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authorBryan Newbold <bnewbold@robocracy.org>2019-12-13 17:43:27 -0800
committerBryan Newbold <bnewbold@robocracy.org>2019-12-13 18:07:53 -0800
commit9c1fd7cb8e60c397fa6defef2f0dc1eacc8d8aa7 (patch)
treec6d3f80610af009ebba799951bfe3a5c56e72694
parent4b2fc499ac77f4b929943b54a4c28b78659468e8 (diff)
downloadfatcat-9c1fd7cb8e60c397fa6defef2f0dc1eacc8d8aa7.tar.gz
fatcat-9c1fd7cb8e60c397fa6defef2f0dc1eacc8d8aa7.zip
update ingest request schema
This is mostly changing ingest_type from 'file' to 'pdf', and adding 'link_source'/'link_source_id', plus some small cleanups.
-rw-r--r--python/fatcat_tools/importers/ingest.py9
-rw-r--r--python/fatcat_tools/transforms/ingest.py27
-rw-r--r--python/fatcat_tools/workers/changelog.py2
-rw-r--r--python/fatcat_web/forms.py14
-rw-r--r--python/fatcat_web/routes.py8
5 files changed, 44 insertions, 16 deletions
diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py
index a4258a38..bd5713c3 100644
--- a/python/fatcat_tools/importers/ingest.py
+++ b/python/fatcat_tools/importers/ingest.py
@@ -132,10 +132,15 @@ class IngestFileResultImporter(EntityImporter):
)
if fatcat and fatcat.get('edit_extra'):
fe.edit_extra = fatcat['edit_extra']
+ else:
+ fe.edit_extra = dict()
if request.get('ingest_request_source'):
- if not fe.edit_extra:
- fe.edit_extra = dict()
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
return fe
def try_update(self, fe):
diff --git a/python/fatcat_tools/transforms/ingest.py b/python/fatcat_tools/transforms/ingest.py
index 988f80a2..e08d56b8 100644
--- a/python/fatcat_tools/transforms/ingest.py
+++ b/python/fatcat_tools/transforms/ingest.py
@@ -1,7 +1,7 @@
from .elasticsearch import release_to_elasticsearch
-def release_ingest_request(release, oa_only=False, ingest_request_source='fatcat', ingest_type='pdf'):
+def release_ingest_request(release, oa_only=False, ingest_request_source='fatcat', ingest_type=None):
"""
Takes a full release entity object and returns an ingest request (as dict),
or None if it seems like this release shouldn't be ingested.
@@ -12,7 +12,7 @@ def release_ingest_request(release, oa_only=False, ingest_request_source='fatcat
The 'oa_only' boolean flag indicates that we should only return an ingest
request if we have reason to believe this is an OA release (or, eg, in
arxiv or pubmed central). Respecting this flag means we are likely to miss
- a lot of "hybrid" and "bronze" content, but could reduce load
+ a lot of "hybrid" and "bronze" content, but could reduce crawl load
significantly.
The type of the ingest request may depend on release type and container
@@ -25,14 +25,22 @@ def release_ingest_request(release, oa_only=False, ingest_request_source='fatcat
# generate a URL where we expect to find fulltext
url = None
+ link_source = None
+ link_source_id = None
if release.ext_ids.arxiv:
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.doi:
url = "https://doi.org/{}".format(release.ext_ids.doi)
- elif release.ext_ids.pmcid:
+ link_source = "doi"
+ link_source_id = release.ext_ids.doi
+ elif release.ext_ids.pmcid and release.ext_ids.pmid:
# 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)
+ link_source = "pubmed"
+ link_source_id = release.ext_ids.pmid
if not url:
return None
@@ -40,21 +48,30 @@ def release_ingest_request(release, oa_only=False, ingest_request_source='fatcat
ext_ids = release.ext_ids.to_dict()
ext_ids = dict([(k, v) for (k, v) in ext_ids.items() if v])
- if oa_only and not ext_ids.get('arxiv') and not ext_ids.get('pmcid'):
+ if oa_only and link_source not in ('arxiv', 'pubmed'):
es = release_to_elasticsearch(release)
if not es['is_oa']:
return None
+ # 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,
'base_url': url,
+ 'release_stage': release.release_stage,
'fatcat': {
- 'release_stage': release.release_stage,
'release_ident': release.ident,
'work_ident': release.work_id,
},
'ext_ids': ext_ids,
}
+
+ if link_source and link_source_id:
+ ingest_request['link_source'] = link_source
+ ingest_request['link_source_id'] = link_source_id
+
return ingest_request
diff --git a/python/fatcat_tools/workers/changelog.py b/python/fatcat_tools/workers/changelog.py
index e1a72217..863ad40a 100644
--- a/python/fatcat_tools/workers/changelog.py
+++ b/python/fatcat_tools/workers/changelog.py
@@ -223,7 +223,7 @@ class EntityUpdatesWorker(FatcatWorker):
# filter to "new" active releases with no matched files
if release.ident in new_release_ids:
ir = release_ingest_request(release, ingest_request_source='fatcat-changelog', oa_only=self.ingest_oa_only)
- if ir and ir['ingest_type'] == 'file' and not release.files:
+ if ir and not release.files:
producer.produce(
self.ingest_file_request_topic,
json.dumps(ir).encode('utf-8'),
diff --git a/python/fatcat_web/forms.py b/python/fatcat_web/forms.py
index bd4e4bbd..5539cc20 100644
--- a/python/fatcat_web/forms.py
+++ b/python/fatcat_web/forms.py
@@ -386,18 +386,16 @@ class SavePaperNowForm(FlaskForm):
choices=release_stage_options,
default='')
- def to_ingest_request(self, release, actor='savepapernow-web'):
+ def to_ingest_request(self, release, ingest_request_source='savepapernow'):
base_url = self.base_url.data
ext_ids = release.ext_ids.to_dict()
# by default this dict has a bunch of empty values
ext_ids = dict([(k, v) for (k, v) in ext_ids.items() if v])
ingest_request = {
'ingest_type': self.ingest_type.data,
- 'ingest_request_source': actor, # TODO: deprecate?
- 'actor': actor,
+ 'ingest_request_source': ingest_request_source,
'base_url': base_url,
'fatcat': {
- 'release_stage': release.release_stage,
'release_ident': release.ident,
'work_ident': release.work_id,
},
@@ -405,8 +403,12 @@ class SavePaperNowForm(FlaskForm):
}
if self.release_stage.data:
ingest_request['release_stage'] = self.release_stage.data
+
if release.ext_ids.doi and base_url == "https://doi.org/{}".format(release.ext_ids.doi):
- ingest_request['source'] = 'doi'
- ingest_request['source_id'] = release.ext_ids.doi
+ ingest_request['link_source'] = 'doi'
+ ingest_request['link_source_id'] = release.ext_ids.doi
+ elif release.ext_ids.arxiv and base_url == "https://arxiv.org/pdf/{}.pdf".format(release.ext_ids.arxiv):
+ ingest_request['link_source'] = 'arxiv'
+ ingest_request['link_source_id'] = release.ext_ids.arxiv
return ingest_request
diff --git a/python/fatcat_web/routes.py b/python/fatcat_web/routes.py
index cc0af5cc..8583d255 100644
--- a/python/fatcat_web/routes.py
+++ b/python/fatcat_web/routes.py
@@ -648,11 +648,11 @@ def release_save(ident):
if form.is_submitted():
if form.validate_on_submit():
# got a valid spn request! try to send to kafka-pixy
- msg = form.to_ingest_request(release)
+ msg = form.to_ingest_request(release, ingest_request_source="savepapernow-web")
try:
kafka_pixy_produce(
Config.KAFKA_SAVEPAPERNOW_TOPIC,
- json.dumps(msg),
+ json.dumps(msg, sort_keys=True),
)
except Exception as e:
print(e, file=sys.stderr)
@@ -666,6 +666,10 @@ def release_save(ident):
form.release_stage.data = release.release_stage
if release.ext_ids.doi:
form.base_url.data = "https://doi.org/{}".format(release.ext_ids.doi)
+ elif release.ext_ids.arxiv:
+ form.base_url.data = "https://arxiv.org/pdf/{}.pdf".format(release.ext_ids.arxiv)
+ elif release.ext_ids.pmcid:
+ form.base_url.data = "http://europepmc.org/backend/ptpmcrender.fcgi?accid={}&blobtype=pdf".format(release.ext_ids.pmcid)
return render_template('release_save.html', entity=release, form=form), 200
### Search ##################################################################