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-rw-r--r--python/fatcat_tools/transforms/__init__.py2
-rw-r--r--python/fatcat_tools/transforms/elasticsearch.py242
2 files changed, 198 insertions, 46 deletions
diff --git a/python/fatcat_tools/transforms/__init__.py b/python/fatcat_tools/transforms/__init__.py
index 6a4b1bba..3f4700ff 100644
--- a/python/fatcat_tools/transforms/__init__.py
+++ b/python/fatcat_tools/transforms/__init__.py
@@ -1,5 +1,5 @@
from .entities import entity_to_dict, entity_from_json, entity_from_dict
-from .elasticsearch import release_to_elasticsearch, container_to_elasticsearch, changelog_to_elasticsearch
+from .elasticsearch import release_to_elasticsearch, container_to_elasticsearch, changelog_to_elasticsearch, file_to_elasticsearch
from .csl import release_to_csl, citeproc_csl
from .ingest import release_ingest_request
diff --git a/python/fatcat_tools/transforms/elasticsearch.py b/python/fatcat_tools/transforms/elasticsearch.py
index 3a53db4d..87e054ec 100644
--- a/python/fatcat_tools/transforms/elasticsearch.py
+++ b/python/fatcat_tools/transforms/elasticsearch.py
@@ -1,6 +1,6 @@
-
import collections
+import tldextract
from fatcat_openapi_client import ApiClient
@@ -20,6 +20,7 @@ def test_check_kbart():
assert check_kbart(1950, dict(year_spans=[[1900, 1920], [1990, 2000]])) == False
assert check_kbart(1950, dict(year_spans=[[1900, 1920], [1930, 2000]])) == True
+
def release_to_elasticsearch(entity, force_bool=True):
"""
Converts from an entity model/schema to elasticsearch oriented schema.
@@ -50,6 +51,10 @@ def release_to_elasticsearch(entity, force_bool=True):
release_stage = release.release_stage,
withdrawn_status = release.withdrawn_status,
language = release.language,
+ volume = release.volume,
+ issue = release.issue,
+ pages = release.pages,
+ number = release.number,
license = release.license_slug,
doi = release.ext_ids.doi,
pmid = release.ext_ids.pmid,
@@ -72,7 +77,7 @@ def release_to_elasticsearch(entity, force_bool=True):
in_dweb = False
in_ia = False
in_ia_sim = False
- in_shadow = False
+ in_shadows = False
release_year = release.release_year
if release.release_date:
@@ -85,11 +90,15 @@ def release_to_elasticsearch(entity, force_bool=True):
t['any_abstract'] = len(release.abstracts or []) > 0
t['ref_count'] = len(release.refs or [])
- t['ref_linked_count'] = 0
- if release.refs:
- t['ref_linked_count'] = len([1 for ref in release.refs if ref.target_release_id])
+ ref_release_ids = []
+ for r in (release.refs or []):
+ if r.target_release_id:
+ ref_release_ids.append(r.target_release_id)
+ t['ref_release_ids'] = ref_release_ids
+ t['ref_linked_count'] = len(ref_release_ids)
t['contrib_count'] = len(release.contribs or [])
contrib_names = []
+ contrib_affiliations = []
creator_ids = []
for c in (release.contribs or []):
if c.raw_name:
@@ -98,8 +107,14 @@ def release_to_elasticsearch(entity, force_bool=True):
contrib_names.append(c.surname)
if c.creator_id:
creator_ids.append(c.creator_id)
+ if c.raw_affiliation:
+ contrib_affiliations.append(c.raw_affiliation)
t['contrib_names'] = contrib_names
t['creator_ids'] = creator_ids
+ t['affiliations'] = contrib_affiliations
+
+ # TODO: mapping... probably by lookup?
+ t['affiliation_rors'] = None
container = release.container
if container:
@@ -134,14 +149,19 @@ def release_to_elasticsearch(entity, force_bool=True):
if c_extra.get('road'):
if c_extra['road'].get('as_of'):
is_oa = True
- if c_extra.get('ezb'):
- if c_extra['ezb'].get('color') == 'green':
- is_oa = True
if c_extra.get('szczepanski'):
if c_extra['szczepanski'].get('as_of'):
is_oa = True
- else:
+ if c_extra.get('country'):
+ t['country_code'] = c_extra['country']
+ t['country_code_upper'] = c_extra['country'].upper()
+
+ # fall back to release-level container metadata if container not linked or
+ # missing context
+ if not t.get('publisher'):
t['publisher'] = release.publisher
+ if not t.get('container_name') and release.extra:
+ t['container_name'] = release.extra.get('container_name')
if release.ext_ids.jstor or (release.ext_ids.doi and release.ext_ids.doi.startswith('10.2307/')):
in_jstor = True
@@ -187,6 +207,8 @@ def release_to_elasticsearch(entity, force_bool=True):
# TODO: more/better checks here, particularly strict *not* OA licenses
if release.license_slug.startswith("CC-"):
is_oa = True
+ if release.license_slug.startswith("ARXIV-"):
+ is_oa = True
extra = release.extra or dict()
if extra:
@@ -203,6 +225,47 @@ def release_to_elasticsearch(entity, force_bool=True):
if extra['crossref'].get('archive'):
# all crossref archives are KBART, I believe
in_kbart = True
+ # backwards compatible subtitle fetching
+ if not t['subtitle'] and extra.get('subtitle'):
+ if type(extra['subtitle']) == list:
+ t['subtitle'] = extra['subtitle'][0]
+ else:
+ t['subtitle'] = extra['subtitle']
+
+ t['first_page'] = None
+ if release.pages:
+ first = release.pages.split('-')[0]
+ first = first.replace('p', '')
+ if first.isdigit():
+ t['first_page'] = first
+ # TODO: non-numerical first pages
+
+ t['ia_microfilm_url'] = None
+ if in_ia_sim:
+ # TODO: determine URL somehow? I think this is in flux. Will probably
+ # need extra metadata in the container extra field.
+ # special case as a demo for now.
+ if release.container_id == "hl5g6d5msjcl7hlbyyvcsbhc2u" \
+ and release.release_year in (2011, 2013) \
+ and release.issue \
+ and release.issue.isdigit() \
+ and t['first_page']:
+ t['ia_microfilm_url'] = "https://archive.org/details/sim_bjog_{}-{:02d}/page/n{}".format(
+ release.release_year,
+ int(release.issue) - 1,
+ t['first_page'],
+ )
+
+ t['doi_registrar'] = None
+ if extra and t['doi']:
+ for k in ('crossref', 'datacite', 'jalc'):
+ if k in extra:
+ t['doi_registrar'] = k
+ if not 'doi_registrar' in t:
+ t['doi_registrar'] = 'crossref'
+
+ if t['doi']:
+ t['doi_prefix'] = t['doi'].split('/')[0]
if is_longtail_oa:
is_oa = True
@@ -215,6 +278,7 @@ def release_to_elasticsearch(entity, force_bool=True):
t['in_jstor'] = bool(in_jstor)
t['in_web'] = bool(in_web)
t['in_dweb'] = bool(in_dweb)
+ t['in_shadows'] = bool(in_shadows)
else:
t['is_oa'] = is_oa
t['is_longtail_oa'] = is_longtail_oa
@@ -223,11 +287,23 @@ def release_to_elasticsearch(entity, force_bool=True):
t['in_jstor'] = in_jstor
t['in_web'] = in_web
t['in_dweb'] = in_dweb
+ t['in_shadows'] = in_shadows
t['in_ia'] = bool(in_ia)
t['is_preserved'] = bool(is_preserved or in_ia or in_kbart or in_jstor)
+
+ if in_ia or t.get('pmcid') or t.get('arxiv_id'):
+ t['preservation'] = 'bright'
+ elif in_kbart or in_jstor:
+ t['preservation'] = 'dark'
+ elif in_shadows:
+ t['preservation'] = 'shadows_only'
+ else:
+ t['preservation'] = 'none'
+
return t
+
def container_to_elasticsearch(entity, force_bool=True):
"""
Converts from an entity model/schema to elasticsearch oriented schema.
@@ -257,23 +333,27 @@ def container_to_elasticsearch(entity, force_bool=True):
wikidata_qid = entity.wikidata_qid,
)
- # TODO: region, discipline
- # TODO: single primary language?
if not entity.extra:
entity.extra = dict()
- for key in ('country', 'languages', 'mimetypes', 'first_year', 'last_year'):
+ for key in ('country', 'languages', 'mimetypes', 'original_name',
+ 'first_year', 'last_year', 'aliases', 'abbrev', 'region',
+ 'discipline'):
if entity.extra.get(key):
t[key] = entity.extra[key]
+ if 'country' in t:
+ t['country_code'] = t.pop('country')
+
+ t['issns'] = []
+ if entity.issnl:
+ t['issns'].append(entity.issnl)
+ for key in ('issnp', 'issne'):
+ if entity.extra.get(key):
+ t['issns'].append(entity.extra[key])
+
in_doaj = None
in_road = None
- # TODO: not currently implemented
- in_doi = None
- # TODO: would be nice to have 'in_doaj_works', or maybe just "any_pid"
- #in_doaj_works = None
- in_sherpa_romeo = None
is_oa = None
- # TODO: not actually set/stored anywhere?
is_longtail_oa = None
any_kbart = None
any_jstor = None
@@ -286,17 +366,15 @@ def container_to_elasticsearch(entity, force_bool=True):
if extra.get('road'):
if extra['road'].get('as_of'):
in_road = True
- if extra.get('ezb'):
- if extra['ezb'].get('color') == 'green':
- is_oa = True
if extra.get('szczepanski'):
if extra['szczepanski'].get('as_of'):
is_oa = True
if extra.get('default_license'):
if extra['default_license'].startswith('CC-'):
is_oa = True
+ t['sherpa_romeo_color'] = None
if extra.get('sherpa_romeo'):
- in_sherpa_romeo = True
+ t['sherpa_romeo_color'] = extra['sherpa_romeo'].get('color')
if extra['sherpa_romeo'].get('color') == 'white':
is_oa = False
if extra.get('kbart'):
@@ -306,54 +384,128 @@ def container_to_elasticsearch(entity, force_bool=True):
if extra.get('ia'):
if extra['ia'].get('sim'):
any_ia_sim = True
+ if extra['ia'].get('longtail_oa'):
+ is_longtail_oa = True
t['is_superceded'] = bool(extra.get('superceded'))
t['in_doaj'] = bool(in_doaj)
t['in_road'] = bool(in_road)
- t['in_sherpa_romeo'] = bool(in_sherpa_romeo)
t['any_kbart'] = bool(any_kbart)
- t['is_longtail_oa'] = bool(is_longtail_oa)
if force_bool:
- t['in_doi'] = bool(in_doi)
- t['is_oa'] = bool(in_doaj or in_road or is_longtail_oa or is_oa)
+ t['is_oa'] = bool(in_doaj or in_road or is_oa)
+ t['is_longtail_oa'] = bool(is_longtail_oa)
t['any_jstor'] = bool(any_jstor)
t['any_ia_sim'] = bool(any_ia_sim)
else:
- t['in_doi'] = in_doi
- t['is_oa'] = in_doaj or in_road or is_longtail_oa or is_oa
+ t['is_oa'] = in_doaj or in_road or is_oa
+ t['is_longtail_oa'] = is_longtail_oa
t['any_jstor'] = any_jstor
t['any_ia_sim'] = any_ia_sim
return t
+def _type_of_edit(edit):
+ if edit.revision == None and edit.redirect_ident == None:
+ return 'delete'
+ elif edit.redirect_ident:
+ # redirect
+ return 'update'
+ elif edit.prev_revision == None and edit.redirect_ident == None and edit.revision:
+ return 'create'
+ else:
+ return 'update'
+
+
def changelog_to_elasticsearch(entity):
+ """
+ Note that this importer requires expanded fill info to work. Calling code
+ may need to re-fetch editgroup from API to get the 'editor' field. Some of
+ the old kafka feed content doesn't includes editor in particular.
+ """
editgroup = entity.editgroup
t = dict(
index=entity.index,
editgroup_id=entity.editgroup_id,
- timestamp=entity.timestamp,
+ timestamp=entity.timestamp.isoformat(),
editor_id=editgroup.editor_id,
+ username=editgroup.editor.username,
+ is_bot=editgroup.editor.is_bot,
+ is_admin=editgroup.editor.is_admin,
)
extra = editgroup.extra or dict()
if extra.get('agent'):
t['agent'] = extra['agent']
- t['containers'] = len(editgroup.edits.containers)
- t['creators'] = len(editgroup.edits.containers)
- t['files'] = len(editgroup.edits.containers)
- t['filesets'] = len(editgroup.edits.containers)
- t['webcaptures'] = len(editgroup.edits.containers)
- t['releases'] = len(editgroup.edits.containers)
- t['works'] = len(editgroup.edits.containers)
-
- # TODO: parse and pull out counts
- #created = 0
- #updated = 0
- #deleted = 0
- #t['created'] = created
- #t['updated'] = updated
- #t['deleted'] = deleted
- #t['total'] = created + updated + deleted
+ containers = [_type_of_edit(e) for e in editgroup.edits.containers]
+ creators = [_type_of_edit(e) for e in editgroup.edits.creators]
+ files = [_type_of_edit(e) for e in editgroup.edits.files]
+ filesets = [_type_of_edit(e) for e in editgroup.edits.filesets]
+ webcaptures = [_type_of_edit(e) for e in editgroup.edits.webcaptures]
+ releases = [_type_of_edit(e) for e in editgroup.edits.releases]
+ works = [_type_of_edit(e) for e in editgroup.edits.works]
+
+ t['containers'] = len(containers)
+ t['new_containers'] = len([e for e in containers if e == 'create'])
+ t['creators'] = len(creators)
+ t['new_creators'] = len([e for e in creators if e == 'create'])
+ t['files'] = len(files)
+ t['new_files'] = len([e for e in files if e == 'create'])
+ t['filesets'] = len(filesets)
+ t['new_filesets'] = len([e for e in filesets if e == 'create'])
+ t['webcaptures'] = len(webcaptures)
+ t['new_webcaptures'] = len([e for e in webcaptures if e == 'create'])
+ t['releases'] = len(releases)
+ t['new_releases'] = len([e for e in releases if e == 'create'])
+ t['works'] = len(works)
+ t['new_works'] = len([e for e in works if e == 'create'])
+
+ all_edits = containers + creators + files + filesets + webcaptures + releases + works
+
+ t['created'] = len([e for e in all_edits if e == 'create'])
+ t['updated'] = len([e for e in all_edits if e == 'update'])
+ t['deleted'] = len([e for e in all_edits if e == 'delete'])
+ t['total'] = len(all_edits)
+ return t
+
+
+def file_to_elasticsearch(entity):
+ """
+ Converts from an entity model/schema to elasticsearch oriented schema.
+
+ Returns: dict
+ Raises exception on error (never returns None)
+ """
+
+ if entity.state in ('redirect', 'deleted'):
+ return dict(
+ ident = entity.ident,
+ state = entity.state,
+ )
+ elif entity.state != 'active':
+ raise ValueError("Unhandled entity state: {}".format(entity.state))
+
+ # First, the easy ones (direct copy)
+ t = dict(
+ ident = entity.ident,
+ state = entity.state,
+ revision = entity.revision,
+ release_ids = entity.release_ids,
+ release_count = len(entity.release_ids),
+ mimetype = entity.mimetype,
+ size_bytes = entity.size,
+ sha1 = entity.sha1,
+ sha256 = entity.sha256,
+ md5 = entity.md5,
+ )
+
+ parsed_urls = [tldextract.extract(u.url) for u in entity.urls]
+ t['hosts'] = list(set(['.'.join([seg for seg in pu if seg]) for pu in parsed_urls]))
+ t['domains'] = list(set([pu.registered_domain for pu in parsed_urls]))
+ t['rels'] = list(set([u.rel for u in entity.urls]))
+
+ t['in_ia'] = bool('archive.org' in t['domains'])
+ t['in_ia_petabox'] = bool('archive.org' in t['hosts'])
+
return t