add functionality and testing around addition of links when publishing a dataset

Author: blue442

foundry/foundry.py

@@ -374,6 +374,8 @@ def publish_dataset(
             dataset_doi (str): The DOI for this dataset (not an associated paper).
             related_dois (list): DOIs related to this dataset,
                     not including the dataset's own DOI (for example, an associated paper's DOI).
+            links (list[dict]): List of dicts describing links associated with the dataset; in the format:
+                {"type":str, "doi":str, "url":str, "description":str, "bibtex":str}
 
         Returns
         -------
@@ -404,6 +406,17 @@ def publish_dataset(
         self.connect_client.set_project_block(
             self.config.metadata_key, foundry_metadata)
 
+        # add links
+        links = kwargs.get("links")
+        if links is not None:
+            # make sure it's a list
+            links = links if isinstance(links, list) else [links]
+            for link in links:
+                # validate links
+                if self.validate_link(link):
+                    # add valid links
+                    self.connect_client.add_links(link)
+
         # upload via HTTPS if specified
         if https_data_path:
             # gather auth'd clients necessary for publication to endpoint
@@ -787,6 +800,15 @@ def validate_metadata(self, metadata):
                 field_name = ".".join([item for item in error['loc'] if isinstance(item, str)])
                 error_description = error['msg']
                 error_message = f"""There is an issue validating the metadata for the field '{field_name}':
-                The error message returned is: '{error_description}'."""
+                                The error message returned is: '{error_description}'."""
                 logger.error(error_message)
             raise e
+
+    def validate_link(self, link):
+        valid_keys = ["type", "doi", "url", "description", "bibtex"]
+        link_keys = [*link]
+        if not all(key in valid_keys for key in link_keys):
+            raise ValueError(f"A key in one of the submitted link ({link_keys}) is not of the valid options: "
+                             f"{valid_keys}")
+        else:
+            return True

tests/test_foundry.py

@@ -366,6 +366,62 @@ def test_publish_with_https():
     _write_test_data(local_path)
 
     res = f.publish_dataset(pub_test_metadata, title, authors, https_data_path=local_path, short_name=short_name)
+    assert res['success']
+    assert res['source_id'] == f"_test_{short_name}_v1.1"
+
+
+@pytest.mark.skipif(bool(is_gha), reason="Not run as part of GHA CI")
+def test_publish_bad_links_with_https():
+    """System test: Assess the end-to-end publication of a dataset via HTTPS
+    """
+
+    f = Foundry(index="mdf-test", authorizers=auths)
+    timestamp = datetime.now().timestamp()
+    title = "https_publish_test_{:.0f}".format(timestamp)
+    short_name = "https_pub_{:.0f}".format(timestamp)
+    authors = ["A Scourtas"]
+    local_path = "./data/https_test"
+    links = {"horse": "link", "doi": "3", "url": "www.test.com", "description": "string", "bibtex": "bib"}
+
+    # create test JSON to upload (if it doesn't already exist)
+    _write_test_data(local_path)
+
+    with pytest.raises(Exception) as exc_info:
+        f.publish_dataset(pub_test_metadata,
+                          title,
+                          authors,
+                          https_data_path=local_path,
+                          short_name=short_name,
+                          links=links)
+    # err = exc_info.value
+    # assert hasattr(err, '__cause__')
+    # assert isinstance(err.__cause__, ValueError)
+    assert isinstance(exc_info.type(), ValueError)
+    _delete_test_data(f)
+
+
+@pytest.mark.skipif(bool(is_gha), reason="Not run as part of GHA CI")
+def test_publish_links_with_https():
+    """System test: Assess the end-to-end publication of a dataset via HTTPS
+    """
+
+    f = Foundry(index="mdf-test", authorizers=auths)
+    timestamp = datetime.now().timestamp()
+    title = "https_publish_test_{:.0f}".format(timestamp)
+    short_name = "https_pub_{:.0f}".format(timestamp)
+    authors = ["A Scourtas"]
+    local_path = "./data/https_test"
+    links = {"type": "link", "doi": "3", "url": "www.test.com", "description": "string", "bibtex": "bib"}
+
+    # create test JSON to upload (if it doesn't already exist)
+    _write_test_data(local_path)
+
+    res = f.publish_dataset(pub_test_metadata,
+                            title,
+                            authors,
+                            https_data_path=local_path,
+                            short_name=short_name,
+                            links=links)
 
     assert res['success']
     assert res['source_id'] == f"_test_{short_name}_v1.1"