Github user stain commented on a diff in the pull request:
https://github.com/apache/incubator-taverna-common-activities/pull/24#discussion_r112030157
--- Diff:
taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/preprocessing/LinkedResolutionUtil.java
---
@@ -0,0 +1,124 @@
+/*******************************************************************************
+ * 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.
+
*******************************************************************************/
+package org.apache.taverna.cwl.utilities.preprocessing;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import org.apache.log4j.Logger;
+
+import java.io.File;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.file.Path;
+
+/**
+ * This class is Util class which is used for resolving Linked resolution
+ * Rules are defined at:
http://www.commonwl.org/draft-3/SchemaSalad.html#Link_resolution
+ */
+public class LinkedResolutionUtil implements CwlPreprocessor {
+
+ final private static Logger logger =
Logger.getLogger(LinkedResolutionUtil.class);
+
+ private JsonNode cwlToolDescription;
+ private JsonNode nameSpace;
+ private URI BASE;
+ private Path path;
+
+ /**
+ *
+ * @param cwlToolDescription CWL tool description
+ * @param path This must be the directory where CWL tool is located
and resolving is done assuming required other files
+ * in the same directory
+ */
+ public LinkedResolutionUtil(JsonNode cwlToolDescription, Path path) {
+ this.cwlToolDescription = cwlToolDescription;
+ this.path = path;
+ setup();
+ }
+
+ private void setBASE(URI BASE) {
+ this.BASE = BASE;
+ }
+
+ /**
+ * This method setup the initial resources for the process
+ */
+ private void setup() {
+ try {
+ if (cwlToolDescription.has("$base"))
+ setBASE(new URI(cwlToolDescription.get("$base").asText()));
+ if (cwlToolDescription.has("$namespaces"))
+ setNameSpace(cwlToolDescription.get("$namespaces"));
+ } catch (URISyntaxException e) {
+ logger.error("Setup function ", e);
+ }
+ }
+
+
+ private void setNameSpace(JsonNode nameSpace) {
+ this.nameSpace = nameSpace;
+ }
+
+ /**
+ * This method is resolving the uri based on the rules mentioned in
the CWL Schema Salad
+ * @param val This is a ValueNode (subclass of a JsonNode) which holds
the link. This must be a single node
+ * @return An URI object which contains absolute is returned
+ * @throws URISyntaxException
+ */
+ @Override
+ public URI process(JsonNode val) throws URISyntaxException {
+
+ String uriString = val.asText();
+ URI uri = new URI(uriString);
+
+ if (uri.isAbsolute()) {
--- End diff --
Not sure if this is the right location, but how can the imports support
relative URIs based on the URI of the CWL document that the `$import` node
comes from?
e.g.
`http://example.com/a/b/c.cwl` imports `../sibling/e.cwl` (aka
`http://example.com/a/sibling/e.cwl`) which then imports `f.cwl` (aka
`http://example.com/a/sibling/f.cwl` - not ``http://example.com/a/b/f.cwl`)
---
If your project is set up for it, you can reply to this email and have your
reply appear on GitHub as well. If your project does not have this feature
enabled and wishes so, or if the feature is enabled but not working, please
contact infrastructure at [email protected] or file a JIRA ticket
with INFRA.
---
