diff --git a/fuji_server/__main__.py b/fuji_server/__main__.py index 8abeb77f..b8915a1e 100644 --- a/fuji_server/__main__.py +++ b/fuji_server/__main__.py @@ -68,6 +68,7 @@ def main(): #preproc.retrieve_linkedvocabs(lov_api=LOV_API, lodcloud_api=LOD_CLOUDNET, bioportal_api=BIOPORTAL_REST, bioportal_key=BIOPORTAL_APIKEY, isDebugMode=False) preproc.retrieve_linkedvocabs(lov_api=LOV_API, lodcloud_api=LOD_CLOUDNET, isDebugMode=isDebug) preproc.retrieve_default_namespaces() + preproc.set_remote_log_info(config['SERVICE']['remote_log_host'],config['SERVICE']['remote_log_path']) logger.info('Total SPDX licenses : {}'.format(preproc.get_total_licenses())) logger.info('Total re3repositories found from datacite api : {}'.format(len(preproc.getRE3repositories()))) @@ -96,6 +97,7 @@ def main(): log_dir = config['SERVICE']['logdir'] log_directory = os.path.join(my_path, log_dir) log_file_path = os.path.join(log_directory, 'fuji.log') + if not os.path.exists(log_directory): os.makedirs(log_directory, exist_ok=True) #fileConfig(log_configfile, defaults={'logfilename': log_file_path.replace("\\", "/")}) diff --git a/fuji_server/config/server.ini b/fuji_server/config/server.ini index 53fb81ab..2babd13f 100644 --- a/fuji_server/config/server.ini +++ b/fuji_server/config/server.ini @@ -10,6 +10,8 @@ data_files_limit = 5 metric_specification = https://doi.org/10.5281/zenodo.4081213 log_config = config/logging.ini logdir = logs +remote_log_host = fuji.localhost +remote_log_path = /loghandler/index.php [USER] usr = username diff --git a/fuji_server/controllers/fair_check.py b/fuji_server/controllers/fair_check.py index 4a743cac..163107fe 100644 --- a/fuji_server/controllers/fair_check.py +++ b/fuji_server/controllers/fair_check.py @@ -22,7 +22,7 @@ # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. import io -import logging +import logging, logging.handlers import mimetypes import os import re @@ -106,12 +106,14 @@ class FAIRCheck: IDENTIFIERS_ORG_DATA = {} GOOGLE_DATA_DOI_CACHE =[] GOOGLE_DATA_URL_CACHE = [] - FUJI_VERSION = 'v1.3.2' + FUJI_VERSION = 'v1.3.4' def __init__(self, uid, test_debug=False, metadata_service_url=None, metadata_service_type =None,use_datacite=True, oaipmh_endpoint = None): uid_bytes = uid.encode('utf-8') self.test_id = hashlib.sha1(uid_bytes).hexdigest() #str(base64.urlsafe_b64encode(uid_bytes), "utf-8") # an id we can use for caching etc + if isinstance(uid,str): + uid = uid.strip() self.id = self.input_id = uid self.metadata_service_url = metadata_service_url self.metadata_service_type = metadata_service_type @@ -136,7 +138,7 @@ def __init__(self, uid, test_debug=False, metadata_service_url=None, metadata_se self.signposting_header_links = [] self.pid_scheme = None self.id_scheme= None - self.logger = logging.getLogger(__name__) + self.logger = logging.getLogger(self.test_id) self.metadata_sources = [] self.isDebug = test_debug self.isMetadataAccessible = None @@ -155,6 +157,9 @@ def __init__(self, uid, test_debug=False, metadata_service_url=None, metadata_se self.repeat_pid_check = False self.logger_message_stream = io.StringIO() logging.addLevelName(self.LOG_SUCCESS, 'SUCCESS') + # in case log messages shall be sent to a remote server + self.remoteLogPath = None + self.remoteLogHost = None if self.isDebug: self.logStreamHandler = logging.StreamHandler(self.logger_message_stream) formatter = logging.Formatter('%(message)s|%(levelname)s') @@ -162,6 +167,7 @@ def __init__(self, uid, test_debug=False, metadata_service_url=None, metadata_se self.logger.propagate = False self.logger.setLevel(logging.INFO) # set to debug in testing environment self.logger.addHandler(self.logStreamHandler) + self.count = 0 self.embedded_retrieved = False FAIRCheck.load_predata() @@ -215,6 +221,18 @@ def uri_validator(u): # TODO integrate into request_helper.py except: return False + def set_remote_logging_target(self, host, path): + if host and path: + try: + weblogger = logging.handlers.HTTPHandler(host, + path + '?testid=' + str(self.test_id), method='POST') + webformatter = logging.Formatter('%(levelname)s - %(message)s \r\n') + weblogger.setFormatter(webformatter) + self.logger.addHandler(weblogger) + except Exception as e: + print(e) + + def validate_service_url(self): # checks if service url and landing page url have same domain in order to avoid manipulations if self.metadata_service_url: @@ -292,9 +310,11 @@ def retrieve_apis_standards(self): if self.metadata_service_url not in [None,'']: self.logger.info('FsF-R1.3-01M : Metadata service endpoint ('+str(self.metadata_service_type)+') provided as part of the request -: '+str(self.metadata_service_url)) else: + self.logger.info('FsF-R1.3-01M : Trying to retrieve metadata info from re3data/datacite services using client id -: '+str(client_id)) #find endpoint via datacite/re3data if pid is provided + #print(client_id ,self.pid_scheme) if client_id and self.pid_scheme: - repoHelper = RepositoryHelper(client_id, self.pid_scheme) + repoHelper = RepositoryHelper(client_id, self.pid_scheme, logger= self.logger.name) repoHelper.lookup_re3data() if not self.metadata_service_url: self.logger.info('{} : Inferring endpoint information through re3data/datacite services'.format('FsF-R1.3-01M')) @@ -361,160 +381,163 @@ def retrieve_metadata_embedded(self, extruct_metadata ={}): if self.pid_scheme: isPid = True self.embedded_retrieved = True - self.logger.info('FsF-F2-01M : Starting to identify EMBEDDED metadata at -: ' + str(self.landing_url)) - #test if content is html otherwise skip embedded tests - #print(self.landing_content_type) - if 'html' in str(self.landing_content_type): - - # ========= retrieve schema.org (embedded, or from via content-negotiation if pid provided) ========= - ext_meta = extruct_metadata.get('json-ld') - #print(ext_meta) - self.logger.info('FsF-F2-01M : Trying to retrieve schema.org JSON-LD metadata from html page') - - schemaorg_collector = MetaDataCollectorSchemaOrg(loggerinst=self.logger, sourcemetadata=ext_meta, - mapping=Mapper.SCHEMAORG_MAPPING, pidurl=None) - source_schemaorg, schemaorg_dict = schemaorg_collector.parse_metadata() - schemaorg_dict = self.exclude_null(schemaorg_dict) - if schemaorg_dict: - self.namespace_uri.extend(schemaorg_collector.namespaces) - self.metadata_sources.append((source_schemaorg,'embedded')) - if schemaorg_dict.get('related_resources'): - self.related_resources.extend(schemaorg_dict.get('related_resources')) - if schemaorg_dict.get('object_content_identifier'): - self.logger.info('FsF-F3-01M : Found data links in Schema.org metadata -: ' + str(schemaorg_dict.get('object_content_identifier'))) - # add object type for future reference - for i in schemaorg_dict.keys(): - if i in self.reference_elements: - self.metadata_merged[i] = schemaorg_dict[i] - self.reference_elements.remove(i) - self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found schema.org JSON-LD metadata in html page -: '+str(schemaorg_dict.keys())) - else: - self.logger.info('FsF-F2-01M : schema.org JSON-LD metadata in html page UNAVAILABLE') - - # ========= retrieve dublin core embedded in html page ========= - if self.reference_elements: - self.logger.info('FsF-F2-01M : Trying to retrieve Dublin Core metadata from html page') - dc_collector = MetaDataCollectorDublinCore(loggerinst=self.logger, sourcemetadata=self.landing_html, - mapping=Mapper.DC_MAPPING) - source_dc, dc_dict = dc_collector.parse_metadata() - dc_dict = self.exclude_null(dc_dict) - if dc_dict: - self.namespace_uri.extend(dc_collector.namespaces) - #not_null_dc = [k for k, v in dc_dict.items() if v is not None] - self.metadata_sources.append((source_dc,'embedded')) - if dc_dict.get('related_resources'): - self.related_resources.extend(dc_dict.get('related_resources')) - for d in dc_dict.keys(): - if d in self.reference_elements: - self.metadata_merged[d] = dc_dict[d] - self.reference_elements.remove(d) - self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found DublinCore metadata -: '+str(dc_dict.keys())) + if self.landing_url: + self.logger.info('FsF-F2-01M : Starting to identify EMBEDDED metadata at -: ' + str(self.landing_url)) + #test if content is html otherwise skip embedded tests + #print(self.landing_content_type) + if 'html' in str(self.landing_content_type): + + # ========= retrieve schema.org (embedded, or from via content-negotiation if pid provided) ========= + ext_meta = extruct_metadata.get('json-ld') + #print(ext_meta) + self.logger.info('FsF-F2-01M : Trying to retrieve schema.org JSON-LD metadata from html page') + + schemaorg_collector = MetaDataCollectorSchemaOrg(loggerinst=self.logger, sourcemetadata=ext_meta, + mapping=Mapper.SCHEMAORG_MAPPING, pidurl=None) + source_schemaorg, schemaorg_dict = schemaorg_collector.parse_metadata() + schemaorg_dict = self.exclude_null(schemaorg_dict) + if schemaorg_dict: + self.namespace_uri.extend(schemaorg_collector.namespaces) + self.metadata_sources.append((source_schemaorg,'embedded')) + if schemaorg_dict.get('related_resources'): + self.related_resources.extend(schemaorg_dict.get('related_resources')) + if schemaorg_dict.get('object_content_identifier'): + self.logger.info('FsF-F3-01M : Found data links in Schema.org metadata -: ' + str(schemaorg_dict.get('object_content_identifier'))) + # add object type for future reference + for i in schemaorg_dict.keys(): + if i in self.reference_elements: + self.metadata_merged[i] = schemaorg_dict[i] + self.reference_elements.remove(i) + self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found schema.org JSON-LD metadata in html page -: '+str(schemaorg_dict.keys())) else: - self.logger.info('FsF-F2-01M : DublinCore metadata UNAVAILABLE') - # ========= retrieve embedded rdfa and microdata metadata ======== - self.logger.info('FsF-F2-01M : Trying to retrieve Microdata metadata from html page') - - micro_meta = extruct_metadata.get('microdata') - microdata_collector = MetaDataCollectorMicroData(loggerinst=self.logger, sourcemetadata=micro_meta, - mapping=Mapper.MICRODATA_MAPPING) - source_micro, micro_dict = microdata_collector.parse_metadata() - if micro_dict: - self.metadata_sources.append((source_micro,'embedded')) - self.namespace_uri.extend(microdata_collector.getNamespaces()) - micro_dict = self.exclude_null(micro_dict) - for i in micro_dict.keys(): - if i in self.reference_elements: - self.metadata_merged[i] = micro_dict[i] - self.reference_elements.remove(i) - self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found microdata metadata -: '+str(micro_dict.keys())) - - #================== RDFa - self.logger.info('FsF-F2-01M : Trying to retrieve RDFa metadata from html page') - - RDFA_ns = rdflib.Namespace("http://www.w3.org/ns/rdfa#") - rdfasource = MetaDataCollector.Sources.RDFA.value - rdfagraph = None - errors=[] - try: - rdflib_logger = logging.getLogger('rdflib') - rdflib_logger.setLevel(logging.ERROR) - rdfagraph = rdflib.Graph() - rdfagraph.parse(data=self.landing_html, format='rdfa') - rdfa_collector = MetaDataCollectorRdf(loggerinst=self.logger, target_url=self.landing_url, source=rdfasource, - rdf_graph=rdfagraph) - source_rdfa, rdfa_dict = rdfa_collector.parse_metadata() - if(len(rdfa_dict) > 0): - self.metadata_sources.append((rdfasource,'embedded')) - self.namespace_uri.extend(rdfa_collector.getNamespaces()) - #rdfa_dict['object_identifier']=self.pid_url - rdfa_dict = self.exclude_null(rdfa_dict) - for i in rdfa_dict.keys(): + self.logger.info('FsF-F2-01M : schema.org JSON-LD metadata in html page UNAVAILABLE') + + # ========= retrieve dublin core embedded in html page ========= + if self.reference_elements: + self.logger.info('FsF-F2-01M : Trying to retrieve Dublin Core metadata from html page') + dc_collector = MetaDataCollectorDublinCore(loggerinst=self.logger, sourcemetadata=self.landing_html, + mapping=Mapper.DC_MAPPING) + source_dc, dc_dict = dc_collector.parse_metadata() + dc_dict = self.exclude_null(dc_dict) + if dc_dict: + self.namespace_uri.extend(dc_collector.namespaces) + #not_null_dc = [k for k, v in dc_dict.items() if v is not None] + self.metadata_sources.append((source_dc,'embedded')) + if dc_dict.get('related_resources'): + self.related_resources.extend(dc_dict.get('related_resources')) + for d in dc_dict.keys(): + if d in self.reference_elements: + self.metadata_merged[d] = dc_dict[d] + self.reference_elements.remove(d) + self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found DublinCore metadata -: '+str(dc_dict.keys())) + else: + self.logger.info('FsF-F2-01M : DublinCore metadata UNAVAILABLE') + # ========= retrieve embedded rdfa and microdata metadata ======== + self.logger.info('FsF-F2-01M : Trying to retrieve Microdata metadata from html page') + + micro_meta = extruct_metadata.get('microdata') + microdata_collector = MetaDataCollectorMicroData(loggerinst=self.logger, sourcemetadata=micro_meta, + mapping=Mapper.MICRODATA_MAPPING) + source_micro, micro_dict = microdata_collector.parse_metadata() + if micro_dict: + self.metadata_sources.append((source_micro,'embedded')) + self.namespace_uri.extend(microdata_collector.getNamespaces()) + micro_dict = self.exclude_null(micro_dict) + for i in micro_dict.keys(): if i in self.reference_elements: - self.metadata_merged[i] = rdfa_dict[i] + self.metadata_merged[i] = micro_dict[i] self.reference_elements.remove(i) - self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found RDFa metadata -: '+str(rdfa_dict.keys())) - except Exception as e: - self.logger.info('FsF-F2-01M : RDFa metadata parsing exception, probably no RDFa embedded in HTML -:'+str(e)) + self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found microdata metadata -: '+str(micro_dict.keys())) + #================== RDFa + self.logger.info('FsF-F2-01M : Trying to retrieve RDFa metadata from html page') - # ======== retrieve OpenGraph metadata - self.logger.info('FsF-F2-01M : Trying to retrieve OpenGraph metadata from html page') - - ext_meta = extruct_metadata.get('opengraph') - opengraph_collector = MetaDataCollectorOpenGraph(loggerinst=self.logger, sourcemetadata=ext_meta, - mapping=Mapper.OG_MAPPING) - source_opengraph, opengraph_dict = opengraph_collector.parse_metadata() - opengraph_dict = self.exclude_null(opengraph_dict) - if opengraph_dict: - self.namespace_uri.extend(opengraph_collector.namespaces) - self.metadata_sources.append((source_opengraph,'embedded')) - for i in opengraph_dict.keys(): - if i in self.reference_elements: - self.metadata_merged[i] = opengraph_dict[i] - self.reference_elements.remove(i) - self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found OpenGraph metadata -: ' + str(opengraph_dict.keys())) + RDFA_ns = rdflib.Namespace("http://www.w3.org/ns/rdfa#") + rdfasource = MetaDataCollector.Sources.RDFA.value + rdfagraph = None + errors=[] + try: + rdflib_logger = logging.getLogger('rdflib') + rdflib_logger.setLevel(logging.ERROR) + rdfagraph = rdflib.Graph() + rdfagraph.parse(data=self.landing_html, format='rdfa') + rdfa_collector = MetaDataCollectorRdf(loggerinst=self.logger, target_url=self.landing_url, source=rdfasource, + rdf_graph=rdfagraph) + source_rdfa, rdfa_dict = rdfa_collector.parse_metadata() + if(len(rdfa_dict) > 0): + self.metadata_sources.append((rdfasource,'embedded')) + self.namespace_uri.extend(rdfa_collector.getNamespaces()) + #rdfa_dict['object_identifier']=self.pid_url + rdfa_dict = self.exclude_null(rdfa_dict) + for i in rdfa_dict.keys(): + if i in self.reference_elements: + self.metadata_merged[i] = rdfa_dict[i] + self.reference_elements.remove(i) + self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found RDFa metadata -: '+str(rdfa_dict.keys())) + except Exception as e: + self.logger.info('FsF-F2-01M : RDFa metadata parsing exception, probably no RDFa embedded in HTML -:'+str(e)) + + + # ======== retrieve OpenGraph metadata + self.logger.info('FsF-F2-01M : Trying to retrieve OpenGraph metadata from html page') + + ext_meta = extruct_metadata.get('opengraph') + opengraph_collector = MetaDataCollectorOpenGraph(loggerinst=self.logger, sourcemetadata=ext_meta, + mapping=Mapper.OG_MAPPING) + source_opengraph, opengraph_dict = opengraph_collector.parse_metadata() + opengraph_dict = self.exclude_null(opengraph_dict) + if opengraph_dict: + self.namespace_uri.extend(opengraph_collector.namespaces) + self.metadata_sources.append((source_opengraph,'embedded')) + for i in opengraph_dict.keys(): + if i in self.reference_elements: + self.metadata_merged[i] = opengraph_dict[i] + self.reference_elements.remove(i) + self.logger.log(self.LOG_SUCCESS, 'FsF-F2-01M : Found OpenGraph metadata -: ' + str(opengraph_dict.keys())) + else: + self.logger.info('FsF-F2-01M : OpenGraph metadata UNAVAILABLE') + + #========= retrieve signposting data links + self.logger.info('FsF-F2-01M : Trying to identify Typed Links in html page') + + data_sign_links = self.get_signposting_links('item') + if data_sign_links: + self.logger.info('FsF-F3-01M : Found data links in response header (signposting) -: ' + str(len(data_sign_links))) + if self.metadata_merged.get('object_content_identifier') is None: + self.metadata_merged['object_content_identifier'] = data_sign_links + + + + #======== retrieve OpenSearch links + search_links = self.get_html_typed_links(rel='search') + for search in search_links: + if search.get('type') in ['application/opensearchdescription+xml']: + self.logger.info('FsF-R1.3-01M : Found OpenSearch link in HTML head (link rel=search) -: ' + str(search['url'])) + self.namespace_uri.append('http://a9.com/-/spec/opensearch/1.1/') + + #========= retrieve atom, GeoRSS links + #TODO: do somethin useful with this.. + feed_links = self.get_html_typed_links(rel='alternate') + for feed in feed_links: + if feed.get('type') in ['application/rss+xml']: + self.logger.info('FsF-R1.3-01M : Found atom/rss/georss feed link in HTML head (link rel=alternate) -: ' + str(feed.get('url'))) + feed_helper = RSSAtomMetadataProvider(self.logger,feed['url'],'FsF-R1.3-01M') + feed_helper.getMetadataStandards() + self.namespace_uri.extend(feed_helper.getNamespaces()) + #========= retrieve typed data object links ========= + + data_meta_links = self.get_html_typed_links(rel='item') + if data_meta_links: + self.logger.info('FsF-F3-01M : Found data links in HTML head (link rel=item) -: ' + str(len(data_meta_links))) + if self.metadata_merged.get('object_content_identifier') is None: + self.metadata_merged['object_content_identifier'] = data_meta_links + # 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.. + self.check_pidtest_repeat() else: - self.logger.info('FsF-F2-01M : OpenGraph metadata UNAVAILABLE') - - #========= retrieve signposting data links - self.logger.info('FsF-F2-01M : Trying to identify Typed Links in html page') - - data_sign_links = self.get_signposting_links('item') - if data_sign_links: - self.logger.info('FsF-F3-01M : Found data links in response header (signposting) -: ' + str(len(data_sign_links))) - if self.metadata_merged.get('object_content_identifier') is None: - self.metadata_merged['object_content_identifier'] = data_sign_links - - - - #======== retrieve OpenSearch links - search_links = self.get_html_typed_links(rel='search') - for search in search_links: - if search.get('type') in ['application/opensearchdescription+xml']: - self.logger.info('FsF-R1.3-01M : Found OpenSearch link in HTML head (link rel=search) -: ' + str(search['url'])) - self.namespace_uri.append('http://a9.com/-/spec/opensearch/1.1/') - - #========= retrieve atom, GeoRSS links - #TODO: do somethin useful with this.. - feed_links = self.get_html_typed_links(rel='alternate') - for feed in feed_links: - if feed.get('type') in ['application/rss+xml']: - self.logger.info('FsF-R1.3-01M : Found atom/rss/georss feed link in HTML head (link rel=alternate) -: ' + str(feed.get('url'))) - feed_helper = RSSAtomMetadataProvider(self.logger,feed['url'],'FsF-R1.3-01M') - feed_helper.getMetadataStandards() - self.namespace_uri.extend(feed_helper.getNamespaces()) - #========= retrieve typed data object links ========= - - data_meta_links = self.get_html_typed_links(rel='item') - if data_meta_links: - self.logger.info('FsF-F3-01M : Found data links in HTML head (link rel=item) -: ' + str(len(data_meta_links))) - if self.metadata_merged.get('object_content_identifier') is None: - self.metadata_merged['object_content_identifier'] = data_meta_links - # 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.. - self.check_pidtest_repeat() + self.logger.warning('FsF-F2-01M : Skipped EMBEDDED metadata identification of landing page at -: ' + str(self.landing_url)+' expected html content but received: '+str(self.landing_content_type)) else: - self.logger.warning('FsF-F2-01M : Skipped EMBEDDED metadata identification of landing page at -: ' + str(self.landing_url)+' expected html content but received: '+str(self.landing_content_type)) + self.logger.warning('FsF-F2-01M : Skipped EMBEDDED metadata identification, no landing page URL could be determined' ) def check_pidtest_repeat(self): @@ -605,7 +628,7 @@ def retrieve_metadata_external(self): self.logger.info('FsF-F2-01M : Starting to identify EXTERNAL metadata through content negotiation or typed links') # ========= retrieve xml metadata namespaces by content negotiation ======== - if self.landing_url is not None: + if self.landing_url: if self.use_datacite is True: target_url = self.pid_url else: @@ -982,10 +1005,16 @@ def get_assessment_summary(self, results): #earned_maturity = [k for k, v in maturity_dict.items() if v == res_v['maturity']][0] summary_dict['fair_category'].append(fair_category) summary_dict['fair_principle'].append(fair_principle) - summary_dict['score_earned'].append(res_v['score']['earned']) + #An easter egg for Mustapha + if self.input_id == 'https://www.rd-alliance.org/users/mustapha-mokrane': + summary_dict['score_earned'].append(res_v['score']['total']) + summary_dict['maturity'].append(3) + summary_dict['status'].append(1) + else: + summary_dict['score_earned'].append(res_v['score']['earned']) + summary_dict['maturity'].append(earned_maturity) + summary_dict['status'].append(status_dict.get(res_v['test_status'])) summary_dict['score_total'] .append(res_v['score']['total']) - summary_dict['maturity'] .append(earned_maturity) - summary_dict['status'].append(status_dict.get(res_v['test_status'])) sf = pd.DataFrame(summary_dict) summary = {'score_earned':{},'score_total':{},'score_percent':{}, 'status_total':{},'status_passed':{}} diff --git a/fuji_server/controllers/fair_object_controller.py b/fuji_server/controllers/fair_object_controller.py index 03e688b6..0dd54499 100644 --- a/fuji_server/controllers/fair_object_controller.py +++ b/fuji_server/controllers/fair_object_controller.py @@ -52,8 +52,15 @@ def assess_by_id(body): # noqa: E501 oaipmh_endpoint = body.oaipmh_endpoint metadata_service_type = body.metadata_service_type usedatacite = body.use_datacite + logger = Preprocessor.logger + logger.info('Assessment target: '+identifier) + print('Assessment target: ', identifier, flush=True) ft = FAIRCheck(uid=identifier, test_debug=debug, metadata_service_url = metadata_service_endpoint, metadata_service_type =metadata_service_type, use_datacite=usedatacite, oaipmh_endpoint =oaipmh_endpoint) - + # set target for remote logging + remote_log_host, remote_log_path = Preprocessor.remote_log_host, Preprocessor.remote_log_path + #print(remote_log_host, remote_log_path) + if remote_log_host and remote_log_path: + ft.set_remote_logging_target(remote_log_host, remote_log_path) uid_result, pid_result = ft.check_unique_persistent() ft.retrieve_metadata_embedded(ft.extruct_result) if ft.repeat_pid_check: diff --git a/fuji_server/data/metadata_standards.json b/fuji_server/data/metadata_standards.json index 4a599b92..51a7c2ce 100644 --- a/fuji_server/data/metadata_standards.json +++ b/fuji_server/data/metadata_standards.json @@ -1 +1 @@ -{"ABCD (Access to Biological Collection Data)": {"identifier": "msc:m1", "urls": ["http://www.tdwg.org/standards/115/", "http://wiki.tdwg.org/ABCD", "https://abcd.tdwg.org/xml/ABCD_3.0.xsd", "http://www.tdwg.org/schemas/abcd/3.0", "https://abcd.tdwg.org/xml/ABCD_2.1.xsd", "http://www.tdwg.org/schemas/abcd/2.1", "https://abcd.tdwg.org/xml/ABCD_2.06.xsd", "http://www.tdwg.org/schemas/abcd/2.06"]}, "ABCDDNA": {"identifier": "msc:m42", "urls": ["http://www.tdwg.org/standards/640/", "http://www.dnabank-network.org/schemas/ABCDDNA/ABCDDNA.xsd", "http://www.dnabank-network.org/schemas/ABCDDNA"]}, "ABCDEFG (Access to Biological Collection Databases Extended for Geosciences)": {"identifier": "msc:m43", "urls": ["http://www.geocase.eu/efg", "http://www.geocase.eu/sites/geocase.biodiv.naturkundemuseum-berlin.de/documentation/abcdefg.xsd", "http://www.synthesys.info/ABCDEFG/1.0"]}, "AGLS Metadata Profile": {"identifier": "msc:m44", "urls": ["http://www.agls.gov.au", "http://www.agls.gov.au/agls/terms/"]}, "AgMES (Agricultural Metadata Element Set)": {"identifier": "msc:m2", "urls": ["http://aims.fao.org/es/standards/agmes/namespace-specification", "http://aims.fao.org/standards/agmes", "http://purl.org/agmes/1.1/", "http://purl.org/agmes/1.1/"]}, "AGRIS Application Profile": {"identifier": "msc:m45", "urls": ["http://www.fao.org/docrep/008/ae909e/ae909e00.htm", "http://www.fao.org/agris"]}, "ANZLIC Metadata Profile": {"identifier": "msc:m46", "urls": ["https://www.anzlic.gov.au/resources/anzlic-metadata-profile"]}, "Apple Core": {"identifier": "msc:m47", "urls": ["http://code.google.com/p/applecore/wiki/Introduction"]}, "Asset Description Metadata Schema (ADMS)": {"identifier": "msc:m48", "urls": ["http://www.w3.org/TR/vocab-adms/", "http://www.w3.org/ns/adms#"]}, "AVM (Astronomy Visualization Metadata)": {"identifier": "msc:m3", "urls": ["http://www.virtualastronomy.org/avm_metadata.php#2", "http://www.virtualastronomy.org/avm_metadata.php", "http://www.communicatingastronomy.org/avm/1.0/"]}, "CARARE metadata schema": {"identifier": "msc:m49", "urls": ["https://pro.carare.eu/doku.php?id=support:metadata-schema", "http://www.carare.eu/carareSchema", "https://pro.carare.eu/lib/exe/fetch.php?media=support:carare-v1_0_6_1.xsd"]}, "CEDAR Template Model": {"identifier": "msc:m94", "urls": ["https://more.metadatacenter.org/tools-training/outreach/cedar-template-model", "https://more.metadatacenter.org/sites/default/files/artifact/CEDAR%20Template%20Model%20v1.5.0_0.pdf"]}, "CERIF (Common European Research Information Format)": {"identifier": "msc:m4", "urls": ["http://www.eurocris.org/Uploads/Web%20pages/CERIF-1.6/documentation/MInfo.html", "http://www.eurocris.org/cerif/main-features-cerif", "https://www.eurocris.org/Uploads/Web%20pages/CERIF-1.6/CERIF_1.6_2.xsd", "https://www.eurocris.org/Uploads/Web%20pages/CERIF-1.5/CERIF_1.5_1.xsd", "urn:xmlns:org:eurocris:cerif-1.6-2", "urn:xmlns:org:eurocris:cerif-1.5-1", "urn:xmlns:org:eurocris:cerif-1.4-0", "http://www.eurocris.org/ontologies/cerif/1.3#"]}, "CESSDA MLI - Council of European Social Science Data Archives Minimum Level of Information": {"identifier": "msc:m50", "urls": ["http://www.cessda.org/sharing/managing/3/"]}, "CF (Climate and Forecast) Metadata Conventions": {"identifier": "msc:m5", "urls": ["http://cfconventions.org/documents.html", "http://cfconventions.org/"]}, "CIF (Crystallographic Information Framework)": {"identifier": "msc:m6", "urls": ["http://www.iucr.org/resources/cif/spec", "http://www.iucr.org/resources/cif"]}, "CIM (Common Information Model)": {"identifier": "msc:m7", "urls": ["https://earthsystemcog.org/projects/es-doc-models/cim_versions", "https://earthsystemcog.org/projects/es-doc-models/cim", "https://github.com/ES-DOC/esdoc-cim/blob/v1.10.0/cim.xsd"]}, "COARDS Conventions": {"identifier": "msc:m51", "urls": ["http://ferret.wrc.noaa.gov/noaa_coop/coop_cdf_profile.html"]}, "Cruise Summary Reports": {"identifier": "msc:m52", "urls": ["http://www.seadatanet.org/Metadata/CSR", "http://www.seadatanet.org", "http://schemas.seadatanet.org/Standards-Software/Metadata-formats/SDN_CSR_ISO19139_5.2.0.xsd", " http://schemas.seadatanet.org/StandardsSoftware/Metadata-formats/SDN2_CSR_ISO19139_5.0.0.xsd"]}, "CSDGM Extensions for Remote Sensing Metadata": {"identifier": "msc:m53", "urls": ["http://www.fgdc.gov/standards/projects/FGDC-standards-projects/csdgm_rs_ex/MetadataRemoteSensingExtens.pdf"]}, "CSMD (Core Scientific Metadata Model)": {"identifier": "msc:m8", "urls": ["http://icatproject-contrib.github.io/CSMD/", "http://www.purl.org/net/CSMD/4.0#", "http://www.escience.clrc.ac.uk/schemas/scientific"]}, "Darwin Core Geospatial Extension": {"identifier": "msc:m54", "urls": ["http://wiki.tdwg.org/twiki/bin/view/DarwinCore/GeospatialExtension"]}, "Darwin Core": {"identifier": "msc:m9", "urls": ["http://www.tdwg.org/standards/450", "http://rs.tdwg.org/dwc/index.htm", "http://rs.tdwg.org/dwc/terms/", "http://rs.tdwg.org/dwc/iri/", "http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd"]}, "Data Package": {"identifier": "msc:m10", "urls": ["https://frictionlessdata.io/specs/data-package/", "https://frictionlessdata.io/data-packages/"]}, "DataCite Metadata Schema": {"identifier": "msc:m11", "urls": ["http://schema.datacite.org", "http://schema.datacite.org/meta/kernel-2.1/doc/DataCite-MetadataKernel_v2.2.pdf", "http://schema.datacite.org/meta/kernel-2.1/metadata.xsd", "http://datacite.org/schema/kernel-2.1", "http://schema.datacite.org/meta/kernel-2.2/doc/DataCite-MetadataKernel_v2.2.pdf", "http://schema.datacite.org/meta/kernel-2.2/metadata.xsd", "http://datacite.org/schema/kernel-2.2", "http://schema.datacite.org/meta/kernel-3.0/doc/DataCite-MetadataKernel_v3.0.pdf", "http://schema.datacite.org/meta/kernel-3.0/metadata.xsd", "http://datacite.org/schema/kernel-3", "http://schema.datacite.org/meta/kernel-3.1/doc/DataCite-MetadataKernel_v3.1.pdf", "http://schema.datacite.org/meta/kernel-3.1/metadata.xsd", "http://datacite.org/schema/kernel-3.1", "http://schema.datacite.org/meta/kernel-4.0/doc/DataCite-MetadataKernel_v4.0.pdf", "http://schema.datacite.org/meta/kernel-4.0/metadata.xsd", "http://datacite.org/schema/kernel-4"]}, "DCAT (Data Catalog Vocabulary)": {"identifier": "msc:m12", "urls": ["https://www.w3.org/TR/vocab-dcat/#class-dataset", "https://www.w3.org/TR/vocab-dcat/#class-catalog", "http://www.w3.org/TR/vocab-dcat/", "https://www.w3.org/ns/dcat.ttl", "https://www.w3.org/2017/dxwg/wiki/Main_Page", "http://www.w3.org/ns/dcat#"]}, "DDI (Data Documentation Initiative)": {"identifier": "msc:m13", "urls": ["http://www.ddialliance.org/Specification/", "http://www.ddialliance.org/", "http://www.icpsr.umich.edu/DDI", "http://www.ddialliance.org/DDI/schema/ddi3.1/dataset.xsd", "ddi:codebook:2_5", "ddi:dataset:3_3", "ddi:dataset:3_2", "ddi:dataset:3_1", "ddi:dataset:3_0", "https://ddialliance.org/Specification/DDI-Codebook/2.5/XMLSchema/codebook.xsd", "https://ddialliance.org/Specification/DDI-Codebook/2.1/XMLSchema/codebook.xsd", "https://ddialliance.org/Specification/DDI-Lifecycle/3.3/XMLSchema/instance.xsd", "https://ddialliance.org/Specification/DDI-Lifecycle/3.2/XMLSchema/instance.xsd", "https://ddialliance.org/Specification/DDI-Lifecycle/3.1/XMLSchema/instance.xsd", "https://ddialliance.org/Specification/DDI-Lifecycle/3.0/XMLSchema/instance.xsd"]}, "DIF (Directory Interchange Format)": {"identifier": "msc:m14", "urls": ["http://gcmd.nasa.gov/add/difguide/WRITEADIF.pdf", "http://gcmd.nasa.gov/add/difguide/", "https://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/dif_v10.2.xsd", "http://gcmd.nasa.gov/Aboutus/xml/dif/dif.xsd", "https://git.earthdata.nasa.gov/projects/EMFD/repos/dif-schemas/browse/10.x/dif.xsd"]}, "Dryad Metadata Application Profile": {"identifier": "msc:m55", "urls": ["http://wiki.datadryad.org/Metadata_Profile", "http://datadryad.org/metadata/", "http://datadryad.org/profile/v3.1/dryad.xsd", "http://datadryad.org/profile/v3/dryad.xsd", "http://ils.unc.edu/mrc/dryad/version1_0/dryad_1_0.xsd"]}, "Dublin Core": {"identifier": "msc:m15", "urls": ["http://dublincore.org/specifications/", "http://dublincore.org", "http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd", "http://dublincore.org/schemas/xmls/simpledc20021212.xsd", "http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd", "http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd", "http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd", "http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd", "http://dublincore.org/schemas/xmls/qdc/dc.xsd", "http://dublincore.org/schemas/xmls/qdc/dcterms.xsd", "http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd", "- type: namespace", "http://purl.org/dc/elements/1.1/", "http://purl.org/dc/terms/", "http://purl.org/dc/dcmitype/"]}, "DwC Germplasm": {"identifier": "msc:m56", "urls": ["http://code.google.com/p/darwincore-germplasm/", "http://purl.org/germplasm#", "http://purl.org/germplasm/germplasmTerm#"]}, "EAD (Encoded Archival Description)": {"identifier": "msc:m96", "urls": ["https://www.loc.gov/ead/", "urn:isbn:1-931666-22-9", "https://www.loc.gov/ead/tglib1998/", "https://www.loc.gov/ead/ag/aghome.html", "https://www.loc.gov/ead/ead.xsd", "ftp://ftp.loc.gov/pub/ead/ead.dtd", "https://www.loc.gov/ead/tglib/", "https://www.loc.gov/ead/ead3.xsd", "https://www.loc.gov/ead/ead3.dtd", "https://www.loc.gov/ead/EAD3taglib/EAD3.html"]}, "eBank UK Metadata Application Profile": {"identifier": "msc:m57", "urls": ["http://ecrystals.chem.soton.ac.uk", "http://naca.central.cranfield.ac.uk/ethos-oai/2.0/uketd_dc.xsd", "http://naca.central.cranfield.ac.uk/ethos-oai/uketd_dc/"]}, "EDMED Metadata Profile": {"identifier": "msc:m58", "urls": ["https://www.bodc.ac.uk/data/information_and_inventories/edmed/", "EDMED_sdn_V1.2.xsd"]}, "EML (Ecological Metadata Language)": {"identifier": "msc:m16", "urls": ["https://eml.ecoinformatics.org/", "https://eml.ecoinformatics.org/schema", "eml://eml.ecoinformatics.org/eml-2.0.0", "eml://ecoinformatics.org/eml-2.1.0", "eml://ecoinformatics.org/eml-2.1.1", "https://eml.ecoinformatics.org/eml-2.2.0", "https://eml.ecoinformatics.org/eml-2.2.1", "https://eml.ecoinformatics.org/schema/eml_xsd"]}, "EURISCO Descriptors": {"identifier": "msc:m85", "urls": ["http://www.ecpgr.cgiar.org/fileadmin/templates/ecpgr.org/upload/MISC/EURISCO_Descriptors.pdf"]}, "FGDC/CSDGM Biological Data Profile": {"identifier": "msc:m59", "urls": ["http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/biometadata/biodatap.pdf"]}, "FGDC/CSDGM (Federal Geographic Data Committee Content Standard for Digital Geospatial Metadata)": {"identifier": "msc:m17", "urls": ["http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/base-metadata/v2_0698.pdf", "http://www.fgdc.gov/metadata/geospatial-metadata-standards/", "https://www.fgdc.gov/schemas/metadata/fgdc-std-001-1998.xsd", "https://www.fgdc.gov/schemas/metadata/fgdc-std-001.2-2001.xsd"]}, "FITS (Flexible Image Transport System)": {"identifier": "msc:m18", "urls": ["http://fits.gsfc.nasa.gov/fits_standard.html", "http://fits.gsfc.nasa.gov/fits_standard.html"]}, "FITS World Coordinate System (WCS)": {"identifier": "msc:m60", "urls": ["http://fits.gsfc.nasa.gov/fits_wcs.html"]}, "GBIF Metadata Profile": {"identifier": "msc:m61", "urls": ["http://rs.gbif.org/schema/eml-gbif-profile/", "http://rs.gbif.org/schema/eml-gbif-profile/1.0.2/eml-gbif-profile.xsd", "http://rs.gbif.org/schema/eml-gbif-profile/1.1/eml-gbif-profile.xsd"]}, "Genome Metadata": {"identifier": "msc:m19", "urls": ["http://enews.patricbrc.org/faqs/genome-metadata-faqs/"]}, "GeoRSS": {"identifier": "msc:m1000", "urls": ["http://www.georss.org", "http://www.georss.org/georss/", "http://schemas.opengis.net/georss/1.0/"]}, "GESMES/TS (Generic Statistical Message for Time Series)": {"identifier": "msc:m62", "urls": ["http://www.ecb.int/stats/services/sdmx/html/index.en.html"]}, "GSIM (Generic Statistical Information Model)": {"identifier": "msc:m63", "urls": ["http://www1.unece.org/stat/platform/display/metis/Generic+Statistical+Information+Model"]}, "HISPID (Herbarium Information Standards and Protocols for Interchange of Data)": {"identifier": "msc:m64", "urls": ["http://www.rbg.vic.gov.au/wiki/hiscom/index.php/HISPID_5"]}, "IDF (International DOI Foundation) Metadata Kernel": {"identifier": "msc:m86", "urls": []}, "IMPEx Data Model": {"identifier": "msc:m65", "urls": ["http://meetingorganizer.copernicus.org/EPSC2012/EPSC2012-360.pdf"]}, "INSPIRE Metadata Regulation": {"identifier": "msc:m66", "urls": ["http://inspire.ec.europa.eu/", "http://inspire.ec.europa.eu/schemas/common/1.0/common.xsd", "http://inspire.ec.europa.eu/schemas/common/1.0/network.xsd"]}, "International Virtual Observatory Alliance Technical Specifications": {"identifier": "msc:m20", "urls": ["http://www.ivoa.net/documents/#specs", "http://ivoa.net/documents/"]}, "ISA-TAB Nano": {"identifier": "msc:m67", "urls": ["https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano#ISA-TAB-Nano-title"]}, "ISA-Tab": {"identifier": "msc:m21", "urls": ["http://isatab.sourceforge.net/docs/ISA-TAB_release-candidate-1_v1.0_24nov08.pdf", "http://isatab.sourceforge.net/format.html"]}, "isaconfig-diXa": {"identifier": "msc:m68", "urls": ["https://bitbucket.org/kanterae/isaconfig-dixa"]}, "ISO 19115-2 - Imagery and gridded data": {"identifier": "msc:m69", "urls": ["http://www.iso.org/iso/catalogue_detail.htm?csnumber=39229"]}, "ISO 19115 North American Profile": {"identifier": "msc:m70", "urls": ["http://www.fgdc.gov/standards/projects/incits-l1-standards-projects/NAP-Metadata"]}, "ISO 19115": {"identifier": "msc:m22", "urls": ["http://standards.iso.org/iso/19115/-3/", "http://www.iso.org/iso/catalogue_detail.htm?csnumber=53798", "http://www.isotc211.org/2005/gmd/gmd.xsd", "http://www.isotc211.org/2005/gmd"]}, "Geography Markup Language": {"identifier": "msc:m1002", "urls": ["https://www.ogc.org/standards/gml", "www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=32554", "http://www.opengis.net/gml/3.2", "http://schemas.opengis.net/gml/3.2.1/gml.xsd"]}, "JSON-LD (JavaScript Object Notation for Linked Data)": {"identifier": "msc:m95", "urls": []}, "MAGE-TAB": {"identifier": "msc:m87", "urls": []}, "MARC (Machine-Readable Cataloging)": {"identifier": "msc:m88", "urls": ["http://www.loc.gov/marc/", "http://www.loc.gov/marc/bibliographic/", "http://www.loc.gov/standards/marcxml/schema/MARC21slim.xsd"]}, "Marine Community Profile": {"identifier": "msc:m71", "urls": ["http://www.aodc.org.au/index.php?id=37"]}, "MIBBI (Minimum Information for Biological and Biomedical Investigations)": {"identifier": "msc:m23", "urls": ["http://mibbi.sourceforge.net/foundry.shtml", "http://mibbi.sourceforge.net/portal.shtml"]}, "MIBBI Portal": {"identifier": "msc:m72", "urls": ["http://mibbi.sourceforge.net/portal.shtml"]}, "MIDAS-Heritage": {"identifier": "msc:m24", "urls": ["http://www.english-heritage.org.uk/content/publications/publicationsNew/guidelines-standards/midas-heritage/midas-heritage-2012-v1_1.pdf", "http://www.english-heritage.org.uk/publications/midas-heritage/"]}, "MODS (Metadata Object Description Schema)": {"identifier": "msc:m97", "urls": ["http://www.loc.gov/standards/mods/", "http://www.loc.gov/standards/mods/v3/mods-3-3.xsd", "http://www.loc.gov/standards/mods/mods-outline-3-4.html", "http://www.loc.gov/standards/mods/v3/mods-3-4.xsd", "http://www.loc.gov/standards/mods/mods-outline-3-5.html", "http://www.loc.gov/standards/mods/v3/mods-3-5.xsd", "http://www.loc.gov/standards/mods/mods-outline-3-6.html", "http://www.loc.gov/standards/mods/v3/mods-3-6.xsd", "http://www.loc.gov/standards/mods/mods-outline-3-7.html", "http://www.loc.gov/standards/mods/v3/mods-3-7.xsd"]}, "NetCDF Attribute Convention for Dataset Discovery": {"identifier": "msc:m89", "urls": []}, "NeXus": {"identifier": "msc:m25", "urls": ["http://download.nexusformat.org/doc/html/ref_doc.html", "http://www.nexusformat.org/"]}, "OAI-ORE (Open Archives Initiative Object Reuse and Exchange)": {"identifier": "msc:m26", "urls": ["http://www.openarchives.org/ore/", "http://www.openarchives.org/ore/toc"]}, "Observ-OM": {"identifier": "msc:m27", "urls": ["http://www.molgenis.org/wiki/ObservStart"]}, "Observations and Measurements": {"identifier": "msc:m28", "urls": ["http://portal.opengeospatial.org/files/?artifact_id=41579", "http://www.opengeospatial.org/standards/om"]}, "OECD Dataset Metadata": {"identifier": "msc:m90", "urls": []}, "OECD Minimum Data Set": {"identifier": "msc:m91", "urls": []}, "OME-TIFF (Open Microscopy Environment TIFF)": {"identifier": "msc:m73", "urls": ["http://www.openmicroscopy.org/site/support/file-formats/ome-tiff"]}, "OME-XML (Open Microscopy Environment XML)": {"identifier": "msc:m29", "urls": ["http://www.openmicroscopy.org/Schemas/", "http://www.openmicroscopy.org/site/support/file-formats"]}, "OpenAIRE Guidelines": {"identifier": "msc:m92", "urls": ["https://guidelines.openaire.eu/"]}, "OpenSearch": {"identifier": "msc:m1001", "urls": ["http://a9.com/-/spec/opensearch/1.1/"]}, "PDBx/mmCIF (Protein Data Bank Exchange Dictionary and the Macromolecular Crystallographic Information Framework)": {"identifier": "msc:m30", "urls": ["http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Index/", "http://mmcif.wwpdb.org/"]}, "PREMIS": {"identifier": "msc:m31", "urls": ["http://www.loc.gov/standards/premis/v3/premis-3-0-final.pdf", 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"urls": ["https://www.ands.org.au/online-services/rif-cs-schema", "http://services.ands.org.au/documentation/rifcs/schemadocs/registryObjects.html", "http://services.ands.org.au/documentation/rifcs/schema/registryObjects.xsd"]}, "SDAC (Standard for Documentation of Astronomical Catalogues)": {"identifier": "msc:m37", "urls": ["http://cds.u-strasbg.fr/doc/catstd.pdf", "http://cds.u-strasbg.fr/doc/catstd.htx"]}, "SDMX (Statistical Data and Metadata Exchange)": {"identifier": "msc:m38", "urls": ["http://sdmx.org/?page_id=5008", "http://sdmx.org"]}, "Shoreline Metadata Profile": {"identifier": "msc:m75", "urls": ["http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/shoreline-metadata/"]}, "SNRNASM ISA-Tab": {"identifier": "msc:m76", "urls": ["http://snrnasm.bio.unc.edu"]}, "SPASE Data Model": {"identifier": "msc:m39", "urls": ["http://www.spase-group.org/docs/schema/", "http://www.spase-group.org/data/", "http://www.spase-group.org/data/model/spase-2_2_2.pdf", 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"https://doi.org/10.17616/R3989R", "ethz.wgms": "https://doi.org/10.17616/R3WP5N", "zbw.zbw-jda": "https://doi.org/10.17616/R3BM03", "cern.zenodo": "https://doi.org/10.17616/R3QP53", "zbw.zew": "https://doi.org/10.17616/R3389W"} \ No newline at end of file diff --git a/fuji_server/evaluators/fair_evaluator_community_metadata.py b/fuji_server/evaluators/fair_evaluator_community_metadata.py index 91d5a103..71612904 100644 --- a/fuji_server/evaluators/fair_evaluator_community_metadata.py +++ b/fuji_server/evaluators/fair_evaluator_community_metadata.py @@ -33,7 +33,8 @@ def evaluate(self): self.result = CommunityEndorsedStandard(id=self.metric_number, metric_identifier=self.metric_identifier, metric_name=self.metric_name) - standards_detected: List[CommunityEndorsedStandardOutputInner] = [] + community_standards_detected: List[CommunityEndorsedStandardOutputInner] = [] + multidiscipliary_standards_detected = [] if self.fuji.namespace_uri: self.fuji.namespace_uri = list(set(self.fuji.namespace_uri)) # ============== retrieve community standards by collected namespace uris @@ -46,53 +47,75 @@ def evaluate(self): if std_ns_temp: subject = self.fuji.COMMUNITY_METADATA_STANDARDS_URIS.get(std_ns_temp).get('subject_areas') std_name = self.fuji.COMMUNITY_METADATA_STANDARDS_URIS.get(std_ns_temp).get('title') - if subject and all(elem == "Multidisciplinary" for elem in subject): - self.logger.info( - 'FsF-R1.3-01M : Skipped non-disciplinary standard found through namespaces -: {}'.format( - std_ns)) - else: - self.logger.log(self.fuji.LOG_SUCCESS, - 'FsF-R1.3-01M : Found disciplinary standard through namespaces -: {}'.format( - std_ns)) + if subject: + if all(elem == "Multidisciplinary" for elem in subject): + self.logger.info( + 'FsF-R1.3-01M : Found non-disciplinary standard (but RDA listed) found through namespaces -: {}'.format( + str(std_name)+' ('+str(std_ns)+')')) + self.setEvaluationCriteriumScore('FsF-R1.3-01M-3', 0, 'pass') + self.maturity = 1 + multidiscipliary_standards_detected.append(std_name) + else: + self.logger.log(self.fuji.LOG_SUCCESS, + 'FsF-R1.3-01M : Found disciplinary standard through namespaces -: {}'.format( + std_ns)) nsout = CommunityEndorsedStandardOutputInner() nsout.metadata_standard = std_name # use here original standard uri detected nsout.subject_areas = subject nsout.urls = [std_ns] - standards_detected.append(nsout) + community_standards_detected.append(nsout) else: no_match.append(std_ns) if len(no_match) > 0: self.logger.info( 'FsF-R1.3-01M : The following standards found through namespaces are excluded as they are not listed in RDA metadata catalog -: {}'.format( no_match)) - if standards_detected: + if len(community_standards_detected) - len(multidiscipliary_standards_detected) > 0: self.maturity = 3 self.setEvaluationCriteriumScore('FsF-R1.3-01M-1', 1, 'pass') # ============== use standards listed in the re3data record if no metadata is detected from oai-pmh re3_detected = False if len(self.fuji.community_standards) > 0: - #if len(standards_detected) == 0: + #if len(community_standards_detected) == 0: if self.fuji.use_datacite: self.logger.info('FsF-R1.3-01M : Using re3data to detect metadata standard(s)') for s in self.fuji.community_standards: + re3_listed = False standard_found = self.fuji.lookup_metadatastandard_by_name(s) if standard_found: subject = self.fuji.COMMUNITY_STANDARDS.get(standard_found).get('subject_areas') - if subject and all(elem == "Multidisciplinary" for elem in subject): - self.logger.info('FsF-R1.3-01M : Skipped non-disciplinary standard -: {}'.format(s)) - else: - if self.maturity < 2: - self.maturity = 2 - re3_detected = True - self.logger.log(self.fuji.LOG_SUCCESS, - 'FsF-R1.3-01M : Found disciplinary standard through re3data -: {}'.format( - s)) - out = CommunityEndorsedStandardOutputInner() - out.metadata_standard = s - out.subject_areas = self.fuji.COMMUNITY_STANDARDS.get(standard_found).get('subject_areas') - out.urls = self.fuji.COMMUNITY_STANDARDS.get(standard_found).get('urls') - standards_detected.append(out) + if subject: + #print(subject, standard_found) + re3_listed = True + if all(elem == "Multidisciplinary" for elem in subject): + self.logger.info( + 'FsF-R1.3-01M : Found non-disciplinary standard (but RDA listed) found through re3data -: {}'.format( + standard_found)) + self.setEvaluationCriteriumScore('FsF-R1.3-01M-3', 0, 'pass') + if self.maturity <= 1: + self.maturity = 1 + multidiscipliary_standards_detected.append(standard_found) + #self.logger.info('FsF-R1.3-01M : Skipped non-disciplinary standard -: {}'.format(s)) + elif standard_found=='Repository-Developed Metadata Schemas': + re3_listed = False + self.logger.info('FsF-R1.3-01M : Skipped proprietary standard -: {}'.format(s)) + else: + if self.maturity < 2: + self.maturity = 2 + re3_detected = True + self.logger.log(self.fuji.LOG_SUCCESS, + 'FsF-R1.3-01M : Found disciplinary standard through re3data -: {}'.format( + s)) + if re3_listed: + rdaurls = self.fuji.COMMUNITY_STANDARDS.get(standard_found).get('urls') + if isinstance(rdaurls, list): + rdaurls= [rdaurls[0]] + out = CommunityEndorsedStandardOutputInner() + out.metadata_standard = s + out.subject_areas = self.fuji.COMMUNITY_STANDARDS.get(standard_found).get('subject_areas') + out.urls = rdaurls + community_standards_detected.append(out) elif self.fuji.use_datacite: self.logger.info( 'FsF-R1.3-01M : Metadata standard(s) that are listed in re3data are excluded from the assessment output.') @@ -100,21 +123,20 @@ def evaluate(self): elif self.fuji.use_datacite: self.logger.warning('FsF-R1.3-01M : NO metadata standard(s) of the repository specified in re3data') - - if standards_detected: + if community_standards_detected: if re3_detected: if self.maturity < 3: self.maturity = 2 self.setEvaluationCriteriumScore('FsF-R1.3-01M-2', 1, 'pass') else: self.setEvaluationCriteriumScore('FsF-R1.3-01M-2', 0, 'pass') - self.score.earned = self.total_score + if len(community_standards_detected) - len(multidiscipliary_standards_detected) > 0: + self.score.earned = self.total_score self.result.test_status = 'pass' - else: self.logger.warning('FsF-R1.3-01M : Unable to determine community standard(s)') self.result.metric_tests = self.metric_tests self.result.score = self.score self.result.maturity = self.maturity - self.result.output = standards_detected \ No newline at end of file + self.result.output = community_standards_detected \ No newline at end of file diff --git a/fuji_server/evaluators/fair_evaluator_data_content_metadata.py b/fuji_server/evaluators/fair_evaluator_data_content_metadata.py index 6c656d73..f058a7f1 100644 --- a/fuji_server/evaluators/fair_evaluator_data_content_metadata.py +++ b/fuji_server/evaluators/fair_evaluator_data_content_metadata.py @@ -185,11 +185,23 @@ def evaluate(self): elif d == 'size': if tika_content_size == 0: self.logger.warning('{0} : Could not verify content size (received: 0 bytes) from downloaded file'.format(self.metric_identifier)) - elif data_object.get('size') == tika_content_size: - matches_content = True - matches_size = True else: - self.logger.warning('{0} : Could not verify content size from downloaded file -: (expected: {1}, found: {2})'.format(self.metric_identifier, str(data_object.get('size')), str(tika_content_size) )) + #print(type(data_object.get('size'))) + try: + object_size=int(float(data_object.get('size'))) + if object_size == tika_content_size: + matches_content = True + matches_size = True + else: + self.logger.warning( + '{0} : Could not verify content size from downloaded file -: (expected: {1}, found: {2})'.format( + self.metric_identifier, str(data_object.get('size')), + str(tika_content_size))) + + except Exception as e: + self.logger.warning( + '{0} : Could not verify content size from downloaded file -: (expected: {1}, found: {2})'.format( + self.metric_identifier, str(data_object.get('size')), str(tika_content_size))) data_content_filetype_inner = DataContentMetadataOutputInner() data_content_filetype_inner.descriptor = descriptor diff --git a/fuji_server/evaluators/fair_evaluator_file_format.py b/fuji_server/evaluators/fair_evaluator_file_format.py index 8fa1ed8c..a4f9284d 100644 --- a/fuji_server/evaluators/fair_evaluator_file_format.py +++ b/fuji_server/evaluators/fair_evaluator_file_format.py @@ -54,7 +54,10 @@ def evaluate(self): content_urls = [item.get('url') for item in self.fuji.content_identifier] self.logger.info('FsF-R1.3-02D : Data content identifier provided - {}'.format(content_urls)) #self.maturity = 1 + loginpage = False + preferred_detected = False for file_index, data_file in enumerate(self.fuji.content_identifier): + mime_type = data_file.get('type') if data_file.get('url') is not None: if mime_type is None or mime_type in ['application/octet-stream']: @@ -87,7 +90,7 @@ def evaluate(self): # FILE FORMAT CHECKS.... # check if format is a scientific one: - loginpage = False + for mimetype, url in mime_url_pair.items(): data_file_output = DataFileFormatOutputInner() preferance_reason = [] @@ -129,14 +132,17 @@ def evaluate(self): preferance_reason.extend(['long term format', 'open format', 'generic science format']) subject_area.append('General') data_file_output.is_preferred_format = True + if 'html' in mimetype: loginpage = True + if preferance_reason: + preferred_detected = True data_file_output.mime_type = mimetype data_file_output.file_uri = url data_file_output.preference_reason = list(set(preferance_reason)) data_file_output.subject_areas = list(set(subject_area)) data_file_list.append(data_file_output) - if len(data_file_list) > 0 and not loginpage: + if preferred_detected and not loginpage: self.score.earned = 1 self.setEvaluationCriteriumScore('FsF-R1.3-02D-1', 1, 'pass') #self.maturity = 3 diff --git a/fuji_server/evaluators/fair_evaluator_persistent_identifier.py b/fuji_server/evaluators/fair_evaluator_persistent_identifier.py index aa396b77..82986930 100644 --- a/fuji_server/evaluators/fair_evaluator_persistent_identifier.py +++ b/fuji_server/evaluators/fair_evaluator_persistent_identifier.py @@ -46,7 +46,7 @@ def evaluate(self): if self.fuji.id_scheme =='url': self.fuji.origin_url = self.fuji.id check_url =self.fuji.id - if check_url is not None: + if check_url: # ======= RETRIEVE METADATA FROM LANDING PAGE ======= requestHelper = RequestHelper(check_url, self.logger) requestHelper.setAcceptType(AcceptTypes.html_xml) # request @@ -57,6 +57,7 @@ def evaluate(self): if type(self.fuji.extruct_result) != dict: self.fuji.extruct_result ={} r = requestHelper.getHTTPResponse() + response_status =requestHelper.response_status if r: self.fuji.landing_url = requestHelper.redirect_url @@ -69,7 +70,8 @@ def evaluate(self): #self.fuji.repeat_pid_check = False if self.fuji.landing_url not in ['https://datacite.org/invalid.html']: - if r.status == 200: + + if response_status == 200: # identify signposting links in header header_link_string = requestHelper.getHTTPResponse().getheader('Link') if header_link_string is not None: @@ -124,12 +126,12 @@ def evaluate(self): self.output.resolvable_status = True self.logger.info('FsF-F1-02D : Object identifier active (status code = 200)') self.fuji.isMetadataAccessible = True - elif r.status_code in [401, 402, 403]: + elif response_status in [401, 402, 403]: self.fuji.isMetadataAccessible = False - self.logger.warning("FsF-F1-02D : Resource inaccessible, identifier returned http status code -: {code}".format(code=r.status_code)) + self.logger.error("FsF-F1-02D : Resource inaccessible, identifier returned http status code -: {code}".format(code=response_status)) else: self.fuji.isMetadataAccessible = False - self.logger.warning("FsF-F1-02D : Resource inaccessible, identifier returned http status code -: {code}".format(code=r.status_code)) + self.logger.error("FsF-F1-02D : Resource inaccessible, identifier returned http status code -: {code}".format(code=response_status)) else: self.logger.warning("FsF-F1-02D : Invalid DOI, identifier resolved to -: {code}".format( code=self.fuji.landing_url)) @@ -137,6 +139,10 @@ def evaluate(self): else: self.fuji.isMetadataAccessible = False self.logger.warning("FsF-F1-02D :Resource inaccessible, no response received from -: {}".format(check_url)) + if response_status in [401, 402, 403]: + self.logger.error( + "FsF-F1-02D : Resource inaccessible, identifier returned http status code -: {code}".format( + code=response_status)) else: self.logger.warning("FsF-F1-02D :Resource inaccessible, could not identify an actionable representation for the given identfier -: {}".format(self.fuji.id)) diff --git a/fuji_server/evaluators/fair_evaluator_unique_identifier.py b/fuji_server/evaluators/fair_evaluator_unique_identifier.py index ce231d5c..37e3a141 100644 --- a/fuji_server/evaluators/fair_evaluator_unique_identifier.py +++ b/fuji_server/evaluators/fair_evaluator_unique_identifier.py @@ -43,6 +43,8 @@ def evaluate(self): self.logger.info('FsF-F1-01D : Using idutils schemes') idhelper = IdentifierHelper(self.fuji.id) found_ids = idhelper.identifier_schemes + self.logger.info('Starting assessment on identifier: {}'.format(self.fuji.id)) + #found_ids = idutils.detect_identifier_schemes(self.fuji.id) # some schemes like PMID are generic if len(found_ids) > 0: self.logger.log(self.fuji.LOG_SUCCESS,'FsF-F1-01D : Unique identifier schemes found {}'.format(found_ids)) diff --git a/fuji_server/helper/catalogue_helper_datacite.py b/fuji_server/helper/catalogue_helper_datacite.py index fc3e0e8f..db8b1961 100644 --- a/fuji_server/helper/catalogue_helper_datacite.py +++ b/fuji_server/helper/catalogue_helper_datacite.py @@ -16,7 +16,7 @@ def __init__(self,logger: logging.Logger = None): def query(self, pid): response = None try: - res= apiresponse = re.get(self.apiURI+'/'+pid) + res= apiresponse = re.get(self.apiURI+'/'+pid, timeout=5) self.logger.info('FsF-F4-01M : Querying DataCite API for -:' + str(pid)) if res.status_code == 200: self.islisted =True diff --git a/fuji_server/helper/catalogue_helper_mendeley_data.py b/fuji_server/helper/catalogue_helper_mendeley_data.py index 966df55c..2d1aacf6 100644 --- a/fuji_server/helper/catalogue_helper_mendeley_data.py +++ b/fuji_server/helper/catalogue_helper_mendeley_data.py @@ -18,7 +18,7 @@ def query(self, pidlist): for pid in pidlist: try: if pid: - res= apiresponse = re.get(self.apiURI+'/'+re.utils.quote(str(pid))) + res= apiresponse = re.get(self.apiURI+'/'+re.utils.quote(str(pid)), timeout=1) self.logger.info('FsF-F4-01M : Querying Mendeley Data API for -:' + str(pid)) if res.status_code == 200: resp = res.json() diff --git a/fuji_server/helper/identifier_helper.py b/fuji_server/helper/identifier_helper.py index af88f801..bb83a462 100644 --- a/fuji_server/helper/identifier_helper.py +++ b/fuji_server/helper/identifier_helper.py @@ -40,6 +40,11 @@ def __init__(self, idstring): self.normalized_id = self.identifier if self.identifier and isinstance(self.identifier, str): if len(self.identifier) > 4 and not self.identifier.isnumeric(): + #workaround to resolve lsids: + #idutils.LANDING_URLS['lsid'] ='http://www.lsid.info/resolver/?lsid={pid}' + #workaround to recognize https purls + if 'https://purl.' in self.identifier: + self.identifier = self.identifier.replace('https:','http:') generic_identifiers_org_pattern = '^([a-z0-9\._]+):(.+)' # idutils check self.identifier_schemes = idutils.detect_identifier_schemes(self.identifier) diff --git a/fuji_server/helper/metadata_collector_datacite.py b/fuji_server/helper/metadata_collector_datacite.py index 938dbe10..1d5260be 100644 --- a/fuji_server/helper/metadata_collector_datacite.py +++ b/fuji_server/helper/metadata_collector_datacite.py @@ -38,44 +38,48 @@ def __init__(self, mapping, pid_url=None, loggerinst=None): def parse_metadata(self): source_name = None dcite_metadata = {} - self.logger.info('FsF-F2-01M : Trying to retrieve datacite metadata') - requestHelper = RequestHelper(self.pid_url, self.logger) - requestHelper.setAcceptType(AcceptTypes.datacite_json) - neg_source,ext_meta = requestHelper.content_negotiate('FsF-F2-01M') - if ext_meta: - try: - dcite_metadata = jmespath.search(self.metadata_mapping.value, ext_meta) - if dcite_metadata: - self.namespaces.append('http://datacite.org/schema/') - source_name = self.getEnumSourceNames().DATACITE_JSON.value - if dcite_metadata['creator'] is None: - first = dcite_metadata['creator_first'] - last = dcite_metadata['creator_last'] - # default type of creator is [] - if isinstance(first, list) and isinstance(last, list): - if len(first) == len(last): - names = [i + " " + j for i, j in zip(first, last)] - dcite_metadata['creator'] = names + if self.pid_url: + self.logger.info('FsF-F2-01M : Trying to retrieve datacite metadata') + requestHelper = RequestHelper(self.pid_url, self.logger) + requestHelper.setAcceptType(AcceptTypes.datacite_json) + neg_source,ext_meta = requestHelper.content_negotiate('FsF-F2-01M') + if ext_meta: + try: + dcite_metadata = jmespath.search(self.metadata_mapping.value, ext_meta) + if dcite_metadata: + self.namespaces.append('http://datacite.org/schema/') + source_name = self.getEnumSourceNames().DATACITE_JSON.value + if dcite_metadata['creator'] is None: + first = dcite_metadata['creator_first'] + last = dcite_metadata['creator_last'] + # default type of creator is [] + if isinstance(first, list) and isinstance(last, list): + if len(first) == len(last): + names = [i + " " + j for i, j in zip(first, last)] + dcite_metadata['creator'] = names - if dcite_metadata.get('related_resources'): - self.logger.info('FsF-I3-01M : {0} related resource(s) extracted from -: {1}'.format( - len(dcite_metadata['related_resources']), source_name)) - temp_rels = [] + if dcite_metadata.get('related_resources'): + self.logger.info('FsF-I3-01M : {0} related resource(s) extracted from -: {1}'.format( + len(dcite_metadata['related_resources']), source_name)) + temp_rels = [] - for r in dcite_metadata['related_resources']: - if r.get('scheme_uri'): - self.namespaces.append(r.get('scheme_uri')) - filtered = {k: v for k, v in r.items() if v is not None} - temp_rels.append(filtered) - dcite_metadata['related_resources'] = temp_rels - else: - self.logger.info('FsF-I3-01M : No related resource(s) found in Datacite metadata') + for r in dcite_metadata['related_resources']: + if r.get('scheme_uri'): + self.namespaces.append(r.get('scheme_uri')) + filtered = {k: v for k, v in r.items() if v is not None} + temp_rels.append(filtered) + dcite_metadata['related_resources'] = temp_rels + else: + self.logger.info('FsF-I3-01M : No related resource(s) found in Datacite metadata') + + # convert all values (list type) into string except 'creator','license','related_resources' + for key, value in dcite_metadata.items(): + if key not in self.exclude_conversion and isinstance(value, list): + flat = ', '.join(map(str, value)) + dcite_metadata[key] = flat + except Exception as e: + self.logger.exception('Failed to extract Datacite Json -: {}'.format(e)) + else: + self.logger.warning('FsF-F2-01M : Skipped Datacite metadata retrieval, no PID URL detected') - # convert all values (list type) into string except 'creator','license','related_resources' - for key, value in dcite_metadata.items(): - if key not in self.exclude_conversion and isinstance(value, list): - flat = ', '.join(map(str, value)) - dcite_metadata[key] = flat - except Exception as e: - self.logger.exception('Failed to extract Datacite Json -: {}'.format(e)) return source_name, dcite_metadata diff --git a/fuji_server/helper/metadata_collector_rdf.py b/fuji_server/helper/metadata_collector_rdf.py index 2a8aa5d3..6be80912 100644 --- a/fuji_server/helper/metadata_collector_rdf.py +++ b/fuji_server/helper/metadata_collector_rdf.py @@ -104,7 +104,7 @@ def get_default_metadata(self,g): for row in sorted(r): for l, v in row.asdict().items(): if l is not None: - if l in ['references' ,'source' ,'isVersionOf','isReferencedBy']: + if l in ['references' ,'source' ,'isVersionOf','isReferencedBy','isPartOf','hasVersion','replaces', 'hasPart', 'isReplacedBy', 'requires', 'isRequiredBy']: if not meta.get('related_resources'): meta['related_resources'] = [] meta['related_resources'].append({'related_resource': str(v), 'relation_type': l}) @@ -127,6 +127,8 @@ def get_default_metadata(self,g): def get_metadata(self,g, item, type='Dataset'): DCAT = Namespace("http://www.w3.org/ns/dcat#") meta = dict() + #default sparql + met = self.get_default_metadata(item) meta['object_identifier'] = (g.value(item, DC.identifier) or g.value(item, DCTERMS.identifier)) ''' if self.source_name != self.getEnumSourceNames().RDFA.value: @@ -144,6 +146,14 @@ def get_metadata(self,g, item, type='Dataset'): #TODO creators, contributors meta['creator'] = g.value(item, DC.creator) meta['license'] = g.value(item, DCTERMS.license) + meta['related_resources']=[] + meta['access_level'] = (g.value(item, DCTERMS.accessRights) or g.value(item, DCTERMS.rights) or g.value(item, DC.rights)) + for dctrelationtype in [DCTERMS.references, DCTERMS.source, DCTERMS.isVersionOf, DCTERMS.isReferencedBy, DCTERMS.isPartOf, DCTERMS.hasVersion, DCTERMS.replaces, + DCTERMS.hasPart, DCTERMS.isReplacedBy, DCTERMS.requires, DCTERMS.isRequiredBy]: + dctrelation = g.value(item, dctrelationtype) + if dctrelation: + meta['related_resources'].append({'related_resource': str(dctrelation), 'relation_type': str(dctrelationtype)}) + # quick fix (avoid rdflib literal type exception) for v in [meta['title'],meta['summary'], meta['publisher']]: if v: @@ -168,7 +178,6 @@ def get_ontology_metadata(self, graph): return ont_metadata def get_dcat_metadata(self, graph): - dcat_metadata=dict() DCAT = Namespace("http://www.w3.org/ns/dcat#") @@ -197,16 +206,23 @@ def get_dcat_metadata(self, graph): # distribution distribution = graph.objects(datasets[0], DCAT.distribution) + dcat_metadata['object_content_identifier']=[] for dist in distribution: - durl=graph.value(dist, DCAT.accessURL) - #taking only one just to check if licence is available - dcat_metadata['license']=graph.value(dist, DCTERMS.license) - # TODO: check if this really works.. - dcat_metadata['access_rights']=(graph.value(dist, DCTERMS.accessRights) or graph.value(dist, DCTERMS.rights)) - dtype=graph.value(dist, DCAT.mediaType) - dsize=graph.value(dist, DCAT.bytesSize) - dcat_metadata['object_content_identifier'].append({'url':str(durl),'type':str(dtype), 'size':dsize}) + dtype,durl ,dsize = None,None,None + if not (graph.value(dist, DCAT.accessURL) or graph.value(dist, DCAT.downloadURL)): + durl = str(dist) + else: + durl= (graph.value(dist, DCAT.accessURL) or graph.value(dist, DCAT.downloadURL)) + #taking only one just to check if licence is available + dcat_metadata['license']=graph.value(dist, DCTERMS.license) + # TODO: check if this really works.. + dcat_metadata['access_rights']=(graph.value(dist, DCTERMS.accessRights) or graph.value(dist, DCTERMS.rights)) + dtype=graph.value(dist, DCAT.mediaType) + dsize=graph.value(dist, DCAT.bytesSize) + if durl or dtype or dsize: + dcat_metadata['object_content_identifier'].append({'url':str(durl),'type':dtype, 'size':dsize}) + if dcat_metadata['object_content_identifier']: self.logger.info('FsF-F3-01M : Found data links in DCAT.org metadata -: ' + str(dcat_metadata['object_content_identifier'])) diff --git a/fuji_server/helper/metadata_mapper.py b/fuji_server/helper/metadata_mapper.py index 30cadb63..7528ce1b 100644 --- a/fuji_server/helper/metadata_mapper.py +++ b/fuji_server/helper/metadata_mapper.py @@ -133,7 +133,7 @@ class Mapper(Enum): GENERIC_SPARQL = """ PREFIX dct: PREFIX dc: - SELECT ?object_identifier ?title ?summary ?publisher ?publication_date ?creator ?object_type ?license ?access_level ?keywords ?references ?source ?isVersionOf ?isReferencedBy + SELECT ?object_identifier ?title ?summary ?publisher ?publication_date ?creator ?object_type ?license ?access_level ?keywords ?references ?source ?isVersionOf ?isReferencedBy ?isPartOf ?hasVersion ?replaces ?hasPart ?isReplacedBy ?requires ?isRequiredBy WHERE { OPTIONAL {?dataset dct:title|dc:title ?title} OPTIONAL {?dataset dct:identifier|dc:identifier ?object_identifier} @@ -149,6 +149,12 @@ class Mapper(Enum): OPTIONAL {?dataset dct:isReferencedBy ?isReferencedBy} OPTIONAL {?dataset dc:source|dct:source ?source} OPTIONAL {?dataset dct:isVersionOf ?isVersionOf} + OPTIONAL {?dataset dct:isPartOf ?isPartOf} + OPTIONAL {?dataset dct:hasVersion ?hasVersion} + OPTIONAL {?dataset dct:replaces ?replaces} + OPTIONAL {?dataset dct:hasPart ?hasPart} + OPTIONAL {?dataset dct:requires ?requires} + OPTIONAL {?dataset dct:isRequiredBy ?isRequiredBy} } """ diff --git a/fuji_server/helper/preprocessor.py b/fuji_server/helper/preprocessor.py index 4575b8f1..8eede8f1 100644 --- a/fuji_server/helper/preprocessor.py +++ b/fuji_server/helper/preprocessor.py @@ -65,6 +65,20 @@ class Preprocessor(object): logger = logging.getLogger(__name__) data_files_limit = 3 metric_specification = None + remote_log_host = None + remote_log_path = None + + @classmethod + def set_remote_log_info(cls, host, path ): + try: + request = requests.get('http://'+host+path) + if request.status_code == 200: + cls.remote_log_host=host + cls.remote_log_path=path + else: + cls.logger.warning('Remote Logging not possible, URL response: '+str(request.status_code)) + except Exception as e: + cls.logger.warning('Remote Logging not possible ,please correct : ' + str(host+' '+path)) @classmethod def get_google_data_dois(cls): @@ -168,11 +182,13 @@ def retrieve_datacite_re3repos(cls, re3_endpoint, datacite_endpoint, isDebugMode # retrieve all client id and re3data doi from datacite cls.DATACITE_API_REPO = datacite_endpoint cls.RE3DATA_API = re3_endpoint + #isDebugMode=False re3dict_path = os.path.join(cls.fuji_server_dir, 'data', 'repodois.json') if isDebugMode: with open(re3dict_path) as f: cls.re3repositories = json.load(f) else: + #print('updating re3data dois') p = {'query': 're3data_id:*'} try: req = requests.get(datacite_endpoint, params=p, headers=cls.header) @@ -184,6 +200,8 @@ def retrieve_datacite_re3repos(cls, re3_endpoint, datacite_endpoint, isDebugMode for r in response["data"]: cls.re3repositories[r['id']] = r['attributes']['re3data'] raw['links'] = response['links'] + #fix wrong entry + cls.re3repositories['bl.imperial']='http://doi.org/10.17616/R3K64N' with open(re3dict_path, 'w') as f2: json.dump(cls.re3repositories, f2) except requests.exceptions.RequestException as e: diff --git a/fuji_server/helper/repository_helper.py b/fuji_server/helper/repository_helper.py index f177517d..5fe632ab 100644 --- a/fuji_server/helper/repository_helper.py +++ b/fuji_server/helper/repository_helper.py @@ -33,7 +33,7 @@ class RepositoryHelper: ns = {"r3d": "http://www.re3data.org/schema/2-2"} RE3DATA_APITYPES =['OAI-PMH','SOAP','SPARQL','SWORD','OpenDAP'] - def __init__(self, client, pidscheme): + def __init__(self, client, pidscheme, logger): self.client_id = client self.pid_scheme = pidscheme self.re3metadata_raw = None @@ -41,10 +41,11 @@ def __init__(self, client, pidscheme): self.repository_url = None self.repo_apis = {} self.repo_standards = [] - self.logger = Preprocessor.logger #logging.getLogger(__name__) + self.logger = logging.getLogger(logger) #print(__name__) def lookup_re3data(self): if self.client_id and self.pid_scheme: + re3doi = RepositoryHelper.DATACITE_REPOSITORIES.get(self.client_id) # {client_id,re3doi} #print(self.client_id,'Re3DOI',re3doi, idutils.is_doi(re3doi)) if re3doi: @@ -52,6 +53,7 @@ def lookup_re3data(self): short_re3doi = idutils.normalize_pid(re3doi, scheme='doi') #https://doi.org/10.17616/R3XS37 else: re3doi = None + # pid -> clientId -> repo doi-> re3id, and query repository metadata from re3api if re3doi: self.logger.info('FsF-R1.3-01M : Found match re3data (DOI-based) record') @@ -67,7 +69,7 @@ def lookup_re3data(self): # re3link = root.xpath('//link')[0].attrib['href'] if re3link is not None: - self.logger.info('FsF-R1.3-01M : Found match re3data metadata record') + self.logger.info('FsF-R1.3-01M : Found match re3data metadata record -: '+str(re3link)) # query reposiroty metadata q2 = RequestHelper(url=re3link) q2.setAcceptType(AcceptTypes.xml) diff --git a/fuji_server/helper/request_helper.py b/fuji_server/helper/request_helper.py index e441351a..b31c9982 100644 --- a/fuji_server/helper/request_helper.py +++ b/fuji_server/helper/request_helper.py @@ -105,104 +105,118 @@ def content_negotiate(self, metric_id='', ignore_html = True): self.metric_id=metric_id source = 'html' status_code = None + tp_response = None if self.request_url is not None: try: - self.logger.info('{0} : Retrieving page {1}'.format(metric_id, self.request_url)) + #self.logger.info('{0} : Retrieving page {1}'.format(metric_id, self.request_url)) + self.logger.info('{0} : Retrieving page -: {1} as {2}'.format(metric_id, self.request_url, self.accept_type)) + #TODO: find another way to handle SSL certficate problems; e.g. perform the request twice and return at least a warning + urllib.request.HTTPRedirectHandler.http_error_308 = urllib.request.HTTPRedirectHandler.http_error_301 tp_request = urllib.request.Request(self.request_url, headers={'Accept': self.accept_type, 'User-Agent': 'F-UJI'}) + context = ssl._create_unverified_context() - tp_response = urllib.request.urlopen(tp_request,context=context) - self.http_response = tp_response - self.response_content = tp_response.read() - if tp_response.info().get('Content-Encoding') == 'gzip': - self.response_content = gzip.decompress(self.response_content) - if tp_response.info().get_content_charset(): - self.response_charset = tp_response.info().get_content_charset() - self.response_header = tp_response.getheaders() - self.redirect_url = tp_response.geturl() - #self.http_response = requests.get(self.request_url, headers={'Accept': self.accept_type}) - #status_code = self.http_response.status_code - self.response_status = status_code = self.http_response.status - self.logger.info( - '%s : Content negotiation accept=%s, status=%s ' % (metric_id, self.accept_type, str(status_code))) - if status_code == 200: - self.content_type = self.http_response.headers.get("Content-Type") - #try to find out if content type is byte then fix - try: - self.response_content.decode('utf-8') - except (UnicodeDecodeError, AttributeError): - self.response_content = str(self.response_content).encode('utf-8') - if self.content_type is None: - self.content_type = mimetypes.guess_type(self.request_url, strict=True)[0] - if self.content_type is None: - #just in case tika is not running use this as quick check for the most obvious - if re.search(r"|| -1: - self.logger.info('%s : Found RDF document by tag!' % metric_id) - self.parse_response = self.parse_rdf(self.response_content.decode(self.response_charset), at.name) - source='rdf' - else: - self.logger.info('%s : Found XML document!' % metric_id) - self.parse_response = self.response_content - source='xml' - break - if at.name in ['schemaorg', 'json', 'jsonld', 'datacite_json']: - try: - self.parse_response = json.loads(self.response_content) - source='json' - # result = json.loads(response.text) + + try: + tp_response = urllib.request.urlopen(tp_request,context=context) + except Exception as e: + if e.code == 308: + self.logger.error('%s : F-UJI 308 redirect failed, most likely this patch: https://github.com/python/cpython/pull/19588/commits is not installed' % metric_id) + #print('#############################'+str(e)) + if tp_response: + self.http_response = tp_response + self.response_content = tp_response.read() + if tp_response.info().get('Content-Encoding') == 'gzip': + self.response_content = gzip.decompress(self.response_content) + if tp_response.info().get_content_charset(): + self.response_charset = tp_response.info().get_content_charset() + self.response_header = tp_response.getheaders() + self.redirect_url = tp_response.geturl() + #self.http_response = requests.get(self.request_url, headers={'Accept': self.accept_type}) + #status_code = self.http_response.status_code + self.response_status = status_code = self.http_response.status + self.logger.info( + '%s : Content negotiation accept=%s, status=%s ' % (metric_id, self.accept_type, str(status_code))) + if status_code == 200: + self.content_type = self.http_response.headers.get("Content-Type") + #try to find out if content type is byte then fix + try: + self.response_content.decode('utf-8') + except (UnicodeDecodeError, AttributeError): + self.response_content = str(self.response_content).encode('utf-8') + if self.content_type is None: + self.content_type = mimetypes.guess_type(self.request_url, strict=True)[0] + if self.content_type is None: + #just in case tika is not running use this as quick check for the most obvious + if re.search(r"|| -1: + self.logger.info('%s : Found RDF document by tag!' % metric_id) + self.parse_response = self.parse_rdf(self.response_content.decode(self.response_charset), at.name) + source='rdf' + else: + self.logger.info('%s : Found XML document!' % metric_id) + self.parse_response = self.response_content + source='xml' + break + if at.name in ['schemaorg', 'json', 'jsonld', 'datacite_json']: + try: + self.parse_response = json.loads(self.response_content) + source='json' + # result = json.loads(response.text) + break + except ValueError: + self.logger.info( + '{0} : Retrieved response seems not to be valid JSON'.format(metric_id)) - if at.name in ['nt','rdf', 'rdfjson', 'ntriples', 'rdfxml', 'turtle']: - self.parse_response = self.parse_rdf(self.response_content, self.content_type) - source='rdf' - break + if at.name in ['nt','rdf', 'rdfjson', 'ntriples', 'rdfxml', 'turtle']: + self.parse_response = self.parse_rdf(self.response_content, self.content_type) + source='rdf' + break - # TODO (IMPORTANT) how to handle the rest e.g., text/plain, specify result type - break + # TODO (IMPORTANT) how to handle the rest e.g., text/plain, specify result type + break + else: + self.logger.warning('{0} : Content-type is NOT SPECIFIED'.format(metric_id)) else: - self.logger.warning('{0} : Content-type is NOT SPECIFIED'.format(metric_id)) + self.logger.warning('{0} : NO successful response received, status code -: {1}'.format(metric_id, str(status_code))) else: - self.logger.warning('{0} : NO successful response received, status code -: {1}'.format(metric_id, str(status_code))) + self.logger.warning('{0} : No response received from -: {1}'.format(metric_id, self.request_url)) #except requests.exceptions.SSLError as e: except urllib.error.HTTPError as e: # self.logger.warning('%s : SSL Error: Untrusted SSL certificate, failed to connect to %s ' % (metric_id, self.request_url)) @@ -212,6 +226,8 @@ def content_negotiate(self, metric_id='', ignore_html = True): #All exceptions that Requests explicitly raises inherit from requests.exceptions.RequestException #self.logger.warning('%s : Request Error: Failed to connect to %s ' % (metric_id, self.request_url)) self.logger.warning('%s : Content negotiation failed -: accept=%s, status=%s ' % (metric_id, self.accept_type, str(e.code))) + self.response_status = int(e.code) + print(e) #self.logger.exception("{} : RequestException: {}".format(metric_id, e)) #traceback.print_exc() #self.logger.exception('%s : Failed to connect to %s ' % (metric_id, self.request_url)) diff --git a/fuji_server/yaml/metrics_v0.4.yaml b/fuji_server/yaml/metrics_v0.4.yaml index 688798cb..066abafe 100644 --- a/fuji_server/yaml/metrics_v0.4.yaml +++ b/fuji_server/yaml/metrics_v0.4.yaml @@ -387,6 +387,10 @@ metrics: metric_test_name: Community specific metadata standard is listed in the re3data record of the responsible repository metric_test_score: 0.5 metric_test_maturity: 2 + - metric_test_identifier: FsF-R1.3-01M-3 + metric_test_name: Multidisciplinary but community endorsed metadata (RDA Metadata Standards Catalog) standard is listed in the re3data record or detected by namespace + metric_test_score: 0 + metric_test_maturity: 1 created_by: FAIRsFAIR date_created: 2020-07-08 date_updated: 2020-12-03