Merge branch 'bnewbold-xml-html-ingest' into 'master'

HTML webcapture ingest (and XML file ingest)

See merge request webgroup/fatcat!88

4 files changed, 291 insertions, 60 deletions

diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index b82eb11a..c08e04c2 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -27,6 +27,6 @@ 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 .ingest import IngestFileResultImporter, SavePaperNowFileImporter
+from .ingest import IngestFileResultImporter, SavePaperNowFileImporter, IngestWebResultImporter
 from .shadow import ShadowLibraryImporter
 from .file_meta import FileMetaImporter
diff --git a/python/fatcat_tools/importers/datacite.py b/python/fatcat_tools/importers/datacite.py
index 86740e80..5cdc5577 100644
--- a/python/fatcat_tools/importers/datacite.py
+++ b/python/fatcat_tools/importers/datacite.py
@@ -151,7 +151,7 @@ UNKNOWN_MARKERS = set(DATACITE_UNKNOWN_MARKERS).union(set((
     'Unknown',
 )))
 
-# UNKNOWN_MARKERS_LOWER are lowercase version of UNKNOWN blacklist.
+# UNKNOWN_MARKERS_LOWER are lowercase version of UNKNOWN blocklist.
 UNKNOWN_MARKERS_LOWER = set((v.lower() for v in UNKNOWN_MARKERS))
 
 # Any "min" number of "tokens" will signal "spam", https://fatcat.wiki/release/rzcpjwukobd4pj36ipla22cnoi
@@ -346,7 +346,7 @@ class DataciteImporter(EntityImporter):
             print('[{}] skipping record w/o title: {}'.format(doi, obj), file=sys.stderr)
             return False
 
-        # check for blacklisted "spam", e.g. "FULL MOVIE"
+        # check for blocklisted "spam", e.g. "FULL MOVIE"
         for rule in DATACITE_TITLE_SPAM_WORDGROUPS:
             seen = set()
             for token in rule.get("tokens", []):
@@ -819,7 +819,7 @@ class DataciteImporter(EntityImporter):
         contribs = []
 
         # Names, that should be ignored right away.
-        name_blacklist = set(('Occdownload Gbif.Org',))
+        name_blocklist = set(('Occdownload Gbif.Org',))
 
         i = 0
         for c in creators:
@@ -861,7 +861,7 @@ class DataciteImporter(EntityImporter):
                     continue
                 if not name:
                     name = "{} {}".format(given_name or '', surname or '').strip()
-                if name in name_blacklist:
+                if name in name_blocklist:
                     continue
                 if name.lower() in UNKNOWN_MARKERS_LOWER:
                     continue
diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py
index 4b1d3702..4fbd19f1 100644
--- a/python/fatcat_tools/importers/ingest.py
+++ b/python/fatcat_tools/importers/ingest.py
@@ -1,4 +1,6 @@
 
+import datetime
+
 import fatcat_openapi_client
 from .common import EntityImporter, make_rel_url
 
@@ -20,10 +22,10 @@ class IngestFileResultImporter(EntityImporter):
         assert self.default_link_rel
         self.require_grobid = require_grobid
         if self.require_grobid:
-            print("Requiring GROBID status == 200")
+            print("Requiring GROBID status == 200 (for PDFs)")
         else:
             print("NOT checking GROBID success")
-        self.ingest_request_source_whitelist = [
+        self.ingest_request_source_allowlist = [
             'fatcat-changelog',
             'fatcat-ingest-container',
             'fatcat-ingest',
@@ -35,23 +37,41 @@ class IngestFileResultImporter(EntityImporter):
             's2-corpus',
             's2',
         ]
-        if kwargs.get('skip_source_whitelist', False):
-            self.ingest_request_source_whitelist = []
+        if kwargs.get('skip_source_allowlist', False):
+            self.ingest_request_source_allowlist = []
 
-    def want(self, row):
+    def want_file(self, row) -> bool:
+        """
+        File-specific part of want(). Generic across general ingest and save-paper-now.
         """
-        Logic here probably needs work (TODO):
 
-        - Direct ingests via DOI from fatcat-changelog should probably go
-          through regardless of GROBID status
-        - We should filter/block things like single-page PDFs here
-        - public/anonymous submissions could require successful biblio-glutton
-          match, or some other sanity check on the fatcat side (eg, fuzzy title
-          match)
-        - handle the case of release_stage not being 'published'; if pre-print,
-          potentially create a new release.
+        if not row.get('file_meta'):
+            self.counts['skip-file-meta'] += 1
+            return False
 
-        The current logic is intentionally conservative as a first step.
+        # type-specific filters
+        if row['request'].get('ingest_type') == 'pdf':
+            if self.require_grobid and row.get('grobid', {}).get('status_code') != 200:
+                self.counts['skip-grobid'] += 1
+                return False
+            if row['file_meta'].get('mimetype') not in ("application/pdf",):
+                self.counts['skip-mimetype'] += 1
+                return False
+        elif row['request'].get('ingest_type') == 'xml':
+            if row['file_meta'].get('mimetype') not in ("application/xml",
+                    "application/jats+xml", "application/tei+xml", "text/xml"):
+                self.counts['skip-mimetype'] += 1
+                return False
+        else:
+            self.counts['skip-ingest-type'] += 1
+            return False
+
+        return True
+
+    def want_ingest(self, row) -> bool:
+        """
+        Sandcrawler ingest-specific part of want(). Generic across file and
+        webcapture ingest.
         """
         if row.get('hit') != True:
             self.counts['skip-hit'] += 1
@@ -60,33 +80,48 @@ class IngestFileResultImporter(EntityImporter):
         if not source:
             self.counts['skip-ingest_request_source'] += 1
             return False
-        if self.ingest_request_source_whitelist and source not in self.ingest_request_source_whitelist:
+        if self.ingest_request_source_allowlist and source not in self.ingest_request_source_allowlist:
             self.counts['skip-ingest_request_source'] += 1
             return False
-        if source.startswith('arabesque'):
-            if row['request'].get('link_source') not in ('arxiv', 'pmc', 'unpaywall', 'doi', 'mag', 's2'):
-                self.counts['skip-arabesque-source'] += 1
-                return False
+
+        if row['request'].get('link_source') not in ('arxiv', 'pmc', 'unpaywall', 'doi', 'mag', 's2'):
+            self.counts['skip-link-source'] += 1
+            return False
+
         if source.startswith('savepapernow'):
             # never process async savepapernow requests
             self.counts['skip-savepapernow'] += 1
             return False
-        if not row.get('file_meta'):
-            self.counts['skip-file-meta'] += 1
+
+        return True
+
+    def want(self, row):
+        """
+        Overall logic here probably needs work (TODO):
+
+        - Direct ingests via DOI from fatcat-changelog should probably go
+          through regardless of GROBID status
+        - We should filter/block things like single-page PDFs here
+        - public/anonymous submissions could require successful biblio-glutton
+          match, or some other sanity check on the fatcat side (eg, fuzzy title
+          match)
+        - handle the case of release_stage not being 'published'; if pre-print,
+          potentially create a new release.
+
+        The current logic is intentionally conservative as a first step.
+        """
+        if not self.want_file(row):
             return False
-        if self.require_grobid and row.get('grobid', {}).get('status_code') != 200:
-            self.counts['skip-grobid'] += 1
+        if not self.want_ingest(row):
             return False
 
         return True
 
-    def parse_record(self, row):
+    def parse_ingest_release_ident(self, row):
 
         request = row['request']
         fatcat = request.get('fatcat')
-        file_meta = row['file_meta']
 
-        # identify release by fatcat ident, or extid lookup, or biblio-glutton match
         release_ident = None
         if fatcat and fatcat.get('release_ident'):
             release_ident = fatcat.get('release_ident')
@@ -112,23 +147,21 @@ class IngestFileResultImporter(EntityImporter):
                         return None
                 release_ident = release.ident
                 break
+
         if self.use_glutton_match and not release_ident and row.get('grobid'):
             # try biblio-glutton extracted hit
             if row['grobid'].get('fatcat_release'):
                 release_ident = row['grobid']['fatcat_release'].split('_')[-1]
                 self.counts['glutton-match'] += 1
 
-        if not release_ident:
-            self.counts['skip-release-not-found'] += 1
-            return None
+        return release_ident
 
+    def parse_terminal(self, row):
         terminal = row.get('terminal')
         if not terminal:
             # support old cdx-only ingest results
             cdx = row.get('cdx')
             if not cdx:
-                # TODO: support archive.org hits?
-                self.counts['skip-no-terminal'] += 1
                 return None
             else:
                 terminal = {
@@ -142,7 +175,15 @@ class IngestFileResultImporter(EntityImporter):
             terminal['terminal_url'] = terminal['url']
         if not 'terminal_dt' in terminal:
             terminal['terminal_dt'] = terminal['dt']
+
+        # convert CDX-style digits to ISO-style timestamp
         assert len(terminal['terminal_dt']) == 14
+        terminal['terminal_timestamp'] = datetime.datetime.strptime(terminal['terminal_dt'], "%Y%m%d%H%M%S").isoformat() + "Z"
+        return terminal
+
+    def parse_urls(self, row, terminal):
+
+        request = row['request']
 
         default_rel = self.default_link_rel
         if request.get('link_source') == 'doi':
@@ -159,6 +200,55 @@ class IngestFileResultImporter(EntityImporter):
         urls = [url, ("webarchive", wayback)]
 
         urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
+        return urls
+
+    def parse_edit_extra(self, row):
+
+        request = row['request']
+        edit_extra = dict()
+
+        if request.get('edit_extra'):
+            edit_extra = request['edit_extra']
+
+        if request.get('ingest_request_source'):
+            edit_extra['ingest_request_source'] = request['ingest_request_source']
+        if request.get('link_source') and request.get('link_source_id'):
+            edit_extra['link_source'] = request['link_source']
+            edit_extra['link_source_id'] = request['link_source_id']
+
+        return edit_extra
+
+    def parse_record(self, row):
+
+        request = row['request']
+        file_meta = row['file_meta']
+
+        # double check that want() filtered request correctly (eg, old requests)
+        if request.get('ingest_type') not in ('pdf', 'xml'):
+            self.counts['skip-ingest-type'] += 1
+            return None
+        assert (request['ingest_type'], file_meta['mimetype']) in [
+            ("pdf", "application/pdf"),
+            ("xml", "application/xml"),
+            ("xml", "application/jats+xml"),
+            ("xml", "application/tei+xml"),
+            ("xml", "text/xml"),
+        ]
+
+        # identify release by fatcat ident, or extid lookup, or biblio-glutton match
+        release_ident = self.parse_ingest_release_ident(row)
+
+        if not release_ident:
+            self.counts['skip-release-not-found'] += 1
+            return None
+
+        terminal = self.parse_terminal(row)
+        if not terminal:
+            # TODO: support archive.org hits?
+            self.counts['skip-no-terminal'] += 1
+            return None
+
+        urls = self.parse_urls(row, terminal)
 
         fe = fatcat_openapi_client.FileEntity(
             md5=file_meta['md5hex'],
@@ -169,17 +259,10 @@ class IngestFileResultImporter(EntityImporter):
             release_ids=[release_ident],
             urls=urls,
         )
-        if request.get('edit_extra'):
-            fe.edit_extra = request['edit_extra']
-        else:
-            fe.edit_extra = dict()
-        if request.get('ingest_request_source'):
-            fe.edit_extra['ingest_request_source'] = request['ingest_request_source']
-        if request.get('link_source') and request.get('link_source_id'):
-            fe.edit_extra['link_source'] = request['link_source']
-            fe.edit_extra['link_source_id'] = request['link_source_id']
-        if not fe.edit_extra:
-            fe.edit_extra = None
+
+        edit_extra = self.parse_edit_extra(row)
+        if edit_extra:
+            fe.edit_extra = edit_extra
         return fe
 
     def try_update(self, fe):
@@ -244,6 +327,9 @@ class SavePaperNowFileImporter(IngestFileResultImporter):
 
     def want(self, row):
 
+        if not self.want_file(row):
+            return False
+
         source = row['request'].get('ingest_request_source')
         if not source:
             self.counts['skip-ingest_request_source'] += 1
@@ -254,12 +340,6 @@ class SavePaperNowFileImporter(IngestFileResultImporter):
         if row.get('hit') != True:
             self.counts['skip-hit'] += 1
             return False
-        if not row.get('file_meta'):
-            self.counts['skip-file-meta'] += 1
-            return False
-        if self.require_grobid and row.get('grobid', {}).get('status_code') != 200:
-            self.counts['skip-grobid'] += 1
-            return False
 
         return True
 
@@ -280,3 +360,154 @@ class SavePaperNowFileImporter(IngestFileResultImporter):
                     description=self.editgroup_description,
                     extra=self.editgroup_extra),
                 entity_list=batch))
+
+
+class IngestWebResultImporter(IngestFileResultImporter):
+    """
+    Variant of IngestFileResultImporter for processing HTML ingest requests
+    into webcapture objects.
+    """
+
+    def __init__(self, api, **kwargs):
+
+        eg_desc = kwargs.pop('editgroup_description', None) or "Webcaptures crawled from web using sandcrawler ingest tool"
+        eg_extra = kwargs.pop('editgroup_extra', dict())
+        eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestWebResultImporter')
+        kwargs['do_updates'] = False
+        super().__init__(api,
+            editgroup_description=eg_desc,
+            editgroup_extra=eg_extra,
+            **kwargs)
+
+    def want(self, row):
+
+        if not self.want_ingest(row):
+            return False
+
+        if not row.get('file_meta'):
+            self.counts['skip-file-meta'] += 1
+            return False
+
+        # webcapture-specific filters
+        if row['request'].get('ingest_type') != 'html':
+            self.counts['skip-ingest-type'] += 1
+            return False
+        if row['file_meta'].get('mimetype') not in ("text/html", "application/xhtml+xml"):
+            self.counts['skip-mimetype'] += 1
+            return False
+
+        return True
+
+    def parse_record(self, row):
+
+        request = row['request']
+        file_meta = row['file_meta']
+
+        # double check that want() filtered request correctly (eg, old requests)
+        if request.get('ingest_type') != "html":
+            self.counts['skip-ingest-type'] += 1
+            return None
+        if file_meta['mimetype'] not in ("text/html", "application/xhtml+xml"):
+            self.counts['skip-mimetype'] += 1
+            return None
+
+        # identify release by fatcat ident, or extid lookup
+        release_ident = self.parse_ingest_release_ident(row)
+
+        if not release_ident:
+            self.counts['skip-release-not-found'] += 1
+            return None
+
+        terminal = self.parse_terminal(row)
+        if not terminal:
+            # TODO: support archive.org hits?
+            self.counts['skip-no-terminal'] += 1
+            return None
+
+        urls = self.parse_urls(row, terminal)
+        archive_urls = [u for u in urls if u.rel == 'webarchive']
+
+        if terminal['terminal_status_code'] != 200:
+            self.counts['skip-terminal-status-code'] += 1
+            return None
+
+        terminal_cdx = row['cdx']
+        if 'revisit_cdx' in row:
+            terminal_cdx = row['revisit_cdx']
+        assert terminal_cdx['surt']
+        assert terminal_cdx['url'] == terminal['terminal_url']
+
+        wc_cdx = []
+        # primary resource first
+        wc_cdx.append(fatcat_openapi_client.WebcaptureCdxLine(
+            surt=terminal_cdx['surt'],
+            timestamp=terminal['terminal_timestamp'],
+            url=terminal['terminal_url'],
+            mimetype=file_meta['mimetype'],
+            status_code=terminal['terminal_status_code'],
+            sha1=file_meta['sha1hex'],
+            sha256=file_meta['sha256hex'],
+            size=file_meta['size_bytes'],
+        ))
+
+        for resource in row.get('html_resources', []):
+            timestamp = resource['timestamp']
+            if not "+" in timestamp and not "Z" in timestamp:
+                timestamp += "Z"
+            wc_cdx.append(fatcat_openapi_client.WebcaptureCdxLine(
+                surt=resource['surt'],
+                timestamp=timestamp,
+                url=resource['url'],
+                mimetype=resource.get('mimetype'),
+                size=resource.get('size'),
+                sha1=resource.get('sha1hex'),
+                sha256=resource.get('sha256hex'),
+            ))
+
+        wc = fatcat_openapi_client.WebcaptureEntity(
+            cdx=wc_cdx,
+            archive_urls=archive_urls,
+            original_url=terminal['terminal_url'],
+            timestamp=terminal['terminal_timestamp'],
+            release_ids=[release_ident],
+        )
+
+        edit_extra = self.parse_edit_extra(row)
+
+        if edit_extra:
+            wc.edit_extra = edit_extra
+        return wc
+
+    def try_update(self, wc):
+
+        # check for existing edits-in-progress with same file hash
+        for other in self._entity_queue:
+            if other.sha1 == wc.sha1:
+                self.counts['skip-in-queue'] += 1
+                return False
+
+        # lookup sha1, or create new entity (TODO: API doesn't support this yet)
+        #existing = None
+
+        # TODO: currently only allow one release per webcapture
+        release = self.api.get_release(wc.release_ids[0], expand="webcaptures")
+        if release.webcaptures:
+            # check if this is an existing match, or just a similar hit
+            for other in release.webcaptures:
+                if wc.original_url == other.original_url:
+                    # TODO: compare very similar timestamps of same time (different formats)
+                    self.counts['exists'] += 1
+                    return False
+            self.counts['skip-release-has-webcapture'] += 1
+            return False
+
+        # TODO: for now, never update
+        self.counts['skip-update-disabled'] += 1
+        return False
+
+    def insert_batch(self, batch):
+        self.api.create_webcapture_auto_batch(fatcat_openapi_client.WebcaptureAutoBatch(
+            editgroup=fatcat_openapi_client.Editgroup(
+                description=self.editgroup_description,
+                extra=self.editgroup_extra),
+            entity_list=batch))
diff --git a/python/fatcat_tools/transforms/ingest.py b/python/fatcat_tools/transforms/ingest.py
index 2f4e2271..59831017 100644
--- a/python/fatcat_tools/transforms/ingest.py
+++ b/python/fatcat_tools/transforms/ingest.py
@@ -15,15 +15,19 @@ def release_ingest_request(release, ingest_request_source='fatcat', ingest_type=
     if release.state != 'active':
         return None
 
+    # TODO: infer ingest type based on release_type or container metadata?
+    if not ingest_type:
+        ingest_type = 'pdf'
+
     # generate a URL where we expect to find fulltext
     url = None
     link_source = None
     link_source_id = None
-    if release.ext_ids.arxiv:
+    if release.ext_ids.arxiv and ingest_type == "pdf":
         url = "https://arxiv.org/pdf/{}.pdf".format(release.ext_ids.arxiv)
         link_source = "arxiv"
         link_source_id = release.ext_ids.arxiv
-    elif release.ext_ids.pmcid:
+    elif release.ext_ids.pmcid and ingest_type == "pdf":
         # TODO: how to tell if an author manuscript in PMC vs. published?
         #url = "https://www.ncbi.nlm.nih.gov/pmc/articles/{}/pdf/".format(release.ext_ids.pmcid)
         url = "http://europepmc.org/backend/ptpmcrender.fcgi?accid={}&blobtype=pdf".format(release.ext_ids.pmcid)
@@ -40,10 +44,6 @@ def release_ingest_request(release, ingest_request_source='fatcat', ingest_type=
     ext_ids = release.ext_ids.to_dict()
     ext_ids = dict([(k, v) for (k, v) in ext_ids.items() if v])
 
-    # TODO: infer ingest type based on release_type or container metadata?
-    if not ingest_type:
-        ingest_type = 'pdf'
-
     ingest_request = {
         'ingest_type': ingest_type,
         'ingest_request_source': ingest_request_source,