refactor python modules

1 files changed, 168 insertions, 0 deletions

diff --git a/python/fatcat_tools/grobid_metadata_importer.py b/python/fatcat_tools/grobid_metadata_importer.py
new file mode 100755
index 00000000..95cc285e
--- /dev/null
+++ b/python/fatcat_tools/grobid_metadata_importer.py
@@ -0,0 +1,168 @@
+#!/usr/bin/env python3
+
+import sys
+import json
+import base64
+import datetime
+import fatcat_client
+from fatcat.importer_common import FatcatImporter
+
+MAX_ABSTRACT_BYTES=4096
+
+
+class FatcatGrobidMetadataImporter(FatcatImporter):
+
+    def __init__(self, host_url, default_link_rel="web"):
+        super().__init__(host_url)
+        self.default_link_rel = default_link_rel
+
+    def parse_grobid_json(self, obj):
+
+        if not obj.get('title'):
+            return None
+
+        release = dict()
+        extra = dict()
+
+        if obj.get('abstract') and len(obj.get('abstract')) < MAX_ABSTRACT_BYTES:
+            abobj = dict(
+                mimetype="text/plain",
+                language=None,
+                content=obj.get('abstract').strip())
+            abstracts = [abobj]
+        else:
+            abstracts = None
+
+        contribs = []
+        for i, a in enumerate(obj.get('authors', [])):
+            c = dict(raw_name=a['name'], role="author")
+            contribs.append(fatcat_client.ReleaseContrib(
+                index=i,
+                raw_name=a['name'],
+                role="author",
+                extra=None))
+
+        refs = []
+        for raw in obj.get('citations', []):
+            cite_extra = dict()
+            ref = dict()
+            ref['key'] = raw.get('id')
+            if raw.get('title'):
+                ref['title'] = raw['title'].strip()
+            if raw.get('date'):
+                try:
+                    year = int(raw['date'].strip()[:4])
+                    ref['year'] = year
+                except:
+                    pass
+            for key in ('volume', 'url', 'issue', 'publisher'):
+                if raw.get(key):
+                    cite_extra[key] = raw[key].strip()
+            if raw.get('authors'):
+                cite_extra['authors'] = [a['name'] for a in raw['authors']]
+            if cite_extra:
+                cite_extra = dict(grobid=cite_extra)
+            else:
+                cite_extra = None
+            ref['extra'] = cite_extra
+            refs.append(ref)
+
+        release_type = "journal-article"
+        release_date = None
+        if obj.get('date'):
+            # TODO: only returns year, ever? how to handle?
+            release_date = datetime.datetime(year=int(obj['date'][:4]), month=1, day=1)
+
+        if obj.get('doi'):
+            extra['doi'] = obj['doi']
+        if obj['journal'] and obj['journal'].get('name'):
+            extra['container_name'] = obj['journal']['name']
+        
+        extra['is_longtail_oa'] = True
+
+        # TODO: ISSN/eISSN handling? or just journal name lookup?
+
+        if extra:
+            extra = dict(grobid=extra)
+        else:
+            extra = None
+
+        re = fatcat_client.ReleaseEntity(
+            title=obj['title'].strip(),
+            contribs=contribs,
+            refs=refs,
+            publisher=obj['journal'].get('publisher'),
+            volume=obj['journal'].get('volume'),
+            issue=obj['journal'].get('issue'),
+            abstracts=abstracts,
+            extra=extra)
+        return re
+    
+    # TODO: make this a common function somewhere
+    def make_url(self, raw):
+        rel = self.default_link_rel
+        # TODO: this is where we could map specific domains to rel types,
+        # and also filter out bad domains, invalid URLs, etc
+        if "//archive.org/" in raw or "//arxiv.org/" in raw:
+            # TODO: special-case the arxiv.org bulk mirror?
+            rel = "repository"
+        elif "//web.archive.org/" in raw or "//archive.is/" in raw:
+            rel = "webarchive"
+        return fatcat_client.FileEntityUrls(url=raw, rel=rel)
+
+    def parse_file_metadata(self, sha1_key, cdx, mimetype, file_size):
+        
+        sha1 = base64.b16encode(base64.b32decode(sha1_key.replace('sha1:', ''))).decode('ascii').lower()
+
+        # lookup existing SHA1, or create new entity
+        try:
+            existing_file = self.api.lookup_file(sha1=sha1)
+        except fatcat_client.rest.ApiException as err:
+            if err.status != 404:
+                raise err
+            existing_file = None
+
+        if existing_file:
+            # if file is already in here, presumably not actually long-tail
+            return None
+        fe = fatcat_client.FileEntity(
+            sha1=sha1,
+            size=int(file_size),
+            mimetype=mimetype,
+            releases=[],
+            urls=[],
+        )
+
+        # parse URLs and CDX
+        original = cdx['url']
+        wayback = "https://web.archive.org/web/{}/{}".format(
+            cdx['dt'],
+            original)
+        fe.urls.append(
+            fatcat_client.FileEntityUrls(url=wayback, rel="webarchive"))
+        original_url = self.make_url(original)
+        if original_url != None:
+            fe.urls.append(original_url)
+
+        return fe
+
+    def create_row(self, row, editgroup=None):
+        if not row:
+            return
+        fields = row.split('\t')
+        sha1_key = fields[0]
+        cdx = json.loads(fields[1])
+        mimetype = fields[2]
+        file_size = int(fields[3])
+        grobid_meta = json.loads(fields[4])
+        fe = self.parse_file_metadata(sha1_key, cdx, mimetype, file_size)
+        re = self.parse_grobid_json(grobid_meta)
+        if fe and re:
+            release_entity = self.api.create_release(re, editgroup=editgroup)
+            # release ident can't already be in release list because we just
+            # created it
+            fe.releases.append(release_entity.ident)
+            file_entity = self.api.create_file(fe, editgroup=editgroup)
+            self.insert_count = self.insert_count + 1
+
+    # NB: batch mode not implemented