Merge pull request #3334 from mashehu/update-crate-with-version-bump

rocrate: Update crate with version bump and handle new contributor field

Author: mashehu

CHANGELOG.md

@@ -64,6 +64,7 @@
 - build: Setup VS Code tests ([#3292](https://github.com/nf-core/tools/pull/3292))
 - Don't break gitpod.yml with template string ([#3332](https://github.com/nf-core/tools/pull/3332))
 - rocrate: remove duplicated entries for name and version ([#3333](https://github.com/nf-core/tools/pull/3333))
+- rocrate: Update crate with version bump and handle new contributor field ([#3334](https://github.com/nf-core/tools/pull/3334))
 
 ### Version updates
 

nf_core/pipelines/bump_version.py

@@ -11,6 +11,7 @@
 from ruamel.yaml import YAML
 
 import nf_core.utils
+from nf_core.pipelines.rocrate import ROCrate
 from nf_core.utils import Pipeline
 
 log = logging.getLogger(__name__)
@@ -127,6 +128,9 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
         yaml_key=["template", "version"],
     )
 
+    # update rocrate
+    ROCrate(pipeline_obj.wf_path).update_rocrate()
+
 
 def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None:
     """Bumps the required Nextflow version number of a pipeline.

nf_core/pipelines/rocrate.py

@@ -267,14 +267,26 @@ def add_main_authors(self, wf_file: rocrate.model.entity.Entity) -> None:
         # add author entity to crate
 
         try:
-            authors = self.pipeline_obj.nf_config["manifest.author"].split(",")
-            # remove spaces
-            authors = [a.strip() for a in authors]
+            authors = []
+            if "manifest.author" in self.pipeline_obj.nf_config:
+                authors.extend([a.strip() for a in self.pipeline_obj.nf_config["manifest.author"].split(",")])
+            if "manifest.contributor" in self.pipeline_obj.nf_config:
+                authors.extend(
+                    [
+                        c.get("name", "").strip()
+                        for c in self.pipeline_obj.nf_config["manifest.contributor"]
+                        if "name" in c
+                    ]
+                )
+            if not authors:
+                raise KeyError("No authors found")
             # add manifest authors as maintainer to crate
 
         except KeyError:
-            log.error("No author field found in manifest of nextflow.config")
+            log.error("No author or contributor fields found in manifest of nextflow.config")
             return
+        # remove duplicates
+        authors = list(set(authors))
         # look at git contributors for author names
         try:
             git_contributors: Set[str] = set()
@@ -336,6 +348,25 @@ def add_main_authors(self, wf_file: rocrate.model.entity.Entity) -> None:
             if author in authors:
                 wf_file.append_to("maintainer", author_entitity)
 
+    def update_rocrate(self) -> bool:
+        """
+        Update the rocrate file
+        """
+        # check if we need to output a json file and/or a zip file based on the file extensions
+        # try to find a json file
+        json_path: Optional[Path] = None
+        potential_json_path = Path(self.pipeline_dir, "ro-crate-metadata.json")
+        if potential_json_path.exists():
+            json_path = potential_json_path
+
+        # try to find a zip file
+        zip_path: Optional[Path] = None
+        potential_zip_path = Path(self.pipeline_dir, "ro-crate.crate.zip")
+        if potential_zip_path.exists():
+            zip_path = potential_zip_path
+
+        return self.create_rocrate(json_path=json_path, zip_path=zip_path)
+
 
 def get_orcid(name: str) -> Optional[str]:
     """

tests/pipelines/test_rocrate.py

@@ -1,5 +1,6 @@
 """Test the nf-core pipelines rocrate command"""
 
+import json
 import shutil
 import tempfile
 from pathlib import Path
@@ -12,6 +13,7 @@
 import nf_core.pipelines.create.create
 import nf_core.pipelines.rocrate
 import nf_core.utils
+from nf_core.pipelines.bump_version import bump_pipeline_version
 
 from ..test_pipelines import TestPipelines
 
@@ -125,3 +127,36 @@ def test_rocrate_creation_for_fetchngs(self):
 
         # Clean up
         shutil.rmtree(tmp_dir)
+
+    def test_update_rocrate(self):
+        """Run the nf-core rocrate command with a zip output"""
+
+        assert self.rocrate_obj.create_rocrate(json_path=self.pipeline_dir, zip_path=self.pipeline_dir)
+
+        # read the crate json file
+        with open(Path(self.pipeline_dir, "ro-crate-metadata.json")) as f:
+            crate = json.load(f)
+
+        # check the old version
+        self.assertEqual(crate["@graph"][2]["version"][0], "1.0.0dev")
+        # check creativeWorkStatus is InProgress
+        self.assertEqual(crate["@graph"][0]["creativeWorkStatus"], "InProgress")
+
+        # bump version
+        bump_pipeline_version(self.pipeline_obj, "1.1.0")
+
+        # Check that the crate was created
+        self.assertTrue(Path(self.pipeline_dir, "ro-crate.crate.zip").exists())
+
+        # Check that the crate was updated
+        self.assertTrue(Path(self.pipeline_dir, "ro-crate-metadata.json").exists())
+
+        # read the crate json file
+        with open(Path(self.pipeline_dir, "ro-crate-metadata.json")) as f:
+            crate = json.load(f)
+
+        # check that the version was updated
+        self.assertEqual(crate["@graph"][2]["version"][0], "1.1.0")
+
+        # check creativeWorkStatus is Stable
+        self.assertEqual(crate["@graph"][0]["creativeWorkStatus"], "Stable")