;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-databundle/src/main/java/org/apache/taverna/databundle/ErrorDocument.java
----------------------------------------------------------------------
diff --git a/taverna-databundle/src/main/java/org/apache/taverna/databundle/ErrorDocument.java b/taverna-databundle/src/main/java/org/apache/taverna/databundle/ErrorDocument.java
deleted file mode 100644
index ec551b8..0000000
--- a/taverna-databundle/src/main/java/org/apache/taverna/databundle/ErrorDocument.java
+++ /dev/null
@@ -1,62 +0,0 @@
-package org.apache.taverna.databundle;
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.List;
-
-public class ErrorDocument {
- private List<Path> causedBy = new ArrayList<>();
- private String message = "";
- private String trace = "";
-
- public List<Path> getCausedBy() {
- return causedBy;
- }
-
- public String getMessage() {
- return message;
- }
-
- public String getTrace() {
- return trace;
- }
-
- public void setCausedBy(List<Path> causedBy) {
- this.causedBy.clear();
- if (causedBy != null)
- this.causedBy.addAll(causedBy);
- }
-
- public void setMessage(String message) {
- if (message == null)
- message = "";
- this.message = message;
- }
-
- public void setTrace(String trace) {
- if (trace == null)
- trace = "";
- this.trace = trace;
- }
-}