Add avu get func and its integration tests

integration_tests.py

@@ -117,6 +117,27 @@ def _test_avu_rmw_collection(ctx, rmw_attributes):
     return result
 
 
+def _test_avu_get_attr_val_of_coll(ctx, attr, value):
+    # Test getting the value of an attribute on a collection
+    tmp_coll = _create_tmp_collection(ctx)
+    ctx.msi_add_avu('-c', tmp_coll, attr, value, "baz")
+    result = avu.get_attr_val_of_coll(ctx, tmp_coll, attr)
+    collection.remove(ctx, tmp_coll)
+    return result
+
+
+def _test_avu_get_attr_val_of_coll_exception(ctx):
+    # Test that getting a non existing attribute on a collection raises an exception (True for exception raised)
+    tmp_coll = _create_tmp_collection(ctx)
+    result = False
+    try:
+        result = avu.get_attr_val_of_coll(ctx, tmp_coll, "foo")
+    except Exception:
+        result = True
+    collection.remove(ctx, tmp_coll)
+    return result
+
+
 def _test_folder_set_retry_avus(ctx):
     tmp_coll = _create_tmp_collection(ctx)
     folder.folder_secure_set_retry_avus(ctx, tmp_coll, 2)
@@ -482,6 +503,12 @@ def _test_folder_secure_func(ctx, func):
      "check": lambda x: (("aap", "noot", "mies") in x
                          and len([a for a in x if a[0] not in ["org_replication_scheduled"]]) == 1
                          )},
+    {"name": "avu.get_attr_val_of_coll.exists.yes",
+     "test": lambda ctx: _test_avu_get_attr_val_of_coll(ctx, "foo", "bar"),
+     "check": lambda x: x == "bar"},
+    {"name": "avu.get_attr_val_of_coll.exists.no",
+     "test": lambda ctx: _test_avu_get_attr_val_of_coll_exception(ctx),
+     "check": lambda x: x},
     {"name": "avu.apply_atomic_operations.collection",
      "test": lambda ctx: _test_msvc_apply_atomic_operations_collection(ctx),
      "check": lambda x: (("foo", "bar", "baz") in x and len(x) == 1)},

troubleshoot_data.py

@@ -119,21 +119,21 @@ def check_datacite_doi_registration(ctx, data_package, offline, write_stdout):
     base_doi_check = False
 
     try:
-        version_doi = get_attribute_value(ctx, data_package, "versionDOI")
+        version_doi = get_val_for_attr_with_pub_prefix(ctx, data_package, "versionDOI")
         status_code = datacite.metadata_get(ctx, version_doi)
         version_doi_check = status_code == 200
     except ValueError as e:
         log.write(ctx, "check_datacite_doi_registration: Error while trying to get versionDOI - {}".format(e), write_stdout)
 
     previous_version = ''
     try:
-        previous_version = get_attribute_value(ctx, data_package, "previous_version")
+        previous_version = get_val_for_attr_with_pub_prefix(ctx, data_package, "previous_version")
     except Exception:
         pass
 
     if previous_version:
         try:
-            base_doi = get_attribute_value(ctx, data_package, "baseDOI")
+            base_doi = get_val_for_attr_with_pub_prefix(ctx, data_package, "baseDOI")
             status_code = datacite.metadata_get(ctx, base_doi)
             base_doi_check = status_code == 200
         except ValueError as e:
@@ -142,7 +142,7 @@ def check_datacite_doi_registration(ctx, data_package, offline, write_stdout):
     return (version_doi_check, base_doi_check)
 
 
-def get_attribute_value(ctx, data_package, attribute_suffix):
+def get_val_for_attr_with_pub_prefix(ctx, data_package, attribute_suffix):
     """
     Retrieves the value given the suffix of the attribute from a data package.
 
@@ -154,21 +154,16 @@ def get_attribute_value(ctx, data_package, attribute_suffix):
 
     :raises ValueError:      If the attribute is not found in the data package's AVU.
     """
-
-    # TODO extract to avu.py? need this?
     attr = constants.UUORGMETADATAPREFIX + "publication_" + attribute_suffix
-    try:
-        return next(m.value for m in avu.of_coll(ctx, data_package) if m.attr == attr)
-    except Exception:
-        raise ValueError("get_attribute_value: Attribute {} not found in AVU".format(attr))
+    return avu.get_attr_val_of_coll(ctx, data_package, attr)
 
 
 def get_landingpage_paths(ctx, data_package, write_stdout):
     """Given a data package get what the path and remote url should be"""
     file_path = ''
     try:
-        file_path = get_attribute_value(ctx, data_package, "landingPagePath")
-        url = get_attribute_value(ctx, data_package, "landingPageUrl")
+        file_path = get_val_for_attr_with_pub_prefix(ctx, data_package, "landingPagePath")
+        url = get_val_for_attr_with_pub_prefix(ctx, data_package, "landingPageUrl")
         return file_path, url
 
     except Exception:
@@ -259,7 +254,7 @@ def check_combi_json(ctx, data_package, publication_config, offline, write_stdou
     # Check that the combi json in irods exists
     file_path = ''
     try:
-        file_path = get_attribute_value(ctx, data_package, "combiJsonPath")
+        file_path = get_val_for_attr_with_pub_prefix(ctx, data_package, "combiJsonPath")
     except Exception:
         pass
     exists = data_object.exists(ctx, file_path)
@@ -275,7 +270,7 @@ def check_combi_json(ctx, data_package, publication_config, offline, write_stdou
     # Get the version doi
     version_doi = ''
     try:
-        version_doi = get_attribute_value(ctx, data_package, "versionDOI")
+        version_doi = get_val_for_attr_with_pub_prefix(ctx, data_package, "versionDOI")
     except Exception:
         pass
     url = "https://{}/oai/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=oai:{}".format(publication_config["publicVHost"], version_doi)

util/avu.py

@@ -35,6 +35,18 @@ def of_coll(ctx, coll):
                                               "COLL_NAME = '{}'".format(coll)))
 
 
+def get_attr_val_of_coll(ctx, coll, attr):
+    """Get the value corresponding to an attr for a given collection."""
+    iter = genquery.Query(
+        ctx,
+        "META_COLL_ATTR_VALUE",
+        "META_COLL_ATTR_NAME = '{}' AND COLL_NAME = '{}'".format(attr, coll))
+
+    for row in iter:
+        return row
+    raise ValueError("Attribute {} not found in AVUs of collection {}".format(attr, coll))
+
+
 def inside_coll(ctx, path, recursive=False):
     """Get a list of all AVUs inside a collection with corresponding paths.