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Universitas Katolik Widya Mandira - Repository Universitas Katolik Widya Mandira", "originalId": "11875", "websiteurl": "http://repository.unwira.ac.id/", "collectedfrom": "roar", "alternativeNames": [], "id": "roar::11875"} +{"name": "Gutenberg Open Science", "originalId": "17028", "websiteurl": "https://openscience.ub.uni-mainz.de/", "collectedfrom": "roar", "alternativeNames": [], "id": "roar::17028"} +{"name": "KuzSTU Bulletin: full texts", "originalId": "8968", "websiteurl": "http://vestnik.kuzstu.ru/", "collectedfrom": "roar", "alternativeNames": [], "id": "roar::8968"} diff --git a/deduplication/ds.tree.conf.json b/deduplication/ds.tree.conf.json new file mode 100644 index 0000000..83ee8b1 --- /dev/null +++ b/deduplication/ds.tree.conf.json @@ -0,0 +1,67 @@ +{ + "wf" : { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "datasource", + "orderField" : "name", + "queueMaxSize" : "2000", + "groupMaxSize" : "50", + "slidingWindowSize" : "200", + "idPath":"$.id", + "rootBuilder" : [ "organization", "projectOrganization_participation_isParticipant", "datasourceOrganization_provision_isProvidedBy" ], + "includeChildren" : "true", + "maxIterations": "20" + }, + "pace" : { + "clustering" : [ + { "name" : "sortedngrampairs", "fields" : [ "name" ], "params" : { "max" : 2, "ngramLen" : "3"} }, + { "name" : "suffixprefix", "fields" : [ "name" ], "params" : { "max" : 1, "len" : "3" } }, + { "name" : "urlclustering", "fields" : [ "websiteurl" ], "params" : { } } + ], + "decisionTree" : { + "start": { + "fields": [ + { + "field": "websiteurl", + "comparator": "domainExactMatch", + "weight": 1, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1, + "aggregation": "AVG", + "positive": "layer2", + "negative": "NO_MATCH", + "undefined": "layer2", + "ignoreUndefined": "true" + }, + "layer2": { + "fields": [ + { + "field": "name", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true", + "params": { + } + } + ], + "threshold": 0.9, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + } + }, + "model" : [ + { "name" : "name", "type" : "String", "path" : "$.name" }, + { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl" } + ], + "blacklists" : { + "legalname" : [] + }, + "synonyms": {} + } +} \ No newline at end of file diff --git a/deduplication/ds_to_json.py b/deduplication/ds_to_json.py new file mode 100644 index 0000000..5c925b4 --- /dev/null +++ b/deduplication/ds_to_json.py @@ -0,0 +1,76 @@ +# coding=utf-8 +from pyspark import SparkContext +from pyspark import SparkConf +from pyspark.sql import SparkSession +import json +#!/usr/bin/python +import os +import sys +import shutil + +def deleteDir(x): + try: + shutil.rmtree(x) + except OSError as e: + print("Error: %s - %s." % (e.filename, e.strerror)) + +def stringToArray(x): + try: + return eval(x) + except: + return [] + +def testValidJSON(x): + try: + json.loads(x) + return True + except: + return False + +conf = SparkConf().setAppName('fairshare').setMaster('local[*]') +sc = SparkContext(conf=conf) +spark = SparkSession.builder.config(conf=conf).getOrCreate() + +deleteDir("datasources") + +fairsharing_path = "../data/raw/fairsharing_dump_api_02_2022.json" +opendoar_path = "../data/raw/openDoar.tsv" +re3data_path = "../data/raw/re3data.tsv" +roar_path = "../data/raw/export_roar_CSV.csv" + +# #FAIRSHARING V1.0 +# #FILE STRUCTURE: Full name of record | Short name | FAIRsharing URL | Homepage URL of the resource | Country Field | Subjects +# fairsharing = sc.textFile("/Users/miconis/Desktop/Fairsharing dedup/registries_analysis/data/raw/FAIRsharingDBrec_summary20210304.csv") +# fairsharing = fairsharing.filter(lambda x: " FAIRsharing URL " not in x.split("|")).map(lambda x: dict(fullname=x.split("|")[0], shortname=x.split("|")[1], fairshare_url=x.split("|")[2], homepage_url=x.split("|")[3], country=x.split("|")[4], subjects=x.split("|")[5])) +# fairsharing = fairsharing.map(lambda x: dict(id=x['fairshare_url'], originalId=x['fairshare_url'], websiteurl=x['homepage_url'], name=x['fullname'], alternativeNames=[x['shortname']], collectedfrom="FAIRsharing")) +# +# print "FAIRSHARING:" + str(fairsharing.count()) + +#FAIRSHARING (file structure: ) +fairsharing = sc.textFile(fairsharing_path).filter(testValidJSON).map(json.loads) +fairsharing = fairsharing.map(lambda x: dict(id=x['attributes']['url'], originalId=x['id'], websiteurl=x['attributes']['metadata']['homepage'], name=x['attributes']['metadata']['name'], alternativeNames=[x['attributes']['abbreviation']], collectedfrom="FAIRsharing")) +print("FAIRSHARING DS", fairsharing.count()) + +#OPENDOAR (file structure: OpenAIREID orgIdentifier repositoryName alternativeNames repositoryURL description type updateDate startDate subject contentType institution metadataPolicy dataPolicy submissionPolicy contentPolicy software api) +opendoar = sc.textFile(opendoar_path) +opendoar = opendoar.filter(lambda x: "system_metadata.id" not in x.split("\t")).map(lambda x: dict(fullname=x.split("\t")[1], shortname=x.split("\t")[1], alternativeNames=x.split("\t")[2], opendoar_id=x.split("\t")[0], homepage_url=x.split("\t")[3], subjects=x.split("\t")[9], openaire_id="opendoar::"+x.split("\t")[0])) +opendoar = opendoar.map(lambda x: dict(id=x['openaire_id'], originalId=x['opendoar_id'], websiteurl=x['homepage_url'], name=json.loads(x['fullname'])['name'], alternativeNames=x['alternativeNames'], collectedfrom="OpenDOAR")) +print("OPENDOAR DS", opendoar.count()) + +#RE3DATA (file structure: openaire_id re3data_id repository_name additional_name repository_url repository_id description type size update_date start_date end_date subject mission_statement content_type provider_type keyword institution policy database_access database_license data_access data_license data_upload data_upload_license software versioning api pid_system citation_guideline_url aid_system enhanced_publication quality_management certificate metadata_standard syndication remarks entry_date last_update) +re3data = sc.textFile(re3data_path) +re3data = re3data.filter(lambda x: "repositoryName.language" not in x.split("\t")).map(lambda x: dict(fullname=x.split("\t")[1], shortname=x.split("\t")[3], re3data_id=x.split("\t")[0], homepage_url=x.split("\t")[4], subjects=x.split("\t")[14], openaire_id="re3data::"+x.split("\t")[0])) +re3data = re3data.map(lambda x: dict(id=x['openaire_id'], originalId=x['re3data_id'], websiteurl=x['homepage_url'], name=x['fullname'], alternativeNames=stringToArray(x['shortname']), collectedfrom="re3data")) +print("RE3DATA", re3data.count()) + +#ROAR (file structure: "eprintid","rev_number","eprint_status","userid","importid","source","dir","datestamp","lastmod","status_changed","type","succeeds","commentary","metadata_visibility","latitude","longitude","relation_type","relation_uri","item_issues_id","item_issues_type","item_issues_description","item_issues_timestamp","item_issues_status","item_issues_reported_by","item_issues_resolved_by","item_issues_comment","item_issues_count","sword_depositor","sword_slug","exemplar","home_page","title","oai_pmh","sword_endpoint","rss_feed","twitter_feed","description","fulltext","open_access","mandate","organisation_title","organisation_home_page","location_country","location_city","location_latitude","location_longitude","software","geoname","version","subjects","date","note","suggestions","activity_low","activity_medium","activity_high","recordcount","recordhistory","fulltexts_total","fulltexts_docs","fulltexts_rtotal","fulltexts_rdocs","registry_name","registry_id","submit_to","submitted_to_name","submitted_to_done","webometrics_rank","webometrics_size","webometrics_visibility","webometrics_rich_files","webometrics_scholar","monthly_deposits","total_deposits","association") +roar = sc.textFile(roar_path) +roar = roar.filter(lambda x: "\"eprintid\"" not in x.split(",")).filter(lambda x: len(x.split(","))>31).map(lambda x: dict(id=x.split(",")[0], homepage_url=x.split(",")[30], title=x.split(",")[31])).filter(lambda x: x['title'] != "" and x['homepage_url'] != "") +roar = roar.map(lambda x: dict(id="roar::"+x['id'].replace("\"",""), originalId=x['id'].replace("\"",""), websiteurl=x['homepage_url'].replace("\"",""), name=x['title'].replace("\"", ""), alternativeNames=[], collectedfrom="roar")) +roar = roar.filter(lambda x: x['id'] != "" and x['name'] != "") +roar = roar.map(lambda x: (x['id'], x)).reduceByKey(lambda x, y: x).map(lambda x: x[1]) +print "ROAR:" + str(roar.count()) + +all_ds = fairsharing.union(opendoar).union(re3data).union(roar) + +all_ds.map(json.dumps).saveAsTextFile("datasources") \ No newline at end of file