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-rw-r--r--python/fatcat_tools/api_auth.py12
-rw-r--r--python/fatcat_tools/importers/arabesque.py16
-rw-r--r--python/fatcat_tools/importers/arxiv.py22
-rwxr-xr-xpython/fatcat_tools/importers/cdl_dash_dat.py6
-rw-r--r--python/fatcat_tools/importers/chocula.py12
-rw-r--r--python/fatcat_tools/importers/common.py6
-rw-r--r--python/fatcat_tools/importers/crossref.py20
-rw-r--r--python/fatcat_tools/importers/grobid_metadata.py24
-rw-r--r--python/fatcat_tools/importers/jalc.py16
-rw-r--r--python/fatcat_tools/importers/journal_metadata.py10
-rw-r--r--python/fatcat_tools/importers/jstor.py18
-rw-r--r--python/fatcat_tools/importers/matched.py18
-rw-r--r--python/fatcat_tools/importers/orcid.py10
-rw-r--r--python/fatcat_tools/importers/pubmed.py32
-rwxr-xr-xpython/fatcat_tools/importers/wayback_static.py2
-rw-r--r--python/fatcat_tools/reviewers/review_common.py6
-rw-r--r--python/fatcat_tools/transforms/csl.py2
-rw-r--r--python/fatcat_tools/transforms/elasticsearch.py2
-rw-r--r--python/fatcat_tools/transforms/entities.py2
-rw-r--r--python/fatcat_tools/workers/elasticsearch.py2
-rw-r--r--python/fatcat_tools/workers/worker_common.py4
21 files changed, 121 insertions, 121 deletions
diff --git a/python/fatcat_tools/api_auth.py b/python/fatcat_tools/api_auth.py
index 3c643cea..add03399 100644
--- a/python/fatcat_tools/api_auth.py
+++ b/python/fatcat_tools/api_auth.py
@@ -1,7 +1,7 @@
import os, sys
-import fatcat_client
-from fatcat_client.rest import ApiException
+import fatcat_openapi_client
+from fatcat_openapi_client.rest import ApiException
def public_api(host_uri):
@@ -10,9 +10,9 @@ def public_api(host_uri):
if the API isn't going to be used, so it's important that it doesn't try to
actually connect to the API host or something.
"""
- conf = fatcat_client.Configuration()
+ conf = fatcat_openapi_client.Configuration()
conf.host = host_uri
- return fatcat_client.DefaultApi(fatcat_client.ApiClient(conf))
+ return fatcat_openapi_client.DefaultApi(fatcat_openapi_client.ApiClient(conf))
def authenticated_api(host_uri, token=None):
"""
@@ -20,7 +20,7 @@ def authenticated_api(host_uri, token=None):
is needed, so it does try to connect and verify credentials.
"""
- conf = fatcat_client.Configuration()
+ conf = fatcat_openapi_client.Configuration()
conf.host = host_uri
if not token:
token = os.environ['FATCAT_API_AUTH_TOKEN']
@@ -31,7 +31,7 @@ def authenticated_api(host_uri, token=None):
conf.api_key["Authorization"] = token
conf.api_key_prefix["Authorization"] = "Bearer"
- api = fatcat_client.DefaultApi(fatcat_client.ApiClient(conf))
+ api = fatcat_openapi_client.DefaultApi(fatcat_openapi_client.ApiClient(conf))
# verify up front that auth is working
api.auth_check()
diff --git a/python/fatcat_tools/importers/arabesque.py b/python/fatcat_tools/importers/arabesque.py
index e9376d96..65597d5c 100644
--- a/python/fatcat_tools/importers/arabesque.py
+++ b/python/fatcat_tools/importers/arabesque.py
@@ -4,7 +4,7 @@ import json
import base64
import sqlite3
import itertools
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean, make_rel_url, SANE_MAX_RELEASES, SANE_MAX_URLS
@@ -105,7 +105,7 @@ class ArabesqueMatchImporter(EntityImporter):
# lookup extid
try:
re = self.api.lookup_release(**{self.extid_type: extid})
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status == 404:
# bail on 404 (release not in DB)
self.counts['skip-extid-not-found'] += 1
@@ -128,13 +128,13 @@ class ArabesqueMatchImporter(EntityImporter):
row['final_url'])
urls = [url, ("webarchive", wayback)]
- urls = [fatcat_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
+ urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
if len(urls) > SANE_MAX_URLS:
self.counts['skip-too-many-url'] += 1
return None
- fe = fatcat_client.FileEntity(
+ fe = fatcat_openapi_client.FileEntity(
sha1=b32_hex(row['final_sha1']),
mimetype=row['final_mimetype'] or self.default_mimetype,
release_ids=[re.ident],
@@ -147,7 +147,7 @@ class ArabesqueMatchImporter(EntityImporter):
existing = None
try:
existing = self.api.lookup_file(sha1=fe.sha1)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
@@ -177,7 +177,7 @@ class ArabesqueMatchImporter(EntityImporter):
# merge the existing into this one and update
existing.urls = list(set([(u.rel, u.url) for u in fe.urls + existing.urls]))
- existing.urls = [fatcat_client.FileUrl(rel=rel, url=url) for (rel, url) in existing.urls]
+ existing.urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in existing.urls]
if len(existing.urls) > SANE_MAX_URLS:
self.counts['skip-update-too-many-url'] += 1
return None
@@ -192,8 +192,8 @@ class ArabesqueMatchImporter(EntityImporter):
return False
def insert_batch(self, batch):
- self.api.create_file_auto_batch(fatcat_client.FileAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ 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))
diff --git a/python/fatcat_tools/importers/arxiv.py b/python/fatcat_tools/importers/arxiv.py
index 71b2d134..c69ee16a 100644
--- a/python/fatcat_tools/importers/arxiv.py
+++ b/python/fatcat_tools/importers/arxiv.py
@@ -6,7 +6,7 @@ import datetime
from bs4 import BeautifulSoup
from pylatexenc.latex2text import LatexNodes2Text
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean
from .crossref import lookup_license_slug
@@ -120,7 +120,7 @@ class ArxivRawImporter(EntityImporter):
doi = None
title = latex_to_text(metadata.title.string)
authors = parse_arxiv_authors(metadata.authors.string)
- contribs = [fatcat_client.ReleaseContrib(index=i, raw_name=a, role='author') for i, a in enumerate(authors)]
+ contribs = [fatcat_openapi_client.ReleaseContrib(index=i, raw_name=a, role='author') for i, a in enumerate(authors)]
lang = "en" # the vast majority in english
if metadata.comments and metadata.comments.string:
@@ -178,12 +178,12 @@ class ArxivRawImporter(EntityImporter):
if '$' in abst or '{' in abst:
mime = "application/x-latex"
abst_plain = latex_to_text(abst)
- abstracts.append(fatcat_client.ReleaseAbstract(content=abst_plain, mimetype="text/plain", lang="en"))
+ abstracts.append(fatcat_openapi_client.ReleaseAbstract(content=abst_plain, mimetype="text/plain", lang="en"))
else:
mime = "text/plain"
- abstracts.append(fatcat_client.ReleaseAbstract(content=abst, mimetype=mime, lang="en"))
+ abstracts.append(fatcat_openapi_client.ReleaseAbstract(content=abst, mimetype=mime, lang="en"))
if orig:
- abstracts.append(fatcat_client.ReleaseAbstract(content=orig, mimetype=mime))
+ abstracts.append(fatcat_openapi_client.ReleaseAbstract(content=orig, mimetype=mime))
# indicates that fulltext probably isn't english either
if lang == 'en':
lang = None
@@ -207,7 +207,7 @@ class ArxivRawImporter(EntityImporter):
release_date = version.date.string.strip()
release_date = datetime.datetime.strptime(release_date, "%a, %d %b %Y %H:%M:%S %Z").date()
# TODO: source_type?
- versions.append(fatcat_client.ReleaseEntity(
+ versions.append(fatcat_openapi_client.ReleaseEntity(
work_id=None,
title=title,
#original_title
@@ -216,7 +216,7 @@ class ArxivRawImporter(EntityImporter):
release_stage='submitted',
release_date=release_date.isoformat(),
release_year=release_date.year,
- ext_ids=fatcat_client.ReleaseExtIds(
+ ext_ids=fatcat_openapi_client.ReleaseExtIds(
arxiv=arxiv_id,
),
number=number,
@@ -270,7 +270,7 @@ class ArxivRawImporter(EntityImporter):
existing_doi = None
try:
existing = self.api.lookup_release(arxiv=v.ext_ids.arxiv)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
@@ -281,7 +281,7 @@ class ArxivRawImporter(EntityImporter):
if v.ext_ids.doi:
try:
existing_doi = self.api.lookup_release(doi=v.ext_ids.doi)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
if existing_doi:
@@ -325,8 +325,8 @@ class ArxivRawImporter(EntityImporter):
# there is no batch/bezerk mode for arxiv importer, except for testing
if self._test_override:
for batch in batch_batch:
- self.api.create_release_auto_batch(fatcat_client.ReleaseAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ self.api.create_release_auto_batch(fatcat_openapi_client.ReleaseAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
diff --git a/python/fatcat_tools/importers/cdl_dash_dat.py b/python/fatcat_tools/importers/cdl_dash_dat.py
index aa7fab2b..536c013b 100755
--- a/python/fatcat_tools/importers/cdl_dash_dat.py
+++ b/python/fatcat_tools/importers/cdl_dash_dat.py
@@ -9,8 +9,8 @@ import hashlib
import mimetypes
import subprocess
-import fatcat_client
-from fatcat_client import *
+import fatcat_openapi_client
+from fatcat_openapi_client import *
from .common import clean
from .crossref import lookup_license_slug
@@ -176,7 +176,7 @@ def auto_cdl_dash_dat(api, dat_path, release_id=None, editgroup_id=None):
try:
r = api.lookup_release(doi=release.ext_ids.doi)
release_id = r.ident
- except fatcat_client.rest.ApiException:
+ except fatcat_openapi_client.rest.ApiException:
pass
if not release_id:
edit = api.create_release(eg.editgroup_id, release)
diff --git a/python/fatcat_tools/importers/chocula.py b/python/fatcat_tools/importers/chocula.py
index d7044ff4..6915ba98 100644
--- a/python/fatcat_tools/importers/chocula.py
+++ b/python/fatcat_tools/importers/chocula.py
@@ -2,7 +2,7 @@
import sys
import json
import itertools
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean
@@ -66,7 +66,7 @@ class ChoculaImporter(EntityImporter):
elif 'journal ' in name.lower():
container_type = 'journal'
- ce = fatcat_client.ContainerEntity(
+ ce = fatcat_openapi_client.ContainerEntity(
issnl=row['issnl'],
ident=row['ident'],
name=name,
@@ -82,7 +82,7 @@ class ChoculaImporter(EntityImporter):
if ce.ident:
try:
existing = self.api.get_container(ce.ident)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
self.counts['exists'] += 1
@@ -97,7 +97,7 @@ class ChoculaImporter(EntityImporter):
# check if existing by ISSN-L
try:
existing = self.api.lookup_container(issnl=ce.issnl)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
if existing:
@@ -157,8 +157,8 @@ class ChoculaImporter(EntityImporter):
raise NotImplementedError
def insert_batch(self, batch):
- self.api.create_container_auto_batch(fatcat_client.ContainerAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ self.api.create_container_auto_batch(fatcat_openapi_client.ContainerAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py
index 2f677be4..093569e1 100644
--- a/python/fatcat_tools/importers/common.py
+++ b/python/fatcat_tools/importers/common.py
@@ -13,8 +13,8 @@ import xml.etree.ElementTree as ET
import pykafka
from bs4 import BeautifulSoup
-import fatcat_client
-from fatcat_client.rest import ApiException
+import fatcat_openapi_client
+from fatcat_openapi_client.rest import ApiException
DATE_FMT = "%Y-%m-%d"
@@ -337,7 +337,7 @@ class EntityImporter:
if not self._editgroup_id:
eg = self.api.create_editgroup(
- fatcat_client.Editgroup(
+ fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra))
self._editgroup_id = eg.editgroup_id
diff --git a/python/fatcat_tools/importers/crossref.py b/python/fatcat_tools/importers/crossref.py
index 4074dfb8..faee6aac 100644
--- a/python/fatcat_tools/importers/crossref.py
+++ b/python/fatcat_tools/importers/crossref.py
@@ -5,7 +5,7 @@ import sqlite3
import datetime
import itertools
import subprocess
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean
@@ -215,7 +215,7 @@ class CrossrefImporter(EntityImporter):
extra = None
assert ctype in ("author", "editor", "translator")
raw_name = clean(raw_name)
- contribs.append(fatcat_client.ReleaseContrib(
+ contribs.append(fatcat_openapi_client.ReleaseContrib(
creator_id=creator_id,
index=index,
raw_name=raw_name,
@@ -244,7 +244,7 @@ class CrossrefImporter(EntityImporter):
container_name = None
if (container_id is None and self.create_containers and (issnl is not None)
and container_name):
- ce = fatcat_client.ContainerEntity(
+ ce = fatcat_openapi_client.ContainerEntity(
issnl=issnl,
publisher=publisher,
container_type=self.map_container_type(release_type),
@@ -300,7 +300,7 @@ class CrossrefImporter(EntityImporter):
ref_extra[k] = clean(rm[k])
if not ref_extra:
ref_extra = None
- refs.append(fatcat_client.ReleaseRef(
+ refs.append(fatcat_openapi_client.ReleaseRef(
index=i,
# doing lookups would be a second import pass
target_release_id=None,
@@ -316,7 +316,7 @@ class CrossrefImporter(EntityImporter):
abstracts = []
abstract = clean(obj.get('abstract'))
if abstract and len(abstract) > 10:
- abstracts.append(fatcat_client.ReleaseAbstract(
+ abstracts.append(fatcat_openapi_client.ReleaseAbstract(
mimetype="application/xml+jats",
content=abstract))
@@ -420,7 +420,7 @@ class CrossrefImporter(EntityImporter):
if not extra:
extra = None
- re = fatcat_client.ReleaseEntity(
+ re = fatcat_openapi_client.ReleaseEntity(
work_id=None,
container_id=container_id,
title=title,
@@ -431,7 +431,7 @@ class CrossrefImporter(EntityImporter):
release_date=release_date,
release_year=release_year,
publisher=publisher,
- ext_ids=fatcat_client.ReleaseExtIds(
+ ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=obj['DOI'].lower(),
pmid=extids['pmid'],
pmcid=extids['pmcid'],
@@ -459,7 +459,7 @@ class CrossrefImporter(EntityImporter):
existing = None
try:
existing = self.api.lookup_release(doi=re.ext_ids.doi)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
# doesn't exist, need to update
@@ -474,8 +474,8 @@ class CrossrefImporter(EntityImporter):
return True
def insert_batch(self, batch):
- self.api.create_release_auto_batch(fatcat_client.ReleaseAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ self.api.create_release_auto_batch(fatcat_openapi_client.ReleaseAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
diff --git a/python/fatcat_tools/importers/grobid_metadata.py b/python/fatcat_tools/importers/grobid_metadata.py
index ea627dd6..2077eae4 100644
--- a/python/fatcat_tools/importers/grobid_metadata.py
+++ b/python/fatcat_tools/importers/grobid_metadata.py
@@ -4,7 +4,7 @@ import sys
import json
import base64
import datetime
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean, make_rel_url
MAX_ABSTRACT_BYTES=4096
@@ -56,7 +56,7 @@ class GrobidMetadataImporter(EntityImporter):
existing = None
try:
existing = self.api.lookup_file(sha1=fe.sha1)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
@@ -82,7 +82,7 @@ class GrobidMetadataImporter(EntityImporter):
abstract = obj.get('abstract')
if abstract and len(abstract) < MAX_ABSTRACT_BYTES and len(abstract) > 10:
- abobj = fatcat_client.ReleaseAbstract(
+ abobj = fatcat_openapi_client.ReleaseAbstract(
mimetype="text/plain",
content=clean(obj.get('abstract')))
abstracts = [abobj]
@@ -91,7 +91,7 @@ class GrobidMetadataImporter(EntityImporter):
contribs = []
for i, a in enumerate(obj.get('authors', [])):
- contribs.append(fatcat_client.ReleaseContrib(
+ contribs.append(fatcat_openapi_client.ReleaseContrib(
index=i,
raw_name=clean(a['name']),
given_name=clean(a.get('given_name')),
@@ -116,7 +116,7 @@ class GrobidMetadataImporter(EntityImporter):
if not cite_extra:
cite_extra = None
- refs.append(fatcat_client.ReleaseRef(
+ refs.append(fatcat_openapi_client.ReleaseRef(
key=clean(raw.get('id')),
year=year,
title=clean(raw['title']),
@@ -147,7 +147,7 @@ class GrobidMetadataImporter(EntityImporter):
if not title or len(title) < 2:
return None
- re = fatcat_client.ReleaseEntity(
+ re = fatcat_openapi_client.ReleaseEntity(
title=title,
release_type="article-journal",
release_date=release_date,
@@ -158,7 +158,7 @@ class GrobidMetadataImporter(EntityImporter):
volume=clean(obj['journal'].get('volume')),
issue=clean(obj['journal'].get('issue')),
abstracts=abstracts,
- ext_ids=fatcat_client.ReleaseExtIds(),
+ ext_ids=fatcat_openapi_client.ReleaseExtIds(),
extra=extra)
return re
@@ -166,7 +166,7 @@ class GrobidMetadataImporter(EntityImporter):
sha1 = base64.b16encode(base64.b32decode(sha1_key.replace('sha1:', ''))).decode('ascii').lower()
- fe = fatcat_client.FileEntity(
+ fe = fatcat_openapi_client.FileEntity(
sha1=sha1,
size=int(file_size),
mimetype=mimetype,
@@ -181,10 +181,10 @@ class GrobidMetadataImporter(EntityImporter):
cdx['dt'],
original)
fe.urls.append(
- fatcat_client.FileUrl(url=wayback, rel="webarchive"))
+ fatcat_openapi_client.FileUrl(url=wayback, rel="webarchive"))
original_url = make_rel_url(original, default_link_rel=self.default_link_rel)
if original_url is not None:
- fe.urls.append(fatcat_client.FileUrl(rel=original_url[0], url=original_url[1]))
+ fe.urls.append(fatcat_openapi_client.FileUrl(rel=original_url[0], url=original_url[1]))
return fe
@@ -193,8 +193,8 @@ class GrobidMetadataImporter(EntityImporter):
return True
def insert_batch(self, batch):
- self.api.create_file_auto_batch(fatcat_client.FileAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ 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))
diff --git a/python/fatcat_tools/importers/jalc.py b/python/fatcat_tools/importers/jalc.py
index c1c13bb7..a0e0086b 100644
--- a/python/fatcat_tools/importers/jalc.py
+++ b/python/fatcat_tools/importers/jalc.py
@@ -7,7 +7,7 @@ import itertools
import subprocess
from bs4 import BeautifulSoup
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean, is_cjk, DATE_FMT
@@ -48,7 +48,7 @@ def parse_jalc_persons(raw_persons):
if lang == 'en' and surname and given_name:
# english names order is flipped
name = "{} {}".format(given_name, surname)
- rc = fatcat_client.ReleaseContrib(
+ rc = fatcat_openapi_client.ReleaseContrib(
raw_name=name,
surname=surname,
given_name=given_name,
@@ -269,7 +269,7 @@ class JalcImporter(EntityImporter):
# extra: issnp, issne, original_name, languages, country
container_extra['country'] = 'jp'
container_extra['languages'] = ['ja']
- ce = fatcat_client.ContainerEntity(
+ ce = fatcat_openapi_client.ContainerEntity(
name=container_name,
container_type='journal',
publisher=publisher,
@@ -303,7 +303,7 @@ class JalcImporter(EntityImporter):
if not title:
return None
- re = fatcat_client.ReleaseEntity(
+ re = fatcat_openapi_client.ReleaseEntity(
work_id=None,
title=title,
original_title=clean(original_title),
@@ -311,7 +311,7 @@ class JalcImporter(EntityImporter):
release_stage='published',
release_date=release_date,
release_year=release_year,
- ext_ids=fatcat_client.ReleaseExtIds(
+ ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=doi,
pmid=extids['pmid'],
pmcid=extids['pmcid'],
@@ -338,7 +338,7 @@ class JalcImporter(EntityImporter):
existing = None
try:
existing = self.api.lookup_release(doi=re.ext_ids.doi)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
# doesn't exist, need to insert
@@ -353,8 +353,8 @@ class JalcImporter(EntityImporter):
return True
def insert_batch(self, batch):
- self.api.create_release_auto_batch(fatcat_client.ReleaseAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ self.api.create_release_auto_batch(fatcat_openapi_client.ReleaseAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
diff --git a/python/fatcat_tools/importers/journal_metadata.py b/python/fatcat_tools/importers/journal_metadata.py
index d24b4103..d439c80a 100644
--- a/python/fatcat_tools/importers/journal_metadata.py
+++ b/python/fatcat_tools/importers/journal_metadata.py
@@ -2,7 +2,7 @@
import sys
import json
import itertools
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean
@@ -93,7 +93,7 @@ class JournalMetadataImporter(EntityImporter):
if not name:
return None
- ce = fatcat_client.ContainerEntity(
+ ce = fatcat_openapi_client.ContainerEntity(
issnl=row['issnl'],
container_type=None, # TODO
name=name,
@@ -107,7 +107,7 @@ class JournalMetadataImporter(EntityImporter):
existing = None
try:
existing = self.api.lookup_container(issnl=ce.issnl)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
@@ -133,8 +133,8 @@ class JournalMetadataImporter(EntityImporter):
raise NotImplementedError
def insert_batch(self, batch):
- self.api.create_container_auto_batch(fatcat_client.ContainerAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ self.api.create_container_auto_batch(fatcat_openapi_client.ContainerAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
diff --git a/python/fatcat_tools/importers/jstor.py b/python/fatcat_tools/importers/jstor.py
index 5016e813..5ff1ecd9 100644
--- a/python/fatcat_tools/importers/jstor.py
+++ b/python/fatcat_tools/importers/jstor.py
@@ -5,7 +5,7 @@ import datetime
import warnings
from bs4 import BeautifulSoup
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean, LANG_MAP_MARC
from .crossref import CONTAINER_TYPE_MAP
@@ -114,7 +114,7 @@ class JstorImporter(EntityImporter):
# create container if it doesn't exist
if (container_id is None and self.create_containers and (issnl is not None)
and journal_title):
- ce = fatcat_client.ContainerEntity(
+ ce = fatcat_openapi_client.ContainerEntity(
issnl=issnl,
publisher=publisher,
container_type=self.map_container_type(release_type),
@@ -158,7 +158,7 @@ class JstorImporter(EntityImporter):
role = JSTOR_CONTRIB_MAP.get(c.get('contrib-type', 'author'))
if not role and c.get('contrib-type'):
sys.stderr.write("NOT IN JSTOR_CONTRIB_MAP: {}\n".format(c['contrib-type']))
- contribs.append(fatcat_client.ReleaseContrib(
+ contribs.append(fatcat_openapi_client.ReleaseContrib(
role=role,
raw_name=raw_name,
given_name=given,
@@ -228,7 +228,7 @@ class JstorImporter(EntityImporter):
if not extra:
extra = None
- re = fatcat_client.ReleaseEntity(
+ re = fatcat_openapi_client.ReleaseEntity(
#work_id
title=title,
#original_title
@@ -236,7 +236,7 @@ class JstorImporter(EntityImporter):
release_stage=release_stage,
release_date=release_date,
release_year=release_year,
- ext_ids=fatcat_client.ReleaseExtIds(
+ ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=doi,
jstor=jstor_id,
),
@@ -270,7 +270,7 @@ class JstorImporter(EntityImporter):
existing = None
try:
existing = self.api.lookup_release(jstor=re.ext_ids.jstor)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
@@ -282,7 +282,7 @@ class JstorImporter(EntityImporter):
doi = "10.2307/{}".format(re.ext_ids.jstor)
try:
existing = self.api.lookup_release(doi=doi)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
@@ -309,8 +309,8 @@ class JstorImporter(EntityImporter):
return True
def insert_batch(self, batch):
- self.api.create_release_auto_batch(fatcat_client.ReleaseAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ self.api.create_release_auto_batch(fatcat_openapi_client.ReleaseAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
diff --git a/python/fatcat_tools/importers/matched.py b/python/fatcat_tools/importers/matched.py
index a94584cd..dbb78ec9 100644
--- a/python/fatcat_tools/importers/matched.py
+++ b/python/fatcat_tools/importers/matched.py
@@ -3,7 +3,7 @@ import sys
import json
import sqlite3
import itertools
-import fatcat_client
+import fatcat_openapi_client
from fatcat_tools.normal import *
from .common import EntityImporter, clean, make_rel_url, SANE_MAX_RELEASES, SANE_MAX_URLS
@@ -61,7 +61,7 @@ class MatchedImporter(EntityImporter):
return None
try:
re = self.api.lookup_release(doi=doi)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
@@ -77,7 +77,7 @@ class MatchedImporter(EntityImporter):
if extid:
try:
re = self.api.lookup_release(**{extid_type: extid})
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
@@ -110,7 +110,7 @@ class MatchedImporter(EntityImporter):
url = make_rel_url(original, default_link_rel=self.default_link_rel)
if url != None:
urls.add(url)
- urls = [fatcat_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
+ urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
if len(urls) == 0:
self.counts['skip-no-urls'] += 1
return None
@@ -127,7 +127,7 @@ class MatchedImporter(EntityImporter):
if urls[0].url.endswith('.pdf'):
mimetype = 'application/pdf'
- fe = fatcat_client.FileEntity(
+ fe = fatcat_openapi_client.FileEntity(
md5=obj.get('md5'),
sha1=obj['sha1'],
sha256=obj.get('sha256'),
@@ -143,7 +143,7 @@ class MatchedImporter(EntityImporter):
existing = None
try:
existing = self.api.lookup_file(sha1=fe.sha1)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
@@ -183,7 +183,7 @@ class MatchedImporter(EntityImporter):
# merge the existing into this one and update
existing.urls = list(set([(u.rel, u.url) for u in fe.urls + existing.urls]))
- existing.urls = [fatcat_client.FileUrl(rel=rel, url=url) for (rel, url) in existing.urls]
+ existing.urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in existing.urls]
if len(existing.urls) > SANE_MAX_URLS:
self.counts['skip-update-too-many-url'] += 1
@@ -203,8 +203,8 @@ class MatchedImporter(EntityImporter):
return False
def insert_batch(self, batch):
- self.api.create_file_auto_batch(fatcat_client.FileAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ 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))
diff --git a/python/fatcat_tools/importers/orcid.py b/python/fatcat_tools/importers/orcid.py
index 0bdd5d19..0a2c8610 100644
--- a/python/fatcat_tools/importers/orcid.py
+++ b/python/fatcat_tools/importers/orcid.py
@@ -2,7 +2,7 @@
import sys
import json
import itertools
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean
def value_or_none(e):
@@ -64,7 +64,7 @@ class OrcidImporter(EntityImporter):
if not display:
# must have *some* name
return None
- ce = fatcat_client.CreatorEntity(
+ ce = fatcat_openapi_client.CreatorEntity(
orcid=orcid,
given_name=clean(given),
surname=clean(sur),
@@ -76,7 +76,7 @@ class OrcidImporter(EntityImporter):
existing = None
try:
existing = self.api.lookup_creator(orcid=raw_record.orcid)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
@@ -89,8 +89,8 @@ class OrcidImporter(EntityImporter):
return True
def insert_batch(self, batch):
- self.api.create_creator_auto_batch(fatcat_client.CreatorAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ self.api.create_creator_auto_batch(fatcat_openapi_client.CreatorAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py
index 4bfbbc79..80cf986c 100644
--- a/python/fatcat_tools/importers/pubmed.py
+++ b/python/fatcat_tools/importers/pubmed.py
@@ -7,7 +7,7 @@ import warnings
from bs4 import BeautifulSoup
from bs4.element import NavigableString
-import fatcat_client
+import fatcat_openapi_client
from .common import EntityImporter, clean, LANG_MAP_MARC
# from: https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T.publication_types/?report=objectonly
@@ -508,7 +508,7 @@ class PubmedImporter(EntityImporter):
and container_name):
# name, type, publisher, issnl
# extra: issnp, issne, original_name, languages, country
- ce = fatcat_client.ContainerEntity(
+ ce = fatcat_openapi_client.ContainerEntity(
name=container_name,
container_type='journal',
#NOTE: publisher not included
@@ -532,7 +532,7 @@ class PubmedImporter(EntityImporter):
primary_abstract = medline.find("Abstract")
if primary_abstract and primary_abstract.AbstractText.get('NlmCategory'):
joined = "\n".join([m.get_text() for m in primary_abstract.find_all("AbstractText")])
- abst = fatcat_client.ReleaseAbstract(
+ abst = fatcat_openapi_client.ReleaseAbstract(
content=joined,
mimetype="text/plain",
lang="en",
@@ -541,7 +541,7 @@ class PubmedImporter(EntityImporter):
abstracts.append(abst)
elif primary_abstract:
for abstract in primary_abstract.find_all("AbstractText"):
- abst = fatcat_client.ReleaseAbstract(
+ abst = fatcat_openapi_client.ReleaseAbstract(
content=abstract.get_text().strip(),
mimetype="text/plain",
lang="en",
@@ -549,7 +549,7 @@ class PubmedImporter(EntityImporter):
if abst.content:
abstracts.append(abst)
if abstract.find('math'):
- abst = fatcat_client.ReleaseAbstract(
+ abst = fatcat_openapi_client.ReleaseAbstract(
# strip the <AbstractText> tags
content=str(abstract)[14:-15],
mimetype="application/mathml+xml",
@@ -562,7 +562,7 @@ class PubmedImporter(EntityImporter):
lang = "en"
if other.get('Language'):
lang = LANG_MAP_MARC.get(other['Language'])
- abst = fatcat_client.ReleaseAbstract(
+ abst = fatcat_openapi_client.ReleaseAbstract(
content=other.AbstractText.get_text().strip(),
mimetype="text/plain",
lang=lang,
@@ -617,7 +617,7 @@ class PubmedImporter(EntityImporter):
if author.find("EqualContrib"):
# TODO: schema for this?
contrib_extra['equal'] = True
- contribs.append(fatcat_client.ReleaseContrib(
+ contribs.append(fatcat_openapi_client.ReleaseContrib(
raw_name=raw_name,
given_name=given_name,
surname=surname,
@@ -628,7 +628,7 @@ class PubmedImporter(EntityImporter):
))
if medline.AuthorList['CompleteYN'] == 'N':
- contribs.append(fatcat_client.ReleaseContrib(raw_name="et al."))
+ contribs.append(fatcat_openapi_client.ReleaseContrib(raw_name="et al."))
for i, contrib in enumerate(contribs):
if contrib.raw_name != "et al.":
@@ -659,7 +659,7 @@ class PubmedImporter(EntityImporter):
ref_extra['unstructured'] = ref_raw.string
if not ref_extra:
ref_extra = None
- refs.append(fatcat_client.ReleaseRef(
+ refs.append(fatcat_openapi_client.ReleaseRef(
target_release_id=ref_release_id,
extra=ref_extra,
))
@@ -682,7 +682,7 @@ class PubmedImporter(EntityImporter):
if not title:
return None
- re = fatcat_client.ReleaseEntity(
+ re = fatcat_openapi_client.ReleaseEntity(
work_id=None,
title=title,
original_title=clean(original_title),
@@ -691,7 +691,7 @@ class PubmedImporter(EntityImporter):
release_date=release_date,
release_year=release_year,
withdrawn_status=withdrawn_status,
- ext_ids=fatcat_client.ReleaseExtIds(
+ ext_ids=fatcat_openapi_client.ReleaseExtIds(
doi=doi,
pmid=pmid,
pmcid=pmcid,
@@ -717,7 +717,7 @@ class PubmedImporter(EntityImporter):
existing = None
try:
existing = self.api.lookup_release(pmid=re.ext_ids.pmid)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
@@ -725,7 +725,7 @@ class PubmedImporter(EntityImporter):
if not existing and re.ext_ids.doi:
try:
existing = self.api.lookup_release(doi=re.ext_ids.doi)
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
if existing and existing.ext_ids.pmid and existing.ext_ids.pmid != re.ext_ids.pmid:
@@ -751,7 +751,7 @@ class PubmedImporter(EntityImporter):
try:
self.api.update_release(self.get_editgroup_id(), existing.ident, existing)
self.counts['update'] += 1
- except fatcat_client.rest.ApiException as err:
+ except fatcat_openapi_client.rest.ApiException as err:
# there is a code path where we try to update the same release
# twice in a row; if that happens, just skip
# NOTE: API behavior might change in the future?
@@ -765,8 +765,8 @@ class PubmedImporter(EntityImporter):
return True
def insert_batch(self, batch):
- self.api.create_release_auto_batch(fatcat_client.ReleaseAutoBatch(
- editgroup=fatcat_client.Editgroup(
+ self.api.create_release_auto_batch(fatcat_openapi_client.ReleaseAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
diff --git a/python/fatcat_tools/importers/wayback_static.py b/python/fatcat_tools/importers/wayback_static.py
index 2125017a..fa0bd4ef 100755
--- a/python/fatcat_tools/importers/wayback_static.py
+++ b/python/fatcat_tools/importers/wayback_static.py
@@ -16,7 +16,7 @@ import argparse
import subprocess
from bs4 import BeautifulSoup
-from fatcat_client import *
+from fatcat_openapi_client import *
CDX_API_BASE = "https://web.archive.org/cdx/search/cdx"
GWB_URL_BASE = "https://web.archive.org/web"
diff --git a/python/fatcat_tools/reviewers/review_common.py b/python/fatcat_tools/reviewers/review_common.py
index bb36d4e3..ecf7da8f 100644
--- a/python/fatcat_tools/reviewers/review_common.py
+++ b/python/fatcat_tools/reviewers/review_common.py
@@ -5,8 +5,8 @@ import datetime
import subprocess
from collections import Counter
-import fatcat_client
-from fatcat_client.rest import ApiException
+import fatcat_openapi_client
+from fatcat_openapi_client.rest import ApiException
"""
checks should return:
@@ -146,7 +146,7 @@ class ReviewBot:
"checks": [check.name for check in self.checks],
"result_counts": dict(result_counts),
})
- annotation = fatcat_client.EditgroupAnnotation(
+ annotation = fatcat_openapi_client.EditgroupAnnotation(
comment_markdown=comment,
editgroup_id=editgroup.editgroup_id,
extra=extra,
diff --git a/python/fatcat_tools/transforms/csl.py b/python/fatcat_tools/transforms/csl.py
index f94fa372..7ab94cac 100644
--- a/python/fatcat_tools/transforms/csl.py
+++ b/python/fatcat_tools/transforms/csl.py
@@ -8,7 +8,7 @@ from citeproc import formatter
from citeproc.source.json import CiteProcJSON
from citeproc_styles import get_style_filepath
-from fatcat_client import ApiClient
+from fatcat_openapi_client import ApiClient
def contribs_by_role(contribs, role):
diff --git a/python/fatcat_tools/transforms/elasticsearch.py b/python/fatcat_tools/transforms/elasticsearch.py
index 303d56a9..3a53db4d 100644
--- a/python/fatcat_tools/transforms/elasticsearch.py
+++ b/python/fatcat_tools/transforms/elasticsearch.py
@@ -1,7 +1,7 @@
import collections
-from fatcat_client import ApiClient
+from fatcat_openapi_client import ApiClient
def check_kbart(year, archive):
diff --git a/python/fatcat_tools/transforms/entities.py b/python/fatcat_tools/transforms/entities.py
index b67df12d..8e5de286 100644
--- a/python/fatcat_tools/transforms/entities.py
+++ b/python/fatcat_tools/transforms/entities.py
@@ -1,7 +1,7 @@
import collections
-from fatcat_client import ApiClient
+from fatcat_openapi_client import ApiClient
def entity_to_dict(entity, api_client=None):
"""
diff --git a/python/fatcat_tools/workers/elasticsearch.py b/python/fatcat_tools/workers/elasticsearch.py
index a91b5098..91224d98 100644
--- a/python/fatcat_tools/workers/elasticsearch.py
+++ b/python/fatcat_tools/workers/elasticsearch.py
@@ -4,7 +4,7 @@ import time
import requests
from pykafka.common import OffsetType
-from fatcat_client import ReleaseEntity, ContainerEntity, ApiClient
+from fatcat_openapi_client import ReleaseEntity, ContainerEntity, ApiClient
from fatcat_tools import *
from .worker_common import FatcatWorker
diff --git a/python/fatcat_tools/workers/worker_common.py b/python/fatcat_tools/workers/worker_common.py
index cb4e5dab..9ffbe5fd 100644
--- a/python/fatcat_tools/workers/worker_common.py
+++ b/python/fatcat_tools/workers/worker_common.py
@@ -8,8 +8,8 @@ from itertools import islice
from pykafka import KafkaClient
from pykafka.common import OffsetType
-import fatcat_client
-from fatcat_client.rest import ApiException
+import fatcat_openapi_client
+from fatcat_openapi_client.rest import ApiException
def most_recent_message(topic):