From c3ff7515c0d77c752a991c58bfc5c78a07a3d146 Mon Sep 17 00:00:00 2001 From: ADS Administration Date: Mon, 6 Oct 2025 14:56:25 -0400 Subject: [PATCH 1/2] SciX ID support for networks --- vis_services/lib/author_network.py | 10 +- vis_services/lib/paper_network.py | 18 +- .../author_network_second_parameter.json | 3222 +- ...aper_network_before_groups_func_large.json | 55998 ++++++++-------- .../author_network_accomazzi,a.json | 3443 +- vis_services/tests/test_internals.py | 5 +- vis_services/views.py | 27 +- 7 files changed, 35194 insertions(+), 27529 deletions(-) diff --git a/vis_services/lib/author_network.py b/vis_services/lib/author_network.py index 470150b..8cd929a 100644 --- a/vis_services/lib/author_network.py +++ b/vis_services/lib/author_network.py @@ -78,7 +78,7 @@ def augment_graph_data(author_graph, data): return {"fullGraph" : author_graph} # make two dicts: a dict with all info for a certain paper (bib_dict) - # and a dict for each author that lists all bibcodes they helped write + # and a dict for each author that lists all identifiers they helped write name_dict = defaultdict(list) bib_dict= {} @@ -90,12 +90,12 @@ def augment_graph_data(author_graph, data): read_count = d.get("read_count") if not read_count: read_count = 0 - bib_dict[d.get("bibcode")] = {"title" : d.get("title", [""])[0], + bib_dict[d.get("scix_id")] = {"title" : d.get("title", [""])[0], "citation_count": citation_count, "read_count": read_count, "authors" : d.get("author_norm", [])} for author in d.get("author_norm", []): - name_dict[author].append(d.get("bibcode")) + name_dict[author].append(d.get("scix_id")) #don't allow any more author nodes than max_num_auth_nodes if len(author_graph['nodes'])>max_num_auth_nodes: node_cutoff = sorted([d["nodeWeight"] for d in author_graph['nodes']], reverse=True)[:max_num_auth_nodes+1][-1] @@ -147,8 +147,8 @@ def augment_graph_data(author_graph, data): name = G.nodes[child].get("nodeName") size = G.nodes[child].get("nodeWeight") bibs = sorted(name_dict[name], key=lambda x:bib_dict[x]["citation_count"], reverse=True) - total_citations = sum([bib_dict[bibcode]["citation_count"] for bibcode in name_dict[name]]) - total_reads = sum([bib_dict[bibcode]["read_count"] for bibcode in name_dict[name]]) + total_citations = sum([bib_dict[scix_id]["citation_count"] for scix_id in name_dict[name]]) + total_reads = sum([bib_dict[scix_id]["read_count"] for scix_id in name_dict[name]]) children.append({"name":name, "size": size, "papers":bibs, "citation_count" : total_citations, "read_count" : total_reads, "numberName" : child}) else: G.remove_node(child) diff --git a/vis_services/lib/paper_network.py b/vis_services/lib/paper_network.py index 7fbd2db..fc69ebd 100644 --- a/vis_services/lib/paper_network.py +++ b/vis_services/lib/paper_network.py @@ -27,12 +27,12 @@ # Helper functions def _get_reference_mapping(data): ''' - Construct the reference dictionary for a set of bibcodes + Construct the reference dictionary for a set of SciX IDs ''' refdict = {} for doc in data: if 'reference' in doc: - refdict[doc['bibcode']] = set(doc['reference']) + refdict[doc['scix_id']] = set(doc['reference']) return refdict def _get_paper_data(data): @@ -41,7 +41,7 @@ def _get_paper_data(data): ''' infodict = {} for doc in data: - infodict[doc['bibcode']] = doc + infodict[doc['scix_id']] = doc return infodict def _sort_and_cut_results(resdict,cutoff=1500): @@ -189,7 +189,7 @@ def augment_graph_data(data, max_groups): # Main machinery def get_papernetwork(solr_data, max_groups, weighted=True, equalization=False, do_cutoff=False): ''' - Given a list of bibcodes, this function builds the papers network based on co-citations + Given a list of identifiers, this function builds the papers network based on co-citations If 'weighted' is true, we will normalize the co-occurence frequency with the total number of papers in the set, otherwise we will work with the actual co-occurence frequencies. If 'equalization' is true, histogram equalization will be applied to the force values in @@ -205,7 +205,7 @@ def get_papernetwork(solr_data, max_groups, weighted=True, equalization=False, d of the number of references in the linked nodes. ''' # Get get paper list from the Solr data - papers_list = [a['bibcode'] for a in solr_data] + papers_list = [a['scix_id'] for a in solr_data] # First construct the reference dictionary, and a unique list of cited papers reference_dictionary = _get_reference_mapping(solr_data) # From now on we'll only work with publications that actually have references @@ -287,11 +287,11 @@ def get_papernetwork(solr_data, max_groups, weighted=True, equalization=False, d #because the nodes must be inserted at the proper index nodes = [None]*len(ref_papers) for paper in solr_data: - if paper['bibcode'] not in selected_papers: + if paper['scix_id'] not in selected_papers: continue - index = ref_papers[paper["bibcode"]] - nodes[index] ={'nodeName':paper['bibcode'], - 'nodeWeight':paper.get('citation_count',1), + index = ref_papers[paper["scix_id"]] + nodes[index] ={'nodeName':paper['scix_id'], + 'nodeWeight':paper.get('citation_count',1), 'citation_count':paper.get('citation_count',0), 'read_count':paper.get('read_count',0), 'title':paper.get('title','NA')[0], diff --git a/vis_services/tests/stubdata/test_input/author_network_second_parameter.json b/vis_services/tests/stubdata/test_input/author_network_second_parameter.json index b1736df..c46ea71 100644 --- a/vis_services/tests/stubdata/test_input/author_network_second_parameter.json +++ b/vis_services/tests/stubdata/test_input/author_network_second_parameter.json @@ -1 +1,3221 @@ -[{"read_count": 0.0, "bibcode": "2002ASPC..281..471R", "pubdate": "2002-00-00", "title": ["Managing the ADS Citation Database"], "citation_count": 0, "author_norm": ["Accomazzi, A", "Eichhorn, G", "Grant, C", "Rey-Bakaikoa, V"]}, {"read_count": 3.0, "bibcode": "2009ASPC..410..160O", "pubdate": "2009-08-00", "title": ["Making Archival Data Available for Research in the Next Decade and Beyond"], "citation_count": 0, "author_norm": ["Accomazzi, A", "Castelaz, M", "Cline, J", "Cudworth, K", "Griffin, R", "Grindlay, J", "Henden, A", "Osborn, 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+318,7 @@ def test_views_helper_functions(self): err = e except Exception as e: err = e - self.assertEqual(str(err), 'No bibcodes found in POST body') + self.assertEqual(str(err), 'No identifiers found in POST body') # Too many bibcodes should result in an Exception max_recs = self.app.config.get("VIS_SERVICE_PN_MAX_RECORDS") params = {} @@ -332,7 +331,7 @@ def test_views_helper_functions(self): err = e except Exception as e: err = e - self.assertEqual(str(err), 'No results: number of submitted bibcodes exceeds maximum number') + self.assertEqual(str(err), 'No results: number of submitted identifiers exceeds maximum number') # Wrongly encoded JSON for a query should result in an exception params = {} params['query'] = {'q':'author:"Henneken,E"'} diff --git a/vis_services/views.py b/vis_services/views.py index b93e175..8085d34 100644 --- a/vis_services/views.py +++ b/vis_services/views.py @@ -18,31 +18,36 @@ class QueryException(Exception): def make_request(request, service_string, required_fields): bibcodes = [] query = None - if 'bibcodes' in request.json: + if 'bibcodes' in request.json or 'identifiers' in request.json: + # The test below seems a bit pedantic. We can just ignore the 'query' part + # if that is included in addition to identifiers if 'query' in request.json and request.json['query']: raise QueryException('Cannot send both bibcodes and query') - bibcodes = list(map(str, request.json['bibcodes'])) + if 'bibcodes' in request.json: + identifiers = list(map(str, request.json['bibcodes'])) + else: + identifiers = list(map(str, request.json['identifiers'])) - if len(bibcodes) > current_app.config.get("VIS_SERVICE_" + service_string + "_MAX_RECORDS"): - raise QueryException('No results: number of submitted bibcodes exceeds maximum number') + if len(identifiers) > current_app.config.get("VIS_SERVICE_" + service_string + "_MAX_RECORDS"): + raise QueryException('No results: number of submitted identifiers exceeds maximum number') - elif len(bibcodes) == 0: - raise QueryException('No bibcodes found in POST body') + elif len(identifiers) == 0: + raise QueryException('No identifiers found in POST body') - #we have bibcodes, which might be up to 1000 ( too long for solr using GET), + #we have identifiers, which might be up to 1000 ( too long for solr using GET), #so use bigquery headers = { 'X-Forwarded-Authorization' : request.headers.get('Authorization'), 'Content-Type': 'big-query/csv', 'Authorization': request.headers.get('X-Forwarded-Authorization', request.headers.get('Authorization', '')) } - big_query_params = {'q':'*:*', 'wt':'json', 'fl': required_fields, 'fq': '{!bitset}', 'rows' : len(bibcodes)} + big_query_params = {'q':'*:*', 'wt':'json', 'fl': required_fields, 'fq': '{!bitset}', 'rows' : len(identifiers)} response = client().post( current_app.config.get("VIS_SERVICE_BIGQUERY_PATH"), params = big_query_params, headers = headers, - data = 'bibcode\n' + '\n'.join(bibcodes) + data = 'identifier\n' + '\n'.join(identifiers) ) return response @@ -118,7 +123,7 @@ class AuthorNetwork(Resource): def post(self): try: - required_fields = ['author_norm', 'title', 'citation_count', 'read_count','bibcode', 'pubdate'] + required_fields = ['author_norm', 'title', 'citation_count', 'read_count', 'scix_id', 'bibcode', 'pubdate'] response = make_request(request, "AN", required_fields) except QueryException as error: return {'Error' : 'there was a problem with your request', 'Error Info': str(error)}, 403 @@ -151,7 +156,7 @@ class PaperNetwork(Resource): def post(self): try: - required_fields = ['bibcode,title,first_author,year,citation_count,read_count,reference'] + required_fields = ['bibcode,scix_id,title,first_author,year,citation_count,read_count,reference'] response = make_request(request, "PN", required_fields) except QueryException as error: return {'Error' : 'there was a problem with your request', 'Error Info': str(error)}, 403 From 265f3bb3197bffff9a88cfc6f2473529e284be63 Mon Sep 17 00:00:00 2001 From: ADS Administration Date: Mon, 6 Oct 2025 15:34:11 -0400 Subject: [PATCH 2/2] unit test fix --- vis_services/tests/test_internals.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vis_services/tests/test_internals.py b/vis_services/tests/test_internals.py index c79dd4a..e4515b9 100644 --- a/vis_services/tests/test_internals.py +++ b/vis_services/tests/test_internals.py @@ -201,9 +201,9 @@ def test_author_helper_functions(self): def test_paper_helper_functions(self): import vis_services.lib.paper_network as PN # Check that the 'get_paper_data' function returns a bibcode-keyed data dictionary - data = [{'bibcode':'a','title':'foo'}, {'bibcode':'b','title':'bar'}] + data = [{'bibcode':'a','scix_id':'scix:a', 'title':'foo'}, {'bibcode':'b', 'scix_id':'scix:b', 'title':'bar'}] res = PN._get_paper_data(data) - expected = {'a': {'bibcode': 'a', 'title': 'foo'}, 'b': {'bibcode': 'b', 'title': 'bar'}} + expected = {'scix:a': {'bibcode': 'a', 'scix_id': 'scix:a', 'title': 'foo'}, 'scix:b': {'bibcode': 'b', 'scix_id': 'scix:b', 'title': 'bar'}} self.assertEqual(res, expected) # A result dictionary with less that 'cutoff' entries should be returned untouched test_dict = {'a':1.0, 'b':0.75, 'c':3.3}