Merge pull request #105 from pangaea-data-publisher/robbranch2

robbranch2

fuji_server/controllers/fair_check.py

@@ -95,6 +95,7 @@ class FAIRCheck:
     FILES_LIMIT = None
     LOG_SUCCESS = 25
     VALID_RESOURCE_TYPES = []
+    FUJI_VERSION = 'v1.0.1'
 
     def __init__(self, uid, test_debug=False, oaipmh=None, use_datacite=True):
         uid_bytes = uid.encode('utf-8')
@@ -105,7 +106,7 @@ def __init__(self, uid, test_debug=False, oaipmh=None, use_datacite=True):
         self.landing_url = None  # url of the landing page of self.pid_url
         self.landing_html = None
         self.landing_origin = None  # schema + authority of the landing page e.g. https://www.pangaea.de
-        self.signposting_header_links = dict()
+        self.signposting_header_links = []
         self.pid_scheme = None
         self.id_scheme= None
         self.logger = logging.getLogger(self.__class__.__name__)
@@ -369,7 +370,7 @@ def retrieve_metadata_embedded(self, extruct_metadata):
                             'FsF-F3-01M : Found data links in HTML head (link rel=item) : ' + str(len(links)))
             if self.metadata_merged.get('object_content_identifier') is None:
                 self.metadata_merged['object_content_identifier'] = links
-            self.metadata_sources.append((MetaDataCollector.Sources.SIGN_POSTING.value,'linked'))
+            self.metadata_sources.append((MetaDataCollector.Sources.TYPED_LINK.value,'linked'))
 
         #Now if an identifier has been detected in the metadata, potentially check for persistent identifier has to be repeated..
         if self.metadata_merged.get('object_identifier'):
@@ -380,7 +381,8 @@ def retrieve_metadata_embedded(self, extruct_metadata):
                         found_pids_in_metadata.remove('url')
                     found_id = found_pids_in_metadata[0]
                     if found_id in Mapper.VALID_PIDS.value:
-                        self.logger.info('FsF-F1-02D : Found object identifier in metadata, repeating PID check')
+                        self.logger.info('FsF-F2-01M : Found object identifier in metadata, repeating PID check for FsF-F1-02D')
+                        self.logger.log(self.LOG_SUCCESS, 'FsF-F1-02D : Found object identifier in metadata during FsF-F2-01M, PID check was repeated')
                         self.repeat_pid_check = True
                         self.pid_scheme = found_id
                         self.id = self.metadata_merged.get('object_identifier')
@@ -405,6 +407,13 @@ def get_html_typed_links(self, rel="item"):
                 datalinks.append({'url': href, 'type': l.attrib.get('type'), 'rel': l.attrib.get('rel'), 'profile': l.attrib.get('format')})
         return datalinks
 
+    def get_signposting_links(self, rel="item"):
+        signlinks =[]
+        for signposting_links in self.signposting_header_links:
+            if signposting_links.get('rel') == rel:
+                signlinks.append(signposting_links)
+        return signlinks
+
     def get_guessed_xml_link(self):
         # in case object landing page URL ends with '.html' or '/html'
         # try to find out if there is some xml content if suffix is replaced by 'xml
@@ -506,16 +515,25 @@ def retrieve_metadata_external(self):
                 self.logger.info('FsF-F2-01M : Datacite metadata UNAVAILABLE')
         else:
             self.logger.info('FsF-F2-01M : Not a PID, therefore Datacite metadata (json) not requested.')
-        #dcat style
+        sign_header_links = []
+        #signposting header links
+        if self.get_signposting_links('describedby'):
+            sign_header_links = self.get_signposting_links('describedby')
+            self.metadata_sources.append((MetaDataCollector.Sources.SIGN_POSTING.value, 'signposting'))
+        #dcat style meta links
         typed_metadata_links = self.get_html_typed_links(rel='alternate')
-        #ddi style
+        #ddi style meta links
         rel_meta_links = self.get_html_typed_links(rel='meta')
-        #signposting style
-        sign_metadata_links = self.get_html_typed_links(rel='describedby')
+        #signposting style meta links
+        sign_meta_links = self.get_html_typed_links(rel='describedby')
+
 
-        typed_metadata_links.extend(sign_metadata_links)
+
+        typed_metadata_links.extend(sign_meta_links)
         typed_metadata_links.extend(rel_meta_links)
+        typed_metadata_links.extend(sign_header_links)
         guessed_metadata_link = self.get_guessed_xml_link()
+
         if guessed_metadata_link is not None:
             typed_metadata_links.append(guessed_metadata_link)
 

fuji_server/controllers/fair_object_controller.py

@@ -99,6 +99,6 @@ def assess_by_id(body):  # noqa: E501
         metric_spec = Preprocessor.metric_specification
         metric_version = os.path.basename(Preprocessor.METRIC_YML_PATH)
         totalmetrics = len(results)
-        final_response = FAIRResults(timestamp= timestmp, test_id= ft.test_id, metric_version=metric_version, metric_specification=metric_spec, total_metrics=totalmetrics, results=results)
+        final_response = FAIRResults(timestamp= timestmp, software_version=ft.FUJI_VERSION,test_id= ft.test_id, metric_version=metric_version, metric_specification=metric_spec, total_metrics=totalmetrics, results=results)
     return final_response
 

fuji_server/evaluators/fair_evaluator_minimal_metadata.py

@@ -81,6 +81,9 @@ def evaluate(self):
             if source_mechanism == 'linked':
                 self.setEvaluationCriteriumScore('FsF-F2-01M-1c', 0,'pass')
                 self.setEvaluationCriteriumScore('FsF-F2-01M-1', 0, 'pass')
+            if source_mechanism == 'signposting':
+                self.setEvaluationCriteriumScore('FsF-F2-01M-1d', 0,'pass')
+                self.setEvaluationCriteriumScore('FsF-F2-01M-1', 0, 'pass')
         self.result.test_status = test_status
         self.result.metric_tests = self.metric_tests
         self.result.score = self.score

fuji_server/evaluators/fair_evaluator_persistent_identifier.py

@@ -56,19 +56,39 @@ def evaluate(self):
                 # identify signposting links in header
                 header_link_string = requestHelper.getHTTPResponse().getheader('Link')
                 if header_link_string is not None:
+                    self.logger.info('FsF-F1-02D : Found signposting links in response header of landingpage')
+
                     for preparsed_link  in header_link_string.split(','):
+                        found_link = None
+                        found_type, type_match = None, None
+                        found_rel, rel_match = None, None
                         parsed_link = preparsed_link.strip().split(';')
                         found_link = parsed_link[0].strip()
-                        found_rel = re.search('rel=\"([a-z-]+)\"', parsed_link[1])
+                        for link_prop in parsed_link[1:]:
+                            if str(link_prop).startswith('rel="'):
+                                rel_match = re.search('rel=\"(.*?)\"', link_prop)
+                            elif str(link_prop).startswith('type="'):
+                                type_match = re.search('type=\"(.*?)\"', link_prop)
+                        if type_match:
+                            found_type = type_match[1]
+                        if rel_match:
+                            found_rel = rel_match[1]
+                        signposting_link_dict = {'url': found_link[1:-1], 'type': found_type, 'rel': found_rel}
+                        if found_link:
+                            self.fuji.signposting_header_links.append(signposting_link_dict)
+                        '''
                         if found_rel:
                             if self.fuji.signposting_header_links.get(found_rel[1]):
                                 self.fuji.signposting_header_links[found_rel[1]].append(found_link[1:-1])
                             else:
                                 self.fuji.signposting_header_links[found_rel[1]]=[found_link[1:-1]]
+                        '''
 
                 #check if there is a cite-as signposting link
                 if self.fuji.pid_scheme is None:
-                    signposting_pid = self.fuji.signposting_header_links.get('cite-as')
+                    signposting_pid_link = self.fuji.get_signposting_links('cite-as')
+                    if signposting_pid_link:
+                        signposting_pid = signposting_pid_link[0].get('url')
                     if signposting_pid:
                         found_ids = idutils.detect_identifier_schemes(signposting_pid[0])
                         if len(found_ids) > 1: