Remove the use of URL fragments

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

Author: bentsherman

docs/reference/channel.md

@@ -72,7 +72,7 @@ The `channel.fromLineage` factory creates a channel that emits files from the {r
 
 ```nextflow
 channel
-    .fromLineage(workflowRun: 'lid://0d1d1622ced3e4edc690bec768919b45', labels: ['alpha', 'beta'])
+    .fromLineage(workflowLaunch: 'lid://0d1d1622ced3e4edc690bec768919b45', labels: ['alpha', 'beta'])
     .view()
 ```
 
@@ -86,7 +86,7 @@ Available options:
 `taskRun`
 : LID of the task run that produced the desired files.
 
-`workflowRun`
+`workflowLaunch`
 : LID of the workflow run that produced the desired files.
 
 (channel-fromlist)=

docs/reference/cli.md

@@ -716,8 +716,8 @@ List the Nextflow runs with lineage metadata enabled, printing the corresponding
 
 ```console
 $ nextflow lineage list
-TIMESTAMP          	RUN NAME              	SESSION ID                          	LINEAGE ID                            
-2025-04-22 14:45:43	backstabbing_heyrovsky	21bc4fad-e8b8-447d-9410-388f926a711f	lid://c914d714877cc5c882c55a5428b510b1
+TIMESTAMP               RUN NAME        SESSION ID                              LAUNCH LID                              RUN LID                               
+2025-05-02 19:06:15 CDT stoic_shaw      bc79451f-c573-4b7d-8e7c-697be8d9cefc    lid://cd7197c02ab1250eafc2bf7499715e5f  lid://304c57e48ab6b324715ad2c5ba55b25e
 ```
 
 View a lineage record.
@@ -726,12 +726,6 @@ View a lineage record.
 $ nextflow lineage view <lid>
 ```
 
-The output of a workflow run can be shown by appending `#output` to the workflow run LID:
-
-```console
-$ nextflow lineage view lid://c914d714877cc5c882c55a5428b510b1#output
-```
-
 :::{tip}
 You can use the [jq](https://jqlang.org/) command-line tool to apply further queries and transformations on the resulting lineage record.
 :::

modules/nextflow/src/main/groovy/nextflow/cli/CmdLineage.groovy

@@ -40,8 +40,8 @@ class CmdLineage extends CmdBase implements UsageAware {
     private static final String NAME = 'lineage'
 
     interface LinCommand extends ExtensionPoint {
-        void log(ConfigMap config)
-        void describe(ConfigMap config, List<String> args)
+        void list(ConfigMap config)
+        void view(ConfigMap config, List<String> args)
         void render(ConfigMap config, List<String> args)
         void diff(ConfigMap config, List<String> args)
         void find(ConfigMap config, List<String> args)
@@ -61,8 +61,8 @@ class CmdLineage extends CmdBase implements UsageAware {
     private ConfigMap config
 
     CmdLineage() {
-        commands << new CmdLog()
-        commands << new CmdDescribe()
+        commands << new CmdList()
+        commands << new CmdView()
         commands << new CmdRender()
         commands << new CmdDiff()
         commands << new CmdFind()
@@ -94,7 +94,7 @@ class CmdLineage extends CmdBase implements UsageAware {
         // load the command operations
         this.operation = Plugins.getExtension(LinCommand)
         if( !operation )
-            throw new IllegalStateException("Unable to load lineage extensions.")
+            throw new IllegalStateException("Unable to load lineage records.")
         // consume the first argument
         getCmd(args).apply(args.drop(1))
     }
@@ -148,7 +148,7 @@ class CmdLineage extends CmdBase implements UsageAware {
         throw new AbortOperationException(msg)
     }
 
-    class CmdLog implements SubCmd {
+    class CmdList implements SubCmd {
 
         @Override
         String getName() {
@@ -157,7 +157,7 @@ class CmdLineage extends CmdBase implements UsageAware {
 
         @Override
         String getDescription() {
-            return 'List the executions with lineage enabled'
+            return 'List all workflow runs with lineage enabled'
         }
 
         @Override
@@ -167,7 +167,7 @@ class CmdLineage extends CmdBase implements UsageAware {
                 usage()
                 return
             }
-            operation.log(config)
+            operation.list(config)
         }
 
         @Override
@@ -177,7 +177,7 @@ class CmdLineage extends CmdBase implements UsageAware {
         }
     }
 
-    class CmdDescribe implements SubCmd{
+    class CmdView implements SubCmd{
 
         @Override
         String getName() {
@@ -186,7 +186,7 @@ class CmdLineage extends CmdBase implements UsageAware {
 
         @Override
         String getDescription() {
-            return 'Print the description of a Lineage ID (lid)'
+            return 'View a lineage record'
         }
 
         void apply(List<String> args) {
@@ -196,7 +196,7 @@ class CmdLineage extends CmdBase implements UsageAware {
                 return
             }
 
-            operation.describe(config, args)
+            operation.view(config, args)
         }
 
         @Override
@@ -229,7 +229,7 @@ class CmdLineage extends CmdBase implements UsageAware {
         @Override
         void usage() {
             println description
-            println "Usage: nextflow $NAME $name <workflow output lid> [<html output file>]"
+            println "Usage: nextflow $NAME $name <lid> [<html output file>]"
         }
 
     }
@@ -241,7 +241,7 @@ class CmdLineage extends CmdBase implements UsageAware {
 
         @Override
         String getDescription() {
-            return 'Show differences between two lineage descriptions'
+            return 'Show differences between two lineage records'
         }
 
         void apply(List<String> args) {
@@ -268,12 +268,12 @@ class CmdLineage extends CmdBase implements UsageAware {
 
         @Override
         String getDescription() {
-            return 'Find lineage metadata descriptions matching with a query'
+            return 'Find lineage records that match a query'
         }
 
         void apply(List<String> args) {
-            if (args.size() != 1) {
-                println("ERROR: Incorrect number of parameters")
+            if (args.size() == 0) {
+                println("ERROR: At least one key-value pair is required")
                 usage()
                 return
             }
@@ -283,7 +283,7 @@ class CmdLineage extends CmdBase implements UsageAware {
         @Override
         void usage() {
             println description
-            println "Usage: nextflow $NAME $name <query>"
+            println "Usage: nextflow $NAME $name <key>=<value> [<key>=<value> ...]"
         }
 
     }

modules/nextflow/src/main/groovy/nextflow/extension/LinExtension.groovy

@@ -29,7 +29,7 @@ interface LinExtension {
     static final Map PARAMS = [
         labels: List,
         taskRun: [String,GString],
-        workflowRun: [String,GString],
+        workflowLaunch: [String,GString],
     ]
 
     /**

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

@@ -38,30 +38,33 @@ class DefaultLinHistoryLog implements LinHistoryLog {
             Files.createDirectories(path)
     }
 
-    void write(String name, UUID key, String runLid, Date date = null) {
-        assert key
+    @Override
+    void write(String name, UUID id, String launchLid, String runLid, Date date = null) {
+        assert id
         def timestamp = date ?: new Date()
-        final recordFile = path.resolve(key.toString())
+        final recordFile = path.resolve(id.toString())
         try {
-            recordFile.text = new LinHistoryRecord(timestamp, name, key, runLid).toString()
-            log.trace("Record for $key written in lineage history log ${FilesEx.toUriString(this.path)}")
+            recordFile.text = new LinHistoryRecord(timestamp, name, id, launchLid, runLid).toString()
+            log.trace("Record for $id written in lineage history log ${FilesEx.toUriString(this.path)}")
         }catch (Throwable e) {
-            log.warn("Can't write record $key file ${FilesEx.toUriString(recordFile)}", e.message)
+            log.warn("Can't write record $id file ${FilesEx.toUriString(recordFile)}", e.message)
         }
     }
 
+    @Override
     void updateRunLid(UUID id, String runLid) {
         assert id
         final recordFile = path.resolve(id.toString())
         try {
             def current = LinHistoryRecord.parse(path.resolve(id.toString()).text)
-            recordFile.text = new LinHistoryRecord(current.timestamp, current.runName, id, runLid).toString()
+            recordFile.text = new LinHistoryRecord(current.timestamp, current.runName, id, current.launchLid, runLid).toString()
         }
         catch (Throwable e) {
             log.warn("Can't read session $id file: ${FilesEx.toUriString(recordFile)}", e.message)
         }
     }
 
+    @Override
     List<LinHistoryRecord> getRecords(){
         List<LinHistoryRecord> list = new LinkedList<LinHistoryRecord>()
         try {
@@ -73,6 +76,7 @@ class DefaultLinHistoryLog implements LinHistoryLog {
         return list.sort {it.timestamp }
     }
 
+    @Override
     LinHistoryRecord getRecord(UUID id) {
         assert id
         final recordFile = path.resolve(id.toString())

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

@@ -49,8 +49,8 @@ class LinExtensionImpl implements LinExtension {
 
     private static Map<String, List<String>> buildQueryParams(Map<String,?> opts) {
         final queryParams = [type: [FileOutput.class.simpleName] ]
-        if( opts.workflowRun )
-            queryParams['workflowRun'] = [opts.workflowRun as String]
+        if( opts.workflowLaunch )
+            queryParams['workflowLaunch'] = [opts.workflowLaunch as String]
         if( opts.taskRun )
             queryParams['taskRun'] = [opts.taskRun as String]
         if( opts.labels )

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

@@ -26,9 +26,10 @@ interface LinHistoryLog {
      *
      * @param name Workflow execution name.
      * @param sessionId Workflow session ID.
+     * @param launchLid Workflow launch Lineage ID.
      * @param runLid Workflow run ID.
      */
-    void write(String name, UUID sessionId, String runLid)
+    void write(String name, UUID sessionId, String launchLid, String runLid)
 
     /**
      * Updates the run LID for a given session ID.

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

@@ -35,12 +35,14 @@ class LinHistoryRecord {
     final Date timestamp
     final String runName
     final UUID sessionId
+    final String launchLid
     final String runLid
 
-    LinHistoryRecord(Date timestamp, String name, UUID sessionId, String runLid) {
+    LinHistoryRecord(Date timestamp, String name, UUID sessionId, String launchLid, String runLid) {
         this.timestamp = timestamp
         this.runName = name
         this.sessionId = sessionId
+        this.launchLid = launchLid
         this.runLid = runLid
     }
 
@@ -51,6 +53,7 @@ class LinHistoryRecord {
             timestamp ? TIMESTAMP_FMT.format(timestamp) : '-',
             runName ?: '-',
             sessionId.toString(),
+            launchLid ?: '-',
             runLid ?: '-',
         )
     }
@@ -62,8 +65,8 @@ class LinHistoryRecord {
 
     static LinHistoryRecord parse(String line) {
         final cols = line.tokenize('\t')
-        if (cols.size() == 4) {
-            return new LinHistoryRecord(TIMESTAMP_FMT.parse(cols[0]), cols[1], UUID.fromString(cols[2]), cols[3])
+        if (cols.size() == 5) {
+            return new LinHistoryRecord(TIMESTAMP_FMT.parse(cols[0]), cols[1], UUID.fromString(cols[2]), cols[3], cols[4])
         }
         throw new IllegalArgumentException("Not a valid history entry: `$line`")
     }