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Merge pull request #158 from common-workflow-language/rdf-permalinks
Consistent RDF permalinks with content negotiation
2 parents 7c99558 + ac24cee commit 6196d34

22 files changed

+952
-339
lines changed

‎pom.xml‎

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@@ -93,6 +93,11 @@
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<artifactId>jena-osgi</artifactId>
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<version>3.3.0</version>
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</dependency>
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<dependency>
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<groupId>com.github.jsonld-java</groupId>
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<artifactId>jsonld-java</artifactId>
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<version>0.9.0</version>
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</dependency>
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<dependency>
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<groupId>org.eclipse.jgit</groupId>
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<artifactId>org.eclipse.jgit</artifactId>

‎src/main/java/org/commonwl/view/GlobalControllerErrorHandling.java‎

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/*
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* Licensed to the Apache Software Foundation (ASF) under one
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* or more contributor license agreements. See the NOTICE file
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* distributed with this work for additional information
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* regarding copyright ownership. The ASF licenses this file
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* to you under the Apache License, Version 2.0 (the
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* "License"); you may not use this file except in compliance
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* with the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing,
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* software distributed under the License is distributed on an
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* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
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* KIND, either express or implied. See the License for the
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* specific language governing permissions and limitations
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* under the License.
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*/
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package org.commonwl.view;
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import org.commonwl.view.workflow.RepresentationNotFoundException;
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import org.commonwl.view.workflow.WorkflowNotFoundException;
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import org.springframework.http.HttpHeaders;
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import org.springframework.http.HttpStatus;
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import org.springframework.http.MediaType;
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import org.springframework.http.ResponseEntity;
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import org.springframework.web.bind.annotation.ControllerAdvice;
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import org.springframework.web.bind.annotation.ExceptionHandler;
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/**
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* Handles exception handling across the application
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*/
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@ControllerAdvice
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public class GlobalControllerErrorHandling {
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/**
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* Workflow can not be found
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* @return A plain text error message
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*/
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@ExceptionHandler(WorkflowNotFoundException.class)
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public ResponseEntity<?> handleNotFound() {
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final HttpHeaders headers = new HttpHeaders();
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headers.setContentType(MediaType.TEXT_PLAIN);
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return new ResponseEntity<>("Workflow could not be found", headers, HttpStatus.NOT_FOUND);
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}
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/**
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* Workflow exists but representation is not found
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* eg Generic git workflow asking for raw workflow URL
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* @return A plain text error message
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*/
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@ExceptionHandler(RepresentationNotFoundException.class)
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public ResponseEntity<?> handleNoRepresentation() {
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final HttpHeaders headers = new HttpHeaders();
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headers.setContentType(MediaType.TEXT_PLAIN);
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return new ResponseEntity<>("The workflow exists but the requested representation could not be found",
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headers, HttpStatus.NOT_FOUND);
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}
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}

‎src/main/java/org/commonwl/view/WebConfig.java‎

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/*
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* Licensed to the Apache Software Foundation (ASF) under one
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* or more contributor license agreements. See the NOTICE file
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* distributed with this work for additional information
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* regarding copyright ownership. The ASF licenses this file
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* to you under the Apache License, Version 2.0 (the
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* "License"); you may not use this file except in compliance
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* with the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing,
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* software distributed under the License is distributed on an
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* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
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* KIND, either express or implied. See the License for the
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* specific language governing permissions and limitations
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* under the License.
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*/
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package org.commonwl.view;
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import org.springframework.context.annotation.Configuration;
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import org.springframework.http.MediaType;
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import org.springframework.web.servlet.config.annotation.ContentNegotiationConfigurer;
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import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
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import static org.springframework.http.MediaType.parseMediaType;
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@Configuration
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public class WebConfig extends WebMvcConfigurerAdapter {
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/**
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* Allows the use of the format query parameter to be used
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* instead of the Accept HTTP header
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*/
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@Override
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public void configureContentNegotiation(ContentNegotiationConfigurer configurer) {
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configurer.favorParameter(true)
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.mediaType("html", MediaType.TEXT_HTML)
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.mediaType("json", MediaType.APPLICATION_JSON)
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.mediaType("turtle", parseMediaType("text/turtle"))
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.mediaType("jsonld", parseMediaType("application/ld+json"))
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.mediaType("rdfxml", parseMediaType("application/rdf+xml"))
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.mediaType("svg", parseMediaType("image/svg+xml"))
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.mediaType("png", MediaType.IMAGE_PNG)
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.mediaType("ro", parseMediaType("application/vnd.wf4ever.robundle+zip"))
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.mediaType("zip", parseMediaType("application/zip"))
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.mediaType("dot", parseMediaType("text/vnd+graphviz"))
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.mediaType("yaml", parseMediaType("text/x-yaml"))
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.mediaType("raw", MediaType.APPLICATION_OCTET_STREAM);
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}
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}

‎src/main/java/org/commonwl/view/cwl/CWLService.java‎

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@@ -52,6 +52,8 @@
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import java.io.File;
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import java.io.IOException;
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import java.io.StringWriter;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.*;
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import static org.apache.commons.io.FileUtils.readFileToString;
@@ -161,14 +163,14 @@ public List<WorkflowOverview> getWorkflowOverviewsFromPacked(File packedFile) th
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* @param packedWorkflowId The ID of the workflow object if the file is packed
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* @return The constructed workflow object
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*/
164-
public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId) throws IOException {
166+
public Workflow parseWorkflowNative(Path workflowFile, String packedWorkflowId) throws IOException {
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166168
// Check file size limit before parsing
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long fileSizeBytes = workflowFile.length();
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long fileSizeBytes = Files.size(workflowFile);
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if (fileSizeBytes <= singleFileSizeLimit) {
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// Parse file as yaml
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JsonNode cwlFile = yamlStringToJson(readFileToString(workflowFile));
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JsonNode cwlFile = yamlStringToJson(readFileToString(workflowFile.toFile()));
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// Check packed workflow occurs
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if (packedWorkflowId != null) {
@@ -199,7 +201,7 @@ public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId)
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// Use filename for label if there is no defined one
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String label = extractLabel(cwlFile);
201203
if (label == null) {
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label = FilenameUtils.getName(workflowFile.getPath());
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label = workflowFile.getFileName().toString();
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}
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// Construct the rest of the workflow model
@@ -221,7 +223,7 @@ public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId)
221223
return workflowModel;
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223225
} else {
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throw new IOException("File '" + workflowFile.getName() + "' is over singleFileSizeLimit - " +
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throw new IOException("File '" + workflowFile.getFileName() + "' is over singleFileSizeLimit - " +
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FileUtils.byteCountToDisplaySize(fileSizeBytes) + "/" +
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FileUtils.byteCountToDisplaySize(singleFileSizeLimit));
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}
@@ -235,29 +237,32 @@ public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId)
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* @return The constructed workflow object
236238
*/
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public Workflow parseWorkflowWithCwltool(Workflow basicModel,
238-
File workflowFile) throws CWLValidationException {
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Path workflowFile,
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Path workTree) throws CWLValidationException {
239242
GitDetails gitDetails = basicModel.getRetrievedFrom();
240243
String latestCommit = basicModel.getLastCommit();
241244
String packedWorkflowID = gitDetails.getPackedId();
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// Get paths to workflow
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String url = gitDetails.getUrl(latestCommit).replace("https://", "");
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String localPath = workflowFile.toPath().toAbsolutePath().toString();
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String url = basicModel.getPermalink();
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String localPath = workflowFile.toAbsolutePath().toString();
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String gitPath = gitDetails.getPath();
247250
if (packedWorkflowID != null) {
248251
if (packedWorkflowID.charAt(0) != '#') {
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localPath += "#";
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url += "#";
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gitPath += "#";
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}
253255
localPath += packedWorkflowID;
254-
url += packedWorkflowID;
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gitPath += packedWorkflowID;
256257
}
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// Get RDF representation from cwltool
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if (!rdfService.graphExists(url)) {
260261
String rdf = cwlTool.getRDF(localPath);
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rdf = rdf.replace("file://" + workTree.toAbsolutePath().toString(),
263+
"https://w3id.org/cwl/view/git/" + latestCommit);
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// Workaround for common-workflow-language/cwltool#427
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rdf = rdf.replace("<rdfs:>", "<http://www.w3.org/2000/01/rdf-schema#>");
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// Create a workflow model from RDF representation
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Model model = ModelFactory.createDefaultModel();
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// Base workflow details
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String label = FilenameUtils.getName(url);
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String doc = null;
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ResultSet labelAndDoc = rdfService.getLabelAndDoc(gitPath, url);
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ResultSet labelAndDoc = rdfService.getLabelAndDoc(url);
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if (labelAndDoc.hasNext()) {
275280
QuerySolution labelAndDocSoln = labelAndDoc.nextSolution();
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if (labelAndDocSoln.contains("label")) {
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// Inputs
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Map<String, CWLElement> wfInputs = new HashMap<>();
286-
ResultSet inputs = rdfService.getInputs(gitPath, url);
291+
ResultSet inputs = rdfService.getInputs(url);
287292
while (inputs.hasNext()) {
288293
QuerySolution input = inputs.nextSolution();
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String inputName = rdfService.stepNameFromURI(gitPath, input.get("name").toString());
@@ -316,7 +321,7 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
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317322
// Outputs
318323
Map<String, CWLElement> wfOutputs = new HashMap<>();
319-
ResultSet outputs = rdfService.getOutputs(gitPath, url);
324+
ResultSet outputs = rdfService.getOutputs(url);
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while (outputs.hasNext()) {
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QuerySolution output = outputs.nextSolution();
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CWLElement wfOutput = new CWLElement();
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356361
// Steps
357362
Map<String, CWLStep> wfSteps = new HashMap<>();
358-
ResultSet steps = rdfService.getSteps(gitPath, url);
363+
ResultSet steps = rdfService.getSteps(url);
359364
while (steps.hasNext()) {
360365
QuerySolution step = steps.nextSolution();
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String uri = rdfService.stepNameFromURI(gitPath, step.get("step").toString());
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// Add new step
377382
CWLStep wfStep = new CWLStep();
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379-
IRI wfStepUri = iriFactory.construct(step.get("wf").asResource().getURI());
380-
IRI workflowPath = wfStepUri.resolve("./");
381-
384+
IRI workflowPath = iriFactory.construct(url).resolve("./");
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IRI runPath = iriFactory.construct(step.get("run").asResource().getURI());
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wfStep.setRun(workflowPath.relativize(runPath).toString());
384387
wfStep.setRunType(rdfService.strToRuntype(step.get("runtype").toString()));
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409412
}
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411414
// Docker link
412-
ResultSet dockerResult = rdfService.getDockerLink(gitPath, url);
415+
ResultSet dockerResult = rdfService.getDockerLink(url);
413416
String dockerLink = null;
414417
if (dockerResult.hasNext()) {
415418
QuerySolution docker = dockerResult.nextSolution();

‎src/main/java/org/commonwl/view/cwl/CWLToolRunner.java‎

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@@ -19,10 +19,6 @@
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2020
package org.commonwl.view.cwl;
2121

22-
import java.io.IOException;
23-
import java.nio.file.Path;
24-
import java.util.Date;
25-
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import org.apache.jena.query.QueryException;
2723
import org.commonwl.view.git.GitDetails;
2824
import org.commonwl.view.git.GitSemaphore;
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4036
import org.springframework.scheduling.annotation.EnableAsync;
4137
import org.springframework.stereotype.Component;
4238

39+
import java.io.IOException;
40+
import java.nio.file.Path;
41+
import java.util.Date;
42+
4343
/**
4444
* Replace existing workflow with the one given by cwltool
4545
*/
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8585
Path workflowFile = localPath.resolve(gitInfo.getPath()).normalize().toAbsolutePath();
8686
Workflow newWorkflow = cwlService.parseWorkflowWithCwltool(
8787
tempWorkflow,
88-
workflowFile.toFile());
88+
workflowFile,
89+
localPath);
8990

9091
// Success
9192
newWorkflow.setRetrievedFrom(tempWorkflow.getRetrievedFrom());

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