Comply with latest validation and add more related links to workflow record

deep_code/constants.py

@@ -29,3 +29,13 @@
     ".json"
 )
 PROJECT_COLLECTION_NAME = "deep-earth-system-data-lab"
+DEEPESDL_GIT_PULL_BASE = (
+    "https://deep.earthsystemdatalab.net/hub/user-redirect/git-pull"
+)
+APPLICATION_TYPE_JUPYTER_SPEC = (
+    "https://raw.githubusercontent.com/EOEPCA/metadata"
+    "-profile/refs/heads/1.0/schemas/application-type-jupyter-notebook"
+)
+APPLICATION_STAC_EXTENSION_SPEC = (
+    "https://stac-extensions.github.io/application/v0.1.0/schema.json"
+)

deep_code/tests/tools/test_publish.py

@@ -4,10 +4,12 @@
 from pathlib import Path
 from unittest.mock import MagicMock, mock_open, patch
 
+import pytest
 import yaml
 from pystac import Catalog
 
 from deep_code.tools.publish import Publisher
+from deep_code.utils.ogc_api_record import LinksBuilder
 
 
 class TestPublisher(unittest.TestCase):
@@ -107,3 +109,59 @@ def test_read_config_files(self):
         # Assertions
         self.assertEqual(self.publisher.dataset_config, dataset_config)
         self.assertEqual(self.publisher.workflow_config, workflow_config)
+
+
+class TestParseGithubNotebookUrl:
+    @pytest.mark.parametrize(
+        "url,repo_url,repo_name,branch,file_path",
+        [
+            (
+                "https://github.com/deepesdl/cube-gen/blob/main/Permafrost/Create-CCI-Permafrost-cube-EarthCODE.ipynb",
+                "https://github.com/deepesdl/cube-gen",
+                "cube-gen",
+                "main",
+                "Permafrost/Create-CCI-Permafrost-cube-EarthCODE.ipynb",
+            ),
+            (
+                "https://github.com/deepesdl/cube-gen/tree/release-1.0/Permafrost/Create-CCI-Permafrost-cube-EarthCODE.ipynb",
+                "https://github.com/deepesdl/cube-gen",
+                "cube-gen",
+                "release-1.0",
+                "Permafrost/Create-CCI-Permafrost-cube-EarthCODE.ipynb",
+            ),
+            (
+                "https://raw.githubusercontent.com/deepesdl/cube-gen/main/Permafrost/Create-CCI-Permafrost-cube-EarthCODE.ipynb",
+                "https://github.com/deepesdl/cube-gen",
+                "cube-gen",
+                "main",
+                "Permafrost/Create-CCI-Permafrost-cube-EarthCODE.ipynb",
+            ),
+        ],
+    )
+    def test_valid_urls(self, url, repo_url, repo_name, branch, file_path):
+        got_repo_url, got_repo_name, got_branch, got_file_path = LinksBuilder._parse_github_notebook_url(
+            url
+        )
+        assert got_repo_url == repo_url
+        assert got_repo_name == repo_name
+        assert got_branch == branch
+        assert got_file_path == file_path
+
+    def test_invalid_domain(self):
+        url = "https://gitlab.com/deepesdl/cube-gen/-/blob/main/Permafrost/Create-CCI-Permafrost-cube-EarthCODE.ipynb"
+        with pytest.raises(ValueError) as e:
+            LinksBuilder._parse_github_notebook_url(url)
+        assert "Only GitHub URLs are supported" in str(e.value)
+
+    def test_unexpected_github_format_missing_blob_or_tree(self):
+        # Missing the "blob" or "tree" segment
+        url = "https://github.com/deepesdl/cube-gen/main/Permafrost/Create-CCI-Permafrost-cube-EarthCODE.ipynb"
+        with pytest.raises(ValueError) as e:
+            LinksBuilder._parse_github_notebook_url(url)
+        assert "Unexpected GitHub URL format" in str(e.value)
+
+    def test_unexpected_raw_format_too_short(self):
+        url = "https://raw.githubusercontent.com/deepesdl/cube-gen/main"
+        with pytest.raises(ValueError) as e:
+            LinksBuilder._parse_github_notebook_url(url)
+        assert "Unexpected raw.githubusercontent URL format" in str(e.value)

deep_code/tests/utils/test_dataset_stac_generator.py

@@ -65,8 +65,11 @@ def setUp(self, mock_data_store):
         self.generator = OscDatasetStacGenerator(
             dataset_id="mock-dataset-id",
             collection_id="mock-collection-id",
+            workflow_id="dummy",
+            workflow_title="test",
             access_link="s3://mock-bucket/mock-dataset",
             documentation_link="https://example.com/docs",
+            license_type="proprietary",
             osc_status="ongoing",
             osc_region="Global",
             osc_themes=["climate", "environment"],

deep_code/tests/utils/test_ogc_api_record.py

@@ -1,6 +1,10 @@
 import unittest
 
-from deep_code.constants import OGC_API_RECORD_SPEC
+from deep_code.constants import (
+    APPLICATION_STAC_EXTENSION_SPEC,
+    APPLICATION_TYPE_JUPYTER_SPEC,
+    OGC_API_RECORD_SPEC,
+)
 from deep_code.utils.ogc_api_record import (
     Contact,
     ExperimentAsOgcRecord,
@@ -136,7 +140,9 @@ def test_record_properties_to_dict(self):
 
 class TestLinksBuilder(unittest.TestCase):
     def test_build_theme_links_for_records(self):
-        links_builder = LinksBuilder(themes=["climate", "ocean"])
+        links_builder = LinksBuilder(
+            themes=["climate", "ocean"], jupyter_kernel_info={}
+        )
         theme_links = links_builder.build_theme_links_for_records()
 
         expected_links = [
@@ -201,7 +207,14 @@ def test_workflow_as_ogc_record_initialization(self):
             workflow_record.jupyter_notebook_url, "https://example.com/notebook.ipynb"
         )
         self.assertEqual(workflow_record.properties, record_properties)
-        self.assertEqual(workflow_record.conformsTo, [OGC_API_RECORD_SPEC])
+        self.assertEqual(
+            workflow_record.conformsTo,
+            [
+                OGC_API_RECORD_SPEC,
+                APPLICATION_TYPE_JUPYTER_SPEC,
+                APPLICATION_STAC_EXTENSION_SPEC,
+            ],
+        )
         self.assertEqual(workflow_record.links[0]["rel"], "root")
         self.assertEqual(workflow_record.links[-1]["rel"], "self")
 

deep_code/tools/new.py

@@ -20,7 +20,11 @@ def generate_workflow_template(output_path: Optional[str] = None) -> str:
                 "title": "[Human-readable title of the workflow]",
                 "description": "[A concise summary of what the workflow does]",
                 "keywords": ["[KEYWORD1]", "[KEYWORD2]"],
-                "themes": ["[Thematic area(s) of focus (e.g. land, ocean, atmosphere)]","[THEME1]", "[THEME2]"],
+                "themes": [
+                    "[Thematic area(s) of focus (e.g. land, ocean, atmosphere)]",
+                    "[THEME1]",
+                    "[THEME2]",
+                ],
                 "license": "[License type (e.g. MIT, Apache-2.0, CC-BY-4.0, proprietary)]",
                 "jupyter_kernel_info": {
                     "name": "[Name of the execution environment or notebook kernel]",
@@ -61,8 +65,11 @@ def generate_dataset_template(output_path: Optional[str] = None) -> str:
         template = {
             "dataset_id": "[The name of the dataset object within your S3 bucket].zarr",
             "collection_id": "[A unique identifier for the dataset collection]",
-            "osc_themes": ["[Oceans]",  "[Open Science theme (choose from "
-                                           "https://opensciencedata.esa.int/themes/catalog)"],
+            "osc_themes": [
+                "[Oceans]",
+                "[Open Science theme (choose from "
+                "https://opensciencedata.esa.int/themes/catalog)",
+            ],
             "osc_region": "[Geographical coverage, e.g. 'global']",
             "dataset_status": "[Status of the dataset: 'ongoing', 'completed', or 'planned']",
             "documentation_link": "[Link to relevant documentation, publication, or handbook]",

deep_code/tools/publish.py

@@ -4,12 +4,12 @@
 # https://opensource.org/licenses/MIT.
 
 import copy
-import json
 import logging
 from datetime import datetime
 from pathlib import Path
 
 import fsspec
+import jsonpickle
 import yaml
 from pystac import Catalog, Link
 
@@ -22,7 +22,6 @@
 )
 from deep_code.utils.dataset_stac_generator import OscDatasetStacGenerator
 from deep_code.utils.github_automation import GitHubAutomation
-from deep_code.utils.helper import serialize
 from deep_code.utils.ogc_api_record import (
     ExperimentAsOgcRecord,
     LinksBuilder,
@@ -130,6 +129,7 @@ def __init__(
         self._read_config_files()
         self.collection_id = self.dataset_config.get("collection_id")
         self.workflow_title = self.workflow_config.get("properties", {}).get("title")
+        self.workflow_id = self.workflow_config.get("workflow_id")
 
         if not self.collection_id:
             raise ValueError("collection_id is missing in dataset config.")
@@ -151,11 +151,12 @@ def _write_to_file(file_path: str, data: dict):
         # Create the directory if it doesn't exist
         Path(file_path).parent.mkdir(parents=True, exist_ok=True)
         try:
-            json_content = json.dumps(data, indent=2, default=serialize)
+            # unpicklable=False -> plain JSON (drops type metadata); cycles are resolved.
+            json_content = jsonpickle.encode(data, unpicklable=False, indent=2)
         except TypeError as e:
             raise RuntimeError(f"JSON serialization failed: {e}")
 
-        with open(file_path, "w") as f:
+        with open(file_path, "w", encoding="utf-8") as f:
             f.write(json_content)
 
     def _update_and_add_to_file_dict(
@@ -217,6 +218,7 @@ def publish_dataset(self, write_to_file: bool = False):
         osc_region = self.dataset_config.get("osc_region")
         osc_themes = self.dataset_config.get("osc_themes")
         cf_params = self.dataset_config.get("cf_parameter")
+        license_type = self.dataset_config.get("license_type")
 
         if not dataset_id or not self.collection_id:
             raise ValueError("Dataset ID or Collection ID missing in the config.")
@@ -226,6 +228,9 @@ def publish_dataset(self, write_to_file: bool = False):
         generator = OscDatasetStacGenerator(
             dataset_id=dataset_id,
             collection_id=self.collection_id,
+            workflow_id=self.workflow_id,
+            workflow_title=self.workflow_title,
+            license_type=license_type,
             documentation_link=documentation_link,
             access_link=access_link,
             osc_status=dataset_status,
@@ -310,7 +315,7 @@ def _update_base_catalog(
 
         return base_catalog
 
-    def publish_workflow_experiment(self, write_to_file: bool = False):
+    def generate_workflow_experiment_records(self, write_to_file: bool = False) -> None:
         """prepare workflow and experiment as ogc api record to publish it to the
         specified GitHub repository."""
         workflow_id = self._normalize_name(self.workflow_config.get("workflow_id"))
@@ -328,16 +333,23 @@ def publish_workflow_experiment(self, write_to_file: bool = False):
         wf_record_properties = rg.build_record_properties(properties_list, contacts)
         # make a copy for experiment record
         exp_record_properties = copy.deepcopy(wf_record_properties)
+        jupyter_kernel_info = wf_record_properties.jupyter_kernel_info.to_dict()
 
-        link_builder = LinksBuilder(osc_themes)
+        link_builder = LinksBuilder(osc_themes, jupyter_kernel_info)
         theme_links = link_builder.build_theme_links_for_records()
+        application_link = link_builder.build_link_to_jnb(
+            self.workflow_title, jupyter_notebook_url
+        )
+        jnb_open_link = link_builder.make_related_link_for_opening_jnb_from_github(
+            jupyter_notebook_url=jupyter_notebook_url
+        )
 
         workflow_record = WorkflowAsOgcRecord(
             id=workflow_id,
             type="Feature",
             title=self.workflow_title,
             properties=wf_record_properties,
-            links=links + theme_links,
+            links=links + theme_links + application_link + jnb_open_link,
             jupyter_notebook_url=jupyter_notebook_url,
             themes=osc_themes,
         )
@@ -347,21 +359,24 @@ def publish_workflow_experiment(self, write_to_file: bool = False):
             del workflow_dict["jupyter_notebook_url"]
         if "osc_workflow" in workflow_dict["properties"]:
             del workflow_dict["properties"]["osc_workflow"]
+        # add workflow record to file_dict
         wf_file_path = f"workflows/{workflow_id}/record.json"
         file_dict = {wf_file_path: workflow_dict}
 
         # Build properties for the experiment record
         exp_record_properties.type = "experiment"
         exp_record_properties.osc_workflow = workflow_id
 
+        dataset_link = link_builder.build_link_to_dataset(self.collection_id)
+
         experiment_record = ExperimentAsOgcRecord(
             id=workflow_id,
             title=self.workflow_title,
             type="Feature",
             jupyter_notebook_url=jupyter_notebook_url,
             collection_id=self.collection_id,
             properties=exp_record_properties,
-            links=links + theme_links,
+            links=links + theme_links + dataset_link,
         )
         # Convert to dictionary and cleanup
         experiment_dict = experiment_record.to_dict()
@@ -371,6 +386,7 @@ def publish_workflow_experiment(self, write_to_file: bool = False):
             del experiment_dict["collection_id"]
         if "osc:project" in experiment_dict["properties"]:
             del experiment_dict["properties"]["osc:project"]
+        # add experiment record to file_dict
         exp_file_path = f"experiments/{workflow_id}/record.json"
         file_dict[exp_file_path] = experiment_dict
 
@@ -397,7 +413,9 @@ def publish_all(self, write_to_file: bool = False):
         """Publish both dataset and workflow/experiment in a single PR."""
         # Get file dictionaries from both methods
         dataset_files = self.publish_dataset(write_to_file=write_to_file)
-        workflow_files = self.publish_workflow_experiment(write_to_file=write_to_file)
+        workflow_files = self.generate_workflow_experiment_records(
+            write_to_file=write_to_file
+        )
 
         # Combine the file dictionaries
         combined_files = {**dataset_files, **workflow_files}

deep_code/utils/custom_xrlint_rules.py

@@ -71,7 +71,7 @@ def export_config() -> list:
                 "content-desc": "off",
                 "no-empty-attrs": "off",
                 "conventions": "off",
-                "time-coordinate": "off"
+                "time-coordinate": "off",
             }
         },
         "deepcode/recommended",

deep_code/utils/dataset_stac_generator.py

@@ -39,6 +39,9 @@ def __init__(
         self,
         dataset_id: str,
         collection_id: str,
+        workflow_id: str,
+        workflow_title: str,
+        license_type: str,
         access_link: str | None = None,
         documentation_link: str | None = None,
         osc_status: str = "ongoing",
@@ -49,6 +52,9 @@ def __init__(
     ):
         self.dataset_id = dataset_id
         self.collection_id = collection_id
+        self.workflow_id = workflow_id
+        self.workflow_title = workflow_title
+        self.license_type = license_type
         self.access_link = access_link or f"s3://deep-esdl-public/{dataset_id}"
         self.documentation_link = documentation_link
         self.osc_status = osc_status
@@ -478,6 +484,17 @@ def build_dataset_stac_collection(self) -> Collection:
             )
         )
 
+        collection.add_link(
+            Link(
+                rel="related",
+                target=f"../../experiments/{self.workflow_id}/record.json",
+                media_type="application/json",
+                title=f"Experiment: {self.workflow_title}",
+            )
+        )
+
+        collection.license = self.license_type
+
         # Validate OSC extension fields
         try:
             osc_extension.validate_extension()