Use lid fragment only to access workflow outputs by name

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

modules/nf-lineage/src/main/nextflow/lineage/DefaultLinStore.groovy

@@ -94,11 +94,8 @@ class DefaultLinStore implements LinStore {
     void close() throws IOException { }
 
     @Override
-    Map<String, LinSerializable> search(String queryString) {
-        def params = null
-        if (queryString) {
-            params = LinUtils.parseQuery(queryString)
-        }
+    Map<String, LinSerializable> search(Map<String,String> params) {
+        new LinPropertyValidator().validateQueryParams(params)
         return searchAllFiles(params)
     }
 

modules/nf-lineage/src/main/nextflow/lineage/LinStore.groovy

@@ -55,9 +55,9 @@ interface LinStore extends Closeable {
 
     /**
      * Search for lineage entries.
-     * @queryString Json-path like query string. (Only simple and nested field operators are supported(No array, wildcards,etc.)
-     * @return Key-lineage entry pairs fulfilling the queryString
+     * @param params map of query params
+     * @return Key-lineage entry pairs fulfilling the query params
      */
-    Map<String,LinSerializable> search(String queryString)
+    Map<String,LinSerializable> search(Map<String,String> params)
 
 }

modules/nf-lineage/src/main/nextflow/lineage/LinUtils.groovy

@@ -37,107 +37,6 @@ class LinUtils {
 
     private static final String[] EMPTY_ARRAY = new String[] {}
 
-    /**
-     * Query a lineage store.
-     *
-     * @param store lineage store to query.
-     * @param uri Query to perform in a URI-like format.
-     *      Format 'lid://<key>[?QueryString][#fragment]' where:
-     *       - Key: Element where the query will be applied. '/' indicates query will be applied in all the elements of the lineage store.
-     *       - QueryString: all param-value pairs that the lineage element should fulfill in a URI's query string format.
-     *       - Fragment: Element fragment to retrieve.
-     * @return Collection of object fulfilling the query
-     */
-    static Collection query(LinStore store, URI uri) {
-        String key = uri.authority ? uri.authority + uri.path : uri.path
-        if (key == LinPath.SEPARATOR) {
-            return globalSearch(store, uri)
-        } else {
-            final parameters = uri.query ? parseQuery(uri.query) : null
-            final children = parseChildrenFromFragment(uri.fragment)
-            return searchPath(store, key, parameters, children )
-        }
-    }
-
-    private static Collection<LinSerializable> globalSearch(LinStore store, URI uri) {
-        final results = store.search(uri.query).values()
-        if (results && uri.fragment) {
-            // If fragment is defined get the property of the object indicated by the fragment
-            return filterResults(results, uri.fragment)
-        }
-        return results
-    }
-
-    private static List filterResults(Collection<LinSerializable> results, String fragment) {
-        final filteredResults = []
-        results.forEach {
-            final output = navigate(it, fragment)
-            if (output) {
-                filteredResults.add(output)
-            }
-        }
-        return filteredResults
-    }
-
-    /**
-     * Get the array of the search path children elements from the fragment string
-     *
-     * @param fragment String containing the elements separated by '.'
-     * @return array with the parsed element
-     */
-    static String[] parseChildrenFromFragment(String fragment) {
-        if( !fragment )
-            return EMPTY_ARRAY
-        final children = fragment.tokenize('.')
-        new LinPropertyValidator().validate(children)
-        return children as String[]
-    }
-
-    /**
-     * Search for objects inside a description
-     *
-     * @param store lineage store
-     * @param key lineage key where to perform the search
-     * @param params Parameter-value pairs to be evaluated in the key
-     * @param children  Sub-objects to evaluate and retrieve
-     * @return List of object
-     */
-    protected static List<Object> searchPath(LinStore store, String key, Map<String, String> params, String[] children = []) {
-        final object = store.load(key)
-        if (!object) {
-            throw new FileNotFoundException("Lineage object $key not found")
-        }
-        final results = new LinkedList<Object>()
-        if (children && children.size() > 0) {
-            treatSubObject(store, key, object, children, params, results)
-        } else {
-            treatObject(object, params, results)
-        }
-
-        return results
-    }
-
-    private static void treatSubObject(LinStore store, String key, LinSerializable object, String[] children, Map<String, String> params, LinkedList<Object> results) {
-        final output = getSubObject(store, key, object, children)
-        if (!output) {
-            throw new FileNotFoundException("Lineage object $key#${children.join('.')} not found")
-        }
-        treatObject(output, params, results)
-    }
-
-    /**
-     * Get a metadata sub-object.
-     *
-     * @param store Store to retrieve lineage metadata objects.
-     * @param key Parent metadata key.
-     * @param object Parent object.
-     * @param children Array of string in indicating the properties to navigate to get the sub-object.
-     * @return Sub-object or null in it does not exist.
-     */
-    static Object getSubObject(LinStore store, String key, LinSerializable object, String[] children) {
-        return navigate(object, children.join('.'))
-    }
-
     /**
      * Evaluates object or the objects in a collection matches a set of parameter-value pairs. It includes in the results collection in case of match.
      *
@@ -157,23 +56,6 @@ class LinUtils {
         }
     }
 
-    /**
-     * Parses a query string and store them in parameter-value Map.
-     *
-     * @param queryString URI-like query string. (e.g. param1=value1&param2=value2).
-     * @return Map containing the parameter-value pairs of the query string.
-     */
-    static Map<String, String> parseQuery(String queryString) {
-        if( !queryString ) {
-            return [:]
-        }
-        final params = queryString.split('&').collectEntries {
-            it.split('=').collect { URLDecoder.decode(it, 'UTF-8') }
-        } as Map<String, String>
-        new LinPropertyValidator().validateQueryParams(params)
-        return params
-    }
-
     /**
      * Check if an object fulfill the parameter-value
      * 

modules/nf-lineage/src/main/nextflow/lineage/cli/LinCommandImpl.groovy

@@ -27,6 +27,7 @@ import nextflow.Session
 import nextflow.cli.CmdLineage
 import nextflow.config.ConfigMap
 import nextflow.dag.MermaidHtmlRenderer
+import nextflow.file.FileHelper
 import nextflow.lineage.LinHistoryRecord
 import nextflow.lineage.LinStore
 import nextflow.lineage.LinStoreFactory
@@ -98,13 +99,8 @@ class LinCommandImpl implements CmdLineage.LinCommand {
             return
         }
         try {
-            def entries = LinUtils.query(store, new URI(args[0]))
-            if( !entries ) {
-                println "No entries found for ${args[0]}"
-                return
-            }
-            entries = entries.size() == 1 ? entries[0] : entries
-            println LinUtils.encodeSearchOutputs(entries, true)
+            final uri = new URI(args[0])
+            println FileHelper.asPath(uri).text
         } catch (Throwable e) {
             println "Error loading ${args[0]} - ${e.message}"
         }
@@ -319,9 +315,15 @@ class LinCommandImpl implements CmdLineage.LinCommand {
             return
         }
         try {
-            println LinUtils.encodeSearchOutputs(store.search(args[0]).keySet().collect {asUriString(it)}, true)
+            final params = args.inject([:]) { acc, entry ->
+                final tokens = entry.tokenize('=')
+                acc[tokens[0]] = tokens[1]
+                acc
+            } as Map<String,String>
+            final results = store.search(params).keySet().collect { asUriString(it) }
+            println LinUtils.encodeSearchOutputs(results, true)
         } catch (Throwable e){
-            println "Error searching for ${args[0]}. ${e.message}"
+            println "Error searching for '${args.join(' ')}' -- ${e.message}"
         }
     }
 }

modules/nf-lineage/src/main/nextflow/lineage/fs/LinMetadataPath.groovy

@@ -29,27 +29,27 @@ import java.nio.file.attribute.FileTime
  */
 @CompileStatic
 class LinMetadataPath extends LinPath {
-    private byte[] results
+    private byte[] bytes
     private FileTime creationTime
 
-    LinMetadataPath(String resultsObject, FileTime creationTime, LinFileSystem fs, String path, String[] childs) {
-        super(fs, "${path}${childs ? '#'+ childs.join('.') : ''}")
-        this.results = resultsObject.getBytes("UTF-8")
+    LinMetadataPath(String object, FileTime creationTime, LinFileSystem fs, String path, String fragment) {
+        super(fs, "${path}${fragment ? '#'+fragment : ''}")
+        this.bytes = object.getBytes("UTF-8")
         this.creationTime = creationTime
     }
 
     InputStream newInputStream() {
-        return new ByteArrayInputStream(results)
+        return new ByteArrayInputStream(bytes)
     }
 
     SeekableByteChannel newSeekableByteChannel(){
-        return new LinMetadataSeekableByteChannel(results)
+        return new LinMetadataSeekableByteChannel(bytes)
     }
 
     <A extends BasicFileAttributes> A readAttributes(Class<A> type){
         return (A) new BasicFileAttributes() {
             @Override
-            long size() { return results.length }
+            long size() { return bytes.length }
 
             @Override
             FileTime lastModifiedTime() { return creationTime }