Remove legacy provenance format (#48)

Author: bentsherman

README.md

@@ -1,6 +1,17 @@
 # nf-prov
 
-Nextflow plugin to render provenance reports for pipeline runs. Now supporting [BioCompute Object](https://biocomputeobject.org/)!
+Nextflow plugin to render provenance reports for pipeline runs. Supports standard formats such as [BioCompute Object](https://biocomputeobject.org/) and [Workflow Run RO-Crate](https://www.researchobject.org/workflow-run-crate/).
+
+## Requirements
+
+| Version |	Minimum Nextflow version |
+| ------- | ------------------------ |
+| 1.5.x   | 25.04 |
+| 1.4.x   | 24.10 |
+| 1.3.x   | 24.10 |
+| 1.2.x   | 23.04 |
+| 1.1.x   | 23.04 |
+| 1.0.x   | 22.04 |
 
 ## Getting Started
 
@@ -14,20 +25,28 @@ plugins {
 prov {
   enabled = true
   formats {
-    legacy {
-      file = 'manifest.json'
+    bco {
+      file = 'bco.json'
+      overwrite = true
+    }
+    wrroc {
+      file = 'ro-crate-metadata.json'
       overwrite = true
     }
   }
 }
 ```
 
-Finally, run your Nextflow pipeline. You do not need to modify your pipeline script in order to use the `nf-prov` plugin. The plugin will automatically produce the specified provenance reports at the end of the workflow run.
+Any number of formats can be specified. You do not need to modify your pipeline script in order to use the `nf-prov` plugin.
+
+When you run your Nextflow pipeline, the plugin will automatically produce the specified provenance reports at the end of the run.
 
 ## Configuration
 
 *The `file`, `format`, and `overwrite` options have been deprecated since version 1.2.0. Use `formats` instead.*
 
+*The `legacy` format was removed in version 1.5.0. Consider using [data lineage](https://nextflow.io/docs/latest/data-lineage.html) instead.*
+
 The following options are available:
 
 `prov.enabled`
@@ -42,31 +61,10 @@ Configuration scope for the desired output formats. The following formats are av
 
 - `dag`: Render the task graph as a Mermaid diagram embedded in an HTML document. Supports the `file` and `overwrite` options.
 
-*Deprecated in version 1.4.0*
-
-- `legacy`: Render the legacy format originally defined in this plugin (default). Supports the `file` and `overwrite` options.
-
 *New in version 1.4.0*
 
 - `wrroc`: Render a [Workflow Run RO-Crate](https://www.researchobject.org/workflow-run-crate/). Includes all three profiles (Process, Workflow, and Provenance). See [WRROC.md](docs/WRROC.md) for more information about the additional config options for WRROC.
 
-Any number of formats can be specified, for example:
-
-```groovy
-prov {
-  formats {
-    bco {
-      file = 'bco.json'
-      overwrite = true
-    }
-    wrroc {
-      file = 'ro-crate-metadata.json'
-      overwrite = true
-    }
-  }
-}
-```
-
 See the [nf-prov-test](./nf-prov-test) directory for an example pipeline that produces every provenance format.
 
 `prov.patterns`

nf-prov-test/nextflow.config

@@ -19,10 +19,6 @@ prov {
             file = "${params.outdir}/dag.html"
             overwrite = true
         }
-        legacy {
-            file = "${params.outdir}/manifest.json"
-            overwrite = true
-        }
         wrroc {
             file = "${params.outdir}/ro-crate-metadata.json"
             overwrite = true

src/main/groovy/nextflow/prov/ProvConfig.groovy

@@ -16,6 +16,8 @@
 
 package nextflow.prov
 
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
 import nextflow.config.schema.ConfigOption
 import nextflow.config.schema.ConfigScope
 import nextflow.config.schema.ScopeName
@@ -25,6 +27,7 @@ import nextflow.script.dsl.Description
 @Description('''
     The `prov` scope allows you to configure the `nf-prov` plugin.
 ''')
+@CompileStatic
 class ProvConfig implements ConfigScope {
 
     @ConfigOption
@@ -54,29 +57,37 @@ class ProvConfig implements ConfigScope {
 }
 
 
+@Slf4j
+@CompileStatic
 class ProvFormatsConfig implements ConfigScope {
 
-    @Description('Configuration scope for the BCO output format.')
+    @Description('''
+        Configuration scope for the BCO output format.
+    ''')
     final ProvBcoConfig bco
 
-    @Description('Configuration scope for the DAG output format.')
+    @Description('''
+        Configuration scope for the DAG output format.
+    ''')
     final ProvDagConfig dag
 
-    @Description('Configuration scope for the legacy output format.')
-    final ProvLegacyConfig legacy
-
-    @Description('Configuration scope for the WRROC output format.')
+    @Description('''
+        Configuration scope for the WRROC output format.
+    ''')
     final ProvWrrocConfig wrroc
 
     ProvFormatsConfig(Map opts) {
         bco = opts.bco ? new ProvBcoConfig(opts.bco as Map) : null
         dag = opts.dag ? new ProvDagConfig(opts.dag as Map) : null
-        legacy = opts.legacy ? new ProvLegacyConfig(opts.legacy as Map) : null
         wrroc = opts.wrroc ? new ProvWrrocConfig(opts.wrroc as Map) : null
+
+        if( opts.legacy )
+            log.warn "The `legacy` provenance format is no longer supported"
     }
 }
 
 
+@CompileStatic
 class ProvBcoConfig implements ConfigScope {
 
     @ConfigOption
@@ -87,7 +98,7 @@ class ProvBcoConfig implements ConfigScope {
 
     @ConfigOption
     @Description('''
-        When `true` overwrites any existing BCO manifest with the same name.
+        When `true` overwrites any existing BCO manifest with the same name (default: `false`).
     ''')
     final boolean overwrite
 
@@ -98,6 +109,7 @@ class ProvBcoConfig implements ConfigScope {
 }
 
 
+@CompileStatic
 class ProvDagConfig implements ConfigScope {
 
     @ConfigOption
@@ -108,7 +120,7 @@ class ProvDagConfig implements ConfigScope {
 
     @ConfigOption
     @Description('''
-        When `true` overwrites any existing DAG diagram with the same name.
+        When `true` overwrites any existing DAG diagram with the same name (default: `false`).
     ''')
     boolean overwrite
 
@@ -119,27 +131,7 @@ class ProvDagConfig implements ConfigScope {
 }
 
 
-class ProvLegacyConfig implements ConfigScope {
-
-    @ConfigOption
-    @Description('''
-        The file name of the legacy manifest.
-    ''')
-    final String file
-
-    @ConfigOption
-    @Description('''
-        When `true` overwrites any existing legacy manifest with the same name.
-    ''')
-    final boolean overwrite
-
-    ProvLegacyConfig(Map opts) {
-        file = opts.file
-        overwrite = opts.overwrite as boolean
-    }
-}
-
-
+@CompileStatic
 class ProvWrrocConfig implements ConfigScope {
 
     @ConfigOption
@@ -150,7 +142,7 @@ class ProvWrrocConfig implements ConfigScope {
 
     @ConfigOption
     @Description('''
-        When `true` overwrites any existing Workflow Run RO-Crate with the same name.
+        When `true` overwrites any existing Workflow Run RO-Crate with the same name (default: `false`).
     ''')
     final boolean overwrite
 

src/main/groovy/nextflow/prov/ProvObserver.groovy

@@ -28,7 +28,6 @@ import nextflow.Session
 import nextflow.processor.TaskRun
 import nextflow.prov.renderers.BcoRenderer
 import nextflow.prov.renderers.DagRenderer
-import nextflow.prov.renderers.LegacyRenderer
 import nextflow.prov.renderers.WrrocRenderer
 import nextflow.trace.TraceObserverV2
 import nextflow.trace.event.FilePublishEvent
@@ -77,11 +76,6 @@ class ProvObserver implements TraceObserverV2 {
         if( config.dag )
             result.add(new DagRenderer(config.dag))
 
-        if( config.legacy ) {
-            log.warn "The legacy format is deprecated -- it will be removed in a future version"
-            result.add(new LegacyRenderer(config.legacy))
-        }
-
         if( config.wrroc )
             result.add(new WrrocRenderer(config.wrroc))
 
@@ -158,7 +152,6 @@ class ProvObserver implements TraceObserverV2 {
         return switch( renderer ) {
             case BcoRenderer -> 'BCO';
             case DagRenderer -> 'DAG';
-            case LegacyRenderer -> 'legacy';
             case WrrocRenderer -> 'WRROC';
             default -> null;
         }

src/main/groovy/nextflow/prov/ProvObserverFactory.groovy

@@ -44,7 +44,7 @@ class ProvObserverFactory implements TraceObserverFactoryV2 {
             return null
 
         if( !config.formats ) {
-            log.warn "Config setting `prov.formats` is not defined, no provenance reports will be produced"
+            log.warn "Config setting `prov.formats` is not defined -- no provenance reports will be produced"
             return null
         }
 

src/main/groovy/nextflow/prov/ProvPlugin.groovy

@@ -18,7 +18,6 @@ package nextflow.prov
 
 import groovy.transform.CompileStatic
 import nextflow.plugin.BasePlugin
-import nextflow.plugin.Scoped
 import org.pf4j.PluginWrapper
 
 /**