cleanup

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

README.md

@@ -69,14 +69,6 @@ prov {
 
 List of file patterns to include in the provenance report, from the set of published files. By default, all published files are included.
 
-## Examples
-
-```bash
-nextflow run https://github.com/ORGANIZATION/REPOSITORY_ID -profile docker
-nextflow run https://bitbucket.org/ORGANIZATION/REPOSITORY_ID -profile docker
-nextflow run https://gitlab.com/PROJECT/REPOSITORY_ID -profile docker
-```
-
 ## Development
 
 Run the following commands to build and test the nf-prov Nextflow plugin. Refer to the [nf-hello](https://github.com/nextflow-io/nf-hello) README for additional instructions (_e.g._ for publishing the plugin).

plugins/nf-prov/src/main/nextflow/prov/BcoRenderer.groovy

@@ -39,58 +39,6 @@ class BcoRenderer implements Renderer {
 
     private boolean overwrite
 
-    private URL repository
-
-    private String commitId
-
-    private String launchDir
-
-    private String projectDir
-
-    private String workDir
-
-    /**
-     * Normalize local paths to remove environment-specific directories.
-     *
-     * @param path
-     */
-    private String normalizePath(Path path) {
-        normalizePath(path.toUriString())
-    }
-
-    private String normalizePath(String path) {
-        // replace work directory with relative path
-        if( path.startsWith(workDir) )
-            return path.replace(workDir, 'work')
-
-        // replace project directory with source URL (if applicable)
-        if( repository && path.startsWith(projectDir) )
-            return getProjectSourceUrl(path)
-
-        // replace launch directory with relative path
-        if( path.startsWith(launchDir) )
-            return path.replace(launchDir + '/', '')
-
-        return path
-    }
-
-    /**
-     * Get the source URL for a project asset.
-     *
-     * @param path
-     */
-    private String getProjectSourceUrl(String path) {
-        // TODO: add other git providers
-        if( repository.host == 'github.com' )
-            return path.replace(projectDir, "${repository}/tree/${commitId}")
-        else if( repository.host == 'bitbucket.org' )
-            return path.replace(projectDir, "${repository}/src/${commitId}")
-        else if( repository.host == 'gitlab.com' )
-            return path.replace(projectDir, "${repository}/-/tree/${commitId}")
-        else
-            return path
-    }
-
     @Delegate
     private PathNormalizer normalizer
 
@@ -114,12 +62,6 @@ class BcoRenderer implements Renderer {
         final manifest = metadata.manifest
         final nextflowMeta = metadata.nextflow
 
-        this.repository = metadata.repository ? new URL(metadata.repository) : null
-        this.commitId = metadata.commitId
-        this.projectDir = metadata.projectDir.toUriString()
-        this.launchDir = metadata.launchDir.toUriString()
-        this.workDir = metadata.workDir.toUriString()
-
         final dateCreated = DateTimeFormatter.ISO_OFFSET_DATE_TIME.format(metadata.start)
         final authors = (manifest.author ?: '').tokenize(',')*.trim()
         final nextflowVersion = nextflowMeta.version.toString()

plugins/nf-prov/src/main/nextflow/prov/PathNormalizer.groovy

@@ -79,11 +79,16 @@ class PathNormalizer {
      * @param path
      */
     private String getProjectSourceUrl(String path) {
-        // TODO: add other git providers
-        if( repository.host == 'github.com' )
+        switch( repository.host ) {
+        case 'bitbucket.org':
+            return path.replace(projectDir, "${repository}/src/${commitId}")
+        case 'github.com':
             return path.replace(projectDir, "${repository}/tree/${commitId}")
-        else
+        case 'gitlab.com':
+            return path.replace(projectDir, "${repository}/-/tree/${commitId}")
+        default:
             return path
+        }
     }
 
 }