From a4db9ee2e18a18b23eb7ece484f95914421f877d Mon Sep 17 00:00:00 2001
From: Bryan Newbold <bnewbold@robocracy.org>
Date: Wed, 13 Nov 2019 00:27:48 -0800
Subject: ingest file result importer

---
 python/fatcat_tools/importers/__init__.py |   3 +-
 python/fatcat_tools/importers/ingest.py   | 134 ++++++++++++++++++++++++++++++
 2 files changed, 135 insertions(+), 2 deletions(-)
 create mode 100644 python/fatcat_tools/importers/ingest.py

(limited to 'python/fatcat_tools')

diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index 5e2948f4..025a111c 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -26,5 +26,4 @@ from .orcid import OrcidImporter
 from .arabesque import ArabesqueMatchImporter, ARABESQUE_MATCH_WHERE_CLAUSE
 from .wayback_static import auto_wayback_static
 from .cdl_dash_dat import auto_cdl_dash_dat
-#from .kafka_source import KafkaSource
-#from .file_source import FileSource
+from .ingest import IngestFileResultImporter
diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py
new file mode 100644
index 00000000..9e75c26f
--- /dev/null
+++ b/python/fatcat_tools/importers/ingest.py
@@ -0,0 +1,134 @@
+
+import sys
+import json
+import base64
+import itertools
+import fatcat_openapi_client
+from .common import EntityImporter, clean, make_rel_url, SANE_MAX_RELEASES, SANE_MAX_URLS, b32_hex
+
+
+class IngestFileResultImporter(EntityImporter):
+
+    def __init__(self, api, require_grobid=True, **kwargs):
+
+        eg_desc = kwargs.get('editgroup_description',
+            "Files crawled from web using sandcrawler ingest tool")
+        eg_extra = kwargs.get('editgroup_extra', dict())
+        eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFileResultImporter')
+        super().__init__(api,
+            editgroup_description=eg_desc,
+            editgroup_extra=eg_extra,
+            **kwargs)
+        self.default_link_rel = kwargs.get("default_link_rel", "web")
+        assert self.default_link_rel
+        self.default_mimetype = kwargs.get("default_mimetype", None)
+        self.do_updates = kwargs.get("do_updates", False)
+        self.require_grobid = require_grobid
+        if self.require_grobid:
+            print("Requiring GROBID status == 200")
+        else:
+            print("NOT checking GROBID success")
+
+    def want(self, row):
+        if self.require_grobid and not row.get('grobid', {}).get('status_code') == 200:
+            return False
+        if row.get('hit') == True and row.get('file_meta'):
+            return True
+        else:
+            return False
+
+    def parse_record(self, row):
+
+        request = row['request']
+        fatcat = request.get('fatcat')
+        file_meta = row['file_meta']
+
+        # identify release by fatcat ident or extid lookup
+        release_ident = None
+        if fatcat and fatcat.get('release_ident'):
+            release_ident = fatcat.get('release_ident')
+        elif request.get('ext_ids'):
+            # if no fatcat ident, try extids
+            for extid_type in ('doi', 'pmid', 'pmcid', 'arxiv'):
+                extid = request['ext_ids'].get(extid_type)
+                if not extid:
+                    continue
+                try:
+                    release = self.api.lookup_release(**{extid_type: extid})
+                except fatcat_openapi_client.rest.ApiException as err:
+                    if err.status == 404:
+                        continue
+                    elif err.status == 400:
+                        self.counts['warn-extid-invalid'] += 1
+                        continue
+                release_ident = release.ident
+                break
+
+        if not release:
+            self.counts['skip-release-not-found'] += 1
+
+        cdx = row.get('cdx')
+        if not cdx:
+            return None
+
+        url = make_rel_url(cdx['url'], self.default_link_rel)
+
+        if not url:
+            self.counts['skip-url'] += 1
+            return None
+        wayback = "https://web.archive.org/web/{}/{}".format(
+            cdx['datetime'],
+            cdx['url'])
+        urls = [url, ("webarchive", wayback)]
+
+        urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
+
+        fe = fatcat_openapi_client.FileEntity(
+            md5=file_meta['md5hex'],
+            sha1=file_meta['sha1hex'],
+            sha256=file_meta['sha256hex'],
+            size=file_meta['size_bytes'],
+            mimetype=file_meta['mimetype'] or self.default_mimetype,
+            release_ids=[release_ident],
+            urls=urls,
+        )
+        if fatcat and fatcat.get('edit_extra'):
+            fe.edit_extra = fatcat['edit_extra']
+        if request.get('project'):
+            if not fe.edit_extra:
+                fe.edit_extra = dict()
+            fe.edit_extra['project'] = request['project']
+        return fe
+
+    def try_update(self, fe):
+        # lookup sha1, or create new entity
+        existing = None
+        try:
+            existing = self.api.lookup_file(sha1=fe.sha1)
+        except fatcat_openapi_client.rest.ApiException as err:
+            if err.status != 404:
+                raise err
+
+        if not existing:
+            return True
+
+        if (fe.release_ids[0] in existing.release_ids) and existing.urls:
+            # TODO: could still, in theory update with the new URL?
+            self.counts['exists'] += 1
+            return False
+
+        if not self.do_updates:
+            self.counts['skip-update-disabled'] += 1
+            return False
+
+        # TODO: for now, never update
+        self.counts['skip-update-disabled'] += 1
+        return False
+
+    def insert_batch(self, batch):
+        self.api.create_file_auto_batch(fatcat_openapi_client.FileAutoBatch(
+            editgroup=fatcat_openapi_client.Editgroup(
+                description=self.editgroup_description,
+                extra=self.editgroup_extra),
+            entity_list=batch))
+
-- 
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