more progress on crossref+orcid importers

6 files changed, 126 insertions, 52 deletions

diff --git a/python/client.py b/python/client.py
index 9631318a..9a2ed50d 100755
--- a/python/client.py
+++ b/python/client.py
@@ -7,13 +7,19 @@ from fatcat.orcid_importer import FatcatOrcidImporter
 
 def run_import_crossref(args):
     fcc = FatcatCrossrefClient(args.host_url)
-    fcc.import_crossref_file(args.json_file)
-    # create_containers=args.create_containers
+    fcc.import_crossref_file(
+        args.json_file,
+        issn_map_file=args.issn_map_file,
+        create_containers=(not args.no_create_containers))
 
 def run_import_orcid(args):
     foi = FatcatOrcidImporter(args.host_url)
     foi.process_batch(args.json_file, size=args.batch_size)
 
+def run_import_manifest(args):
+    fmi = FatcatManifestImporter(args.host_url)
+    fmi.process_db(args.db_path, size=args.batch_size)
+
 def health(args):
     rfac = RawFatcatApiClient(args.host_url)
     print(rfac.health())
@@ -32,10 +38,11 @@ def main():
     sub_import_crossref.set_defaults(func=run_import_crossref)
     sub_import_crossref.add_argument('json_file',
         help="crossref JSON file to import from")
-    # TODO:
-    #sub_import_crossref.add_argument('--create-containers',
-    #    action='store_true',
-    #    help="if true, create containers based on ISSN")
+    sub_import_crossref.add_argument('issn_map_file',
+        help="ISSN to ISSN-L mapping file")
+    sub_import_crossref.add_argument('--no-create-containers',
+        action='store_true',
+        help="skip creation of new container entities based on ISSN")
 
     sub_import_orcid = subparsers.add_parser('import-orcid')
     sub_import_orcid.set_defaults(func=run_import_orcid)
@@ -46,6 +53,15 @@ def main():
         help="size of batch to send",
         default=50, type=int)
 
+    sub_import_manifest = subparsers.add_parser('import-orcid')
+    sub_import_manifest.set_defaults(func=run_import_orcid)
+    sub_import_manifest.add_argument('db_path',
+        help="sqlite3 database to import from",
+        type=argparse.FileType('r'))
+    sub_import_orcid.add_argument('--batch-size',
+        help="size of batch to send",
+        default=50, type=int)
+
     sub_health = subparsers.add_parser('health')
     sub_health.set_defaults(func=health)
 
diff --git a/python/fatcat/crossref_importer.py b/python/fatcat/crossref_importer.py
index 4c68230d..a7166bc3 100644
--- a/python/fatcat/crossref_importer.py
+++ b/python/fatcat/crossref_importer.py
@@ -8,7 +8,9 @@ from fatcat.importer_common import FatcatImporter
 
 class FatcatCrossrefImporter(FatcatImporter):
 
-    # TODO: overload __init__ to handle create_containers
+    def __init__(self, host_url, issn_map_file, create_containers=True):
+        super().__init__(host_url, issn_map_file)
+        self.create_containers = create_containers
 
     def parse_crossref_dict(self, obj):
         """
@@ -19,50 +21,49 @@ class FatcatCrossrefImporter(FatcatImporter):
         # contribs
         contribs = []
         for i, am in enumerate(obj['author']):
+            creator_id = None
+            if 'ORCID' in am.keys():
+                creator_id = self.lookup_orcid(am['ORCID'].split('/')[-1])
             contribs.append(fatcat_client.ReleaseContrib(
-                creator_id=None, # TODO: orcid lookup
-                index=i,
+                creator_id=creator_id,
+                index=i+1,
                 # Sorry humans :(
                 raw="{} {}".format(am['given'], am['family']),
                 role="author"))
 
         # container
-        # TODO: ISSN vs. ISSN-L
         issn = obj.get('ISSN', [None])[0]
-        container_id = self.lookup_issnl(issn)
+        issnl = self.issn2issnl(issn)
+        container_id = None
+        if issnl:
+            container_id = self.lookup_issnl(issnl)
+        publisher = obj['publisher']
 
-        ## TODO: create containers in-line like this?
-        #container = dict(
-        #    issn=issn,
-        #    name=obj['container-title'][0],
-        #    container=container_id,
-        #    #sortname=obj['short-container-title'][0])
-        #    publisher=obj['publisher'])
-        #if container_id is None and self.create_containers and issn != None:
-        #    rv = self.post('/v0/container', data=dict(
-        #        issn=container['issn'],
-        #        publisher=container['publisher']))
-        #    assert rv.status_code == 201
-        #    container_id = rv.json()['id']
-        #    print("created container: {}".format(issn))
-        #    container['id'] = container_id
-        #    self._issn_map[issn] = container_id
+        ce = None
+        if container_id is None and self.create_containers and issnl != None:
+            ce = fatcat_client.ContainerEntity(
+                issnl=issnl,
+                publisher=publisher,
+                name=obj['container-title'][0])
+            print("created container: {}".format(issnl))
 
         # references
         refs = []
         for i, rm in enumerate(obj.get('reference', [])):
+            try:
+                year = int(rm.get('year'))
+            except:
+                year = None
             refs.append(fatcat_client.ReleaseRef(
-                index=i,
+                index=i+1,
                 target_release_id=None, # TODO: DOI lookup: rm.get("DOI", None),
-                # TODO: all these
-                key=None,
-                year=None,
-                container_title=None,
-                title=None,
-                locator=None,
-                # TODO: how to generate a proper stub here from k/v objdata?
-                # TODO: just dump JSON here if we didn't get a match?
-                raw="| ".join(rm.values())))
+                # unreliable for crossref: key=rm['key'].split('|')[-1],
+                year=year,
+                container_title=rm.get('volume-title'),
+                title=rm.get('title'),
+                locator=rm.get('first-page'),
+                # TODO: just dump JSON somewhere here?
+                raw=rm.get('unstructured')))
 
         # work
         we = fatcat_client.WorkEntity(
@@ -73,34 +74,38 @@ class FatcatCrossrefImporter(FatcatImporter):
         extra = dict(crossref={
             'links': obj.get('link', []),
             'subject': obj.get('subject'),
-            'crossref-type': obj['type'],
+            'type': obj['type'],
+            'license': obj.get('license', [dict(URL=None)])[0]['URL'] or None,
             'alternative-id': obj.get('alternative-id', [])})
 
         re = fatcat_client.ReleaseEntity(
-            work_id='null', # XXX:
+            work_id='tbd', # gets set later, I promise!
             title=obj['title'][0],
             contribs=contribs,
             refs=refs,
             container_id=container_id,
             release_type=obj['type'],
-            doi=obj['DOI'],
+            doi=obj['DOI'].lower(),
             release_date=obj['created']['date-time'],
-            #license=obj.get('license', [dict(URL=None)])[0]['URL'] or None,
             issue=obj.get('issue'),
             volume=obj.get('volume'),
             pages=obj.get('page'),
             extra=extra)
-        return (we, re)
+        return (we, re, ce)
 
     def create_row(self, row, editgroup_id=None):
         if row is None:
-            continue
+            return
         obj = json.loads(row)
-        both = self.parse_crossref_dict(obj)
-        if both is not None:
-            (we, re) = both
+        entities = self.parse_crossref_dict(obj)
+        if entities is not None:
+            (we, re, ce) = entities
             we.editgroup_id = editgroup_id
             re.editgroup_id = editgroup_id
+            if ce is not None:
+                ce.editgroup_id = editgroup_id
+                container = self.api.create_container(ce)
+                re.container_id = container.ident
             created = self.api.create_work(we)
             re.work_id = created.ident
             self.api.create_release(re)
diff --git a/python/fatcat/importer_common.py b/python/fatcat/importer_common.py
index 98bfb26e..c24565b4 100644
--- a/python/fatcat/importer_common.py
+++ b/python/fatcat/importer_common.py
@@ -13,11 +13,15 @@ def grouper(iterable, n, fillvalue=None):
 
 class FatcatImporter:
 
-    def __init__(self, host_url):
+    def __init__(self, host_url, issn_map_file=None):
         conf = fatcat_client.Configuration()
         conf.host = host_url
         self.api = fatcat_client.DefaultApi(fatcat_client.ApiClient(conf))
-        self._issnl_map = dict()
+        self._issnl_id_map = dict()
+        self._orcid_id_map = dict()
+        self._issn_issnl_map = None
+        if issn_map_file:
+            self.read_issn_map_file(issn_map_file)
 
     def process_source(self, source, group_size=100):
         """Creates and auto-accepts editgropu every group_size rows"""
@@ -40,8 +44,8 @@ class FatcatImporter:
     def lookup_issnl(self, issnl):
         """Caches calls to the ISSN-L lookup API endpoint in a local dict"""
         assert len(issnl) == 9 and issnl[4] == '-'
-        if issnl in self._issnl_map:
-            return self._issnl_map[issn]
+        if issnl in self._issnl_id_map:
+            return self._issnl_id_map[issn]
         container_id = None
         try:
             rv = self.api.lookup_container(issnl=issnl)
@@ -49,5 +53,35 @@ class FatcatImporter:
         except ApiException as ae:
             # If anything other than a 404 (not found), something is wrong
             assert ae.status == 404
-        self._issnl_map[issnl] = container_id # might be None
+        self._issnl_id_map[issnl] = container_id # might be None
         return container_id
+
+    def lookup_orcid(self, orcid):
+        """Caches calls to the Orcid lookup API endpoint in a local dict"""
+        assert len(orcid) == 19 and orcid[4] == '-'
+        if orcid in self._orcid_id_map:
+            return self._orcid_id_map[orcid]
+        creator_id = None
+        try:
+            rv = self.api.lookup_creator(orcid=orcid)
+            creator_id = rv.ident
+        except ApiException as ae:
+            # If anything other than a 404 (not found), something is wrong
+            assert ae.status == 404
+        self._orcid_id_map[orcid] = creator_id # might be None
+        return creator_id
+
+    def read_issn_map_file(self, issn_map_file):
+        self._issn_issnl_map = dict()
+        for line in issn_map_file:
+            if line.startswith("ISSN") or len(line) == 0:
+                continue
+            (issn, issnl) = line.split()[0:2]
+            self._issn_issnl_map[issn] = issnl
+            # double mapping makes lookups easy
+            self._issn_issnl_map[issnl] = issnl
+
+    def issn2issnl(self, issn):
+        if issn is None:
+            return None
+        self._issn_issnl_map.get(issn)
diff --git a/python/tests/crossref.py b/python/tests/crossref.py
index e72f7d02..402195d7 100644
--- a/python/tests/crossref.py
+++ b/python/tests/crossref.py
@@ -5,7 +5,8 @@ from fatcat.crossref_importer import FatcatCrossrefImporter
 
 @pytest.fixture(scope="function")
 def crossref_importer():
-    yield FatcatCrossrefImporter("http://localhost:9411/v0")
+    with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
+        yield FatcatCrossrefImporter("http://localhost:9411/v0", issn_file)
 
 def test_crossref_importer_batch(crossref_importer):
     with open('tests/files/crossref-works.2018-01-21.badsample.json', 'r') as f:
@@ -14,3 +15,8 @@ def test_crossref_importer_batch(crossref_importer):
 def test_crossref_importer(crossref_importer):
     with open('tests/files/crossref-works.2018-01-21.badsample.json', 'r') as f:
         crossref_importer.process_source(f)
+
+def test_crossref_importer_create(crossref_importer):
+    crossref_importer.create_containers = True
+    with open('tests/files/crossref-works.2018-01-21.badsample.json', 'r') as f:
+        crossref_importer.process_source(f)
diff --git a/python/tests/files/ISSN-to-ISSN-L.snip.txt b/python/tests/files/ISSN-to-ISSN-L.snip.txt
new file mode 100644
index 00000000..965a49d6
--- /dev/null
+++ b/python/tests/files/ISSN-to-ISSN-L.snip.txt
@@ -0,0 +1,10 @@
+ISSN	ISSN-L
+0000-0019	0000-0019
+0000-0027	0000-0027
+0000-0043	0000-0043
+0000-0051	0000-0051
+0000-006X	0000-006X
+0000-0078	0000-0078
+0000-0094	0000-0094
+0000-0108	0000-0108
+0000-0140	0000-0140
diff --git a/python/tests/files/crossref-works.2018-01-21.badsample.json b/python/tests/files/crossref-works.2018-01-21.badsample.json
index 143adf3e..84271489 100644
--- a/python/tests/files/crossref-works.2018-01-21.badsample.json
+++ b/python/tests/files/crossref-works.2018-01-21.badsample.json
@@ -8,3 +8,6 @@
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