Snakemake prototype support

findbugs-exclude.xml

@@ -1,5 +1,5 @@
 <!--
-  ~    Copyright 2016 OICR
+  ~    Copyright 2025 OICR and UCSC
   ~
   ~    Licensed under the Apache License, Version 2.0 (the "License");
   ~    you may not use this file except in compliance with the License.

pom.xml

@@ -3,16 +3,16 @@
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>io.dockstore</groupId>
-    <artifactId>silly-workflow-language-interface</artifactId>
+    <artifactId>snakemake-language-interface</artifactId>
     <packaging>jar</packaging>
-    <name>silly-workflow-language-interface</name>
-    <version>0.0.1-SNAPSHOT</version>
+    <name>snakemake-language-interface</name>
+    <version>0.0.4-SNAPSHOT</version>
 
     <properties>
-        <github.url>scm:git:git@github.com:dockstore/silly-workflow-language-interface.git</github.url>
+        <github.url>scm:git:git@github.com:dockstore/snakemake-language-interface.git</github.url>
         <dockstore.version>1.16.0</dockstore.version>
         <plugin.id>${project.artifactId}</plugin.id>
-        <plugin.class>io.dockstore.language.SillyWorkflowLanguagePlugin</plugin.class>
+        <plugin.class>io.dockstore.language.SnakemakeWorkflowPlugin</plugin.class>
         <plugin.version>${project.version}</plugin.version>
         <plugin.provider>John Sheridan</plugin.provider>
         <plugin.dependencies />
@@ -176,6 +176,18 @@
             <artifactId>guava</artifactId>
             <version>32.0.0-jre</version>
         </dependency>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>2.9.0</version>
+            <scope>test</scope>
+        </dependency>
+        <!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.18.0</version>
+        </dependency>
     </dependencies>
 </project>
 

src/main/java/io/dockstore/language/SnakemakeWorkflowPlugin.java

@@ -0,0 +1,181 @@
+/*
+ *    Copyright 2025 OICR and UCSC
+ *
+ *    Licensed 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 io.dockstore.language;
+
+import com.google.common.collect.Lists;
+import com.google.common.collect.Sets;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Pattern;
+
+import io.dockstore.common.DescriptorLanguage;
+import io.dockstore.common.VersionTypeValidation;
+import org.pf4j.Extension;
+import org.pf4j.Plugin;
+import org.pf4j.PluginWrapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * @author dyuen
+ */
+public class SnakemakeWorkflowPlugin extends Plugin {
+
+    public static final Logger LOG = LoggerFactory.getLogger(SnakemakeWorkflowPlugin.class);
+    public static final String SNAKEMAKE_WORKFLOW_CATALOG_YML = "/.snakemake-workflow-catalog.yml";
+
+
+    /**
+     * Constructor to be used by plugin manager for plugin instantiation. Your plugins have to provide
+     * constructor with this exact signature to be successfully loaded by manager.
+     *
+     * @param wrapper
+     */
+    public SnakemakeWorkflowPlugin(PluginWrapper wrapper) {
+        super(wrapper);
+    }
+
+    @Extension
+    public static class SnakemakeWorkflowPluginImpl implements RecommendedLanguageInterface {
+
+        @Override
+        public String launchInstructions(String trsID) {
+            return null;
+        }
+
+
+        @Override
+        public VersionTypeValidation validateWorkflowSet(String initialPath, String contents, Map<String, FileMetadata> indexedFiles) {
+            VersionTypeValidation validation = new VersionTypeValidation(indexedFiles.containsKey(SNAKEMAKE_WORKFLOW_CATALOG_YML), new HashMap<>());
+            // TODO hook up some real validation
+            return validation;
+        }
+
+        @Override
+        public VersionTypeValidation validateTestParameterSet(Map<String, FileMetadata> indexedFiles) {
+            return new VersionTypeValidation(true, new HashMap<>());
+        }
+
+
+        @Override
+        public DescriptorLanguage getDescriptorLanguage() {
+            return DescriptorLanguage.SMK;
+        }
+
+        /**
+         * TODO: non-standardized Snakemake files can technically have their Snakefile in the root, supporting this probably
+         * affects some assumptions about folder structure below https://github.com/snakemake/snakemake-workflow-catalog?tab=readme-ov-file#standardized-usage-workflows
+         * @return
+         */
+        @Override
+        public Pattern initialPathPattern() {
+            return Pattern.compile("workflow/Snakefile");
+        }
+
+        @Override
+        public Map<String, FileMetadata> indexWorkflowFiles(String initialPath, String contents, FileReader reader) {
+            Map<String, FileMetadata> results = new HashMap<>();
+            // start with the workflow/Snakemake, some notes on workflow structure at https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html
+            results.put(
+                initialPath,
+                //TODO: get real snakemake version number, if they have one
+                new FileMetadata(contents, GenericFileType.IMPORTED_DESCRIPTOR, "1.0"));
+            // there can be  licenses, readme files and other useful stuff in the root
+            processFolder("/", null, reader, results);
+
+
+            // Snakefile might be in same directory as catalog file or up in a workflow directory (a workflow directory will have other folders), is not named in the catalog file
+            processFolder(initialPath, "/workflow", reader, results);
+            if (results.containsKey("/workflow/Snakefile")) {
+                processWorkflowFolders(reader, results);
+            }
+            // sometimes there is a config folder
+            processFolder(initialPath, "/config", reader, results);
+            // there are results and resources folders, developers are encouraged to keep the latter small
+            // processFolder(initialPath, "results", reader, results);
+            processFolder(initialPath, "/resources", reader, results);
+
+            /// TODO modules support
+
+            // workflow hub extensions
+            // TODO will need to be recursive
+            processFolder(initialPath, ".tests", reader, results);
+
+
+            return results;
+        }
+
+        private void processWorkflowFolders(FileReader reader, Map<String, FileMetadata> results) {
+            processFolder("/workflow", "/workflow/envs", reader, results);
+            processFolder("/workflow", "/workflow/report", reader, results);
+            processFolder("/workflow", "/workflow/rules", reader, results);
+            // TODO see comment in https://github.com/dockstore/snakemake-language-interface/pull/2#discussion_r2014758910
+            // the schemas directory may be optional and potentially added by a `validate` call, investigate
+            processFolder("/workflow", "/workflow/schemas", reader, results);
+            processFolder("/workflow", "/workflow/scripts", reader, results);
+            processFolder("/workflow", "/workflow/notebooks", reader, results);
+        }
+
+        // TODO determine how to process non-descriptor content https://ucsc-cgl.atlassian.net/browse/DOCK-262
+        private void processFolder(String initialPath, String folder, FileReader reader, Map<String, FileMetadata> results) {
+            List<String> files = findFiles(initialPath, folder, reader);
+            for (String file : files) {
+                results.put(file, new FileMetadata(reader.readFile(file), GenericFileType.IMPORTED_DESCRIPTOR, null));
+            }
+        }
+
+        // TODO: folderToCheck should probably be dealt with recursively
+        // TODO: use typed files instead of FileUtils from Apache (Galaxy plugin)
+        protected List<String> findFiles(final String initialPath, final String folderToCheck, final FileReader reader) {
+
+            final int extensionPos = initialPath.lastIndexOf("/");
+            final String base = initialPath.substring(0, extensionPos);
+
+            final Path pathsInDir = folderToCheck == null ? Paths.get(base) : Paths.get(base, folderToCheck);
+            // listing files is more rate limit friendly (e.g. GitHub counts each 404 "miss" as an API
+            // call,
+            // but listing a directory can be free if previously requested/cached)
+            List<String> filennamesInDir = reader.listFiles(pathsInDir.toString());
+            if (filennamesInDir == null) {
+                return Lists.newArrayList();
+            }
+            final Set<String> filenameSet = Sets.newHashSet(filennamesInDir);
+            return filenameSet.stream().map(s ->  (folderToCheck == null ? "/" : folderToCheck + "/") + s).toList();
+        }
+
+        @Override
+        public WorkflowMetadata parseWorkflowForMetadata(String initialPath, String contents, Map<String, FileMetadata> indexedFiles) {
+            WorkflowMetadata metadata = new WorkflowMetadata();
+            // TODO: grab real metadata, this is carried over from SWL and is non-functional
+            for (String line : contents.split("\\r?\\n")) {
+                if (line.startsWith("author")) {
+                    final String[] s = line.split(":");
+                    metadata.setAuthor(s[1].trim());
+                }
+                if (line.startsWith("description")) {
+                    final String[] s = line.split(":");
+                    metadata.setDescription(s[1].trim());
+                }
+            }
+            return metadata;
+        }
+    }
+}
+

src/main/java/io/dockstore/language/package-info.java

@@ -1,5 +1,5 @@
 /*
- *    Copyright 2016 OICR
+ *    Copyright 2025 OICR and UCSC
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.