ro_crate -> rocrate

nf_core/__main__.py

@@ -35,6 +35,7 @@
     pipelines_launch,
     pipelines_lint,
     pipelines_list,
+    pipelines_rocrate,
     pipelines_schema_build,
     pipelines_schema_docs,
     pipelines_schema_lint,
@@ -85,7 +86,7 @@
         },
         {
             "name": "For developers",
-            "commands": ["create", "lint", "bump-version", "sync", "schema", "create-logo"],
+            "commands": ["create", "lint", "bump-version", "sync", "schema", "rocrate", "create-logo"],
         },
     ],
     "nf-core modules": [
@@ -569,8 +570,8 @@ def command_pipelines_list(ctx, keywords, sort, json, show_archived):
     pipelines_list(ctx, keywords, sort, json, show_archived)
 
 
-# nf-core pipelines ro-crate
-@pipelines.command("ro-crate")
+# nf-core pipelines rocrate
+@pipelines.command("rocrate")
 @click.argument(
     "pipeline_dir",
     type=click.Path(exists=True),
@@ -594,7 +595,7 @@ def command_pipelines_list(ctx, keywords, sort, json, show_archived):
     default="",
 )
 @click.pass_context
-def ro_crate(
+def rocrate(
     ctx,
     pipeline_dir: str,
     json_path: str,
@@ -604,7 +605,7 @@ def ro_crate(
     """
     Make an Research Object Crate
     """
-    pipelines_ro_crate(ctx, pipeline_dir, json_path, zip_path, pipeline_version)
+    pipelines_rocrate(ctx, pipeline_dir, json_path, zip_path, pipeline_version)
 
 
 # nf-core pipelines sync

nf_core/commands_pipelines.py

@@ -278,8 +278,8 @@ def pipelines_list(ctx, keywords, sort, json, show_archived):
     stdout.print(list_workflows(keywords, sort, json, show_archived))
 
 
-# nf-core pipelines ro-crate
-def pipelines_ro_crate(
+# nf-core pipelines rocrate
+def pipelines_rocrate(
     ctx,
     pipeline_dir: Union[str, Path],
     json_path: Optional[Union[str, Path]],
@@ -299,7 +299,7 @@ def pipelines_ro_crate(
             zip_path = Path(zip_path)
         try:
             rocrate_obj = ROCrate(pipeline_dir, pipeline_version)
-            rocrate_obj.create_ro_crate(pipeline_dir, metadata_path=json_path, zip_path=zip_path)
+            rocrate_obj.create_rocrate(pipeline_dir, metadata_path=json_path, zip_path=zip_path)
         except (UserWarning, LookupError, FileNotFoundError) as e:
             log.error(e)
             sys.exit(1)

nf_core/pipelines/rocrate.py

@@ -3,15 +3,14 @@
 
 import logging
 import os
+import re
 import sys
 import tempfile
 from datetime import datetime
 from pathlib import Path
 from typing import Dict, List, Optional, Set, Union
-from urllib.parse import quote
 
 import requests
-import rocrate.model.entity
 import rocrate.rocrate
 from git import GitCommandError, InvalidGitRepositoryError
 from rich.progress import BarColumn, Progress
@@ -52,7 +51,7 @@ def __init__(self, pipeline_dir: Path, version="") -> None:
 
         setup_requests_cachedir()
 
-    def create_ro_crate(
+    def create_rocrate(
         self, outdir: Path, metadata_path: Union[None, Path] = None, zip_path: Union[None, Path] = None
     ) -> None:
         """
@@ -96,7 +95,7 @@ def create_ro_crate(
                     log.error(f"Could not checkout version {self.version}")
                     sys.exit(1)
         self.version = self.pipeline_obj.nf_config.get("manifest.version", "")
-        self.make_workflow_ro_crate()
+        self.make_workflow_rocrate()
 
         # Save just the JSON metadata file
         if metadata_path is not None:
@@ -123,7 +122,7 @@ def create_ro_crate(
         # Change back to the original directory
         os.chdir(current_path)
 
-    def make_workflow_ro_crate(self) -> None:
+    def make_workflow_rocrate(self) -> None:
         """
         Create an RO Crate for a pipeline
         """
@@ -258,7 +257,7 @@ def set_main_entity(self, main_entity_filename: str):
         log.debug(f"Adding topics: {topics}")
         self.crate.mainEntity.append_to("keywords", topics)
 
-        # self.add_main_authors(self.crate.mainEntity)
+        self.add_main_authors(self.crate.mainEntity)
 
         self.crate.mainEntity = self.crate.mainEntity
 
@@ -323,9 +322,14 @@ def add_main_authors(self, wf_file: rocrate.model.entity.Entity) -> None:
 
         for author in named_contributors:
             log.debug(f"Adding author: {author}")
+            assert self.pipeline_obj.repo is not None  # mypy
+            # get email from git log
+            email = self.pipeline_obj.repo.git.log(f"--author={author}", "--pretty=format:%ae", "-1")
             orcid = get_orcid(author)
             author_entitity = self.crate.add(
-                Person(self.crate, orcid if orcid is not None else "#" + quote(author), properties={"name": author})
+                Person(
+                    self.crate, orcid if orcid is not None else "#" + email, properties={"name": author, "email": email}
+                )
             )
             wf_file.append_to("creator", author_entitity)
             if author in authors:
@@ -335,7 +339,6 @@ def add_workflow_files(self):
         """
         Add workflow files to the RO Crate
         """
-        import re
 
         import nf_core.utils
 
@@ -360,7 +363,7 @@ def add_workflow_files(self):
                     wf_dir,
                     dest_path=wf_dir,
                     properties={
-                        "description": f"nf-core {component_type} [{component_name}](https://nf-co.re/{component_type}/{component_name}) installed from the [nf-core/modules repository](https://github.com/nf-core/modules/)."
+                        "description": f"nf-core {re.sub('s$', '', component_type)} [{component_name}](https://nf-co.re/{component_type}/{component_name}) installed from the [nf-core/modules repository](https://github.com/nf-core/modules/)."
                     },
                 )
         wf_locals = [

tests/test_rocrate.py

@@ -54,7 +54,7 @@ def test_rocrate_creation(self):
 
         # Run the command
         self.rocrate_obj = nf_core.pipelines.rocrate.ROCrate(self.test_pipeline_dir)
-        self.rocrate_obj.create_ro_crate(self.test_pipeline_dir, metadata_path=Path(self.test_pipeline_dir))
+        self.rocrate_obj.create_rocrate(self.test_pipeline_dir, metadata_path=Path(self.test_pipeline_dir))
 
         # Check that the crate was created
         self.assertTrue(Path(self.test_pipeline_dir, "ro-crate-metadata.json").exists())