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import os
import io
import sys
import sqlite3
import argparse
import requests
from pydantic import BaseModel, validator
from typing import List, Dict, Tuple, Optional, Any, Sequence
from fatcat_openapi_client import ReleaseEntity, FileEntity
import internetarchive
from fatcat_scholar.api_entities import *
from fatcat_scholar.djvu import djvu_extract_leaf_texts
from fatcat_scholar.sandcrawler import SandcrawlerPostgrestClient, SandcrawlerMinioClient
from fatcat_scholar.issue_db import IssueDB, SimIssueRow
from fatcat_scholar.schema import es_biblio_from_release, es_release_from_release, DocType, IntermediateBundle
def truncate_pub_meta(full: Dict[str, Any]) -> Dict[str, Any]:
"""
Takes a complete archive.org metadata dictionary for a publication
collection, and simplifies it by removing fields. Motivation is to make
intermediate bundle files smaller.
"""
full.pop('files')
if 'ulrichs' in full and full['ulrichs']:
full['ulrichs'][0].pop('reviews_mfl')
full['ulrichs'][0].pop('editorial_description')
# these are interesting, but just too long
full['ulrichs'][0].pop('online_availability_full_text')
full['ulrichs'][0].pop('abstracting_indexing')
full['ulrichs'][0].pop('publisher_and_ordering_details')
return full
def truncate_issue_meta(full: Dict[str, Any]) -> Dict[str, Any]:
"""
Same as truncate_pub_meta() but for issue item metadata
"""
full.pop('files')
return full
class SimPipeline():
def __init__(self, issue_db: IssueDB):
self.issue_db: IssueDB = issue_db
self.ia_client = internetarchive.get_session()
def fetch_sim_issue(self, issue_db_row: Any) -> Optional[Any]:
"""
issue_item
pages: str
page_texts: list
raw_text
page_num
leaf_num
release_ident: Optional[str]
pub_item_metadata
issue_item_metadata
"""
# fetch full metadata from API
issue_meta = self.ia_client.get_metadata(issue_db_row['issue_item'])
pub_meta = self.ia_client.get_metadata(issue_db_row['pub_collection'])
leaf_index = dict()
leaf_list = []
if not 'page_numbers' in issue_meta:
# TODO: warn
return None
for entry in issue_meta['page_numbers'].get('pages', []):
page_num = entry['pageNumber']
leaf_index[entry['leafNum']] = page_num
if not (page_num and page_num.isdigit()):
continue
page_num = int(page_num)
leaf_list.append(entry['leafNum'])
if not leaf_list:
return None
page_texts: List[Dict[str, Any]] = []
issue_item = self.ia_client.get_item(issue_db_row['issue_item'])
issue_item_djvu = issue_item.get_file(issue_db_row['issue_item'] + "_djvu.xml")
# override 'close()' method so we can still read out contents
djvu_bytes = io.BytesIO()
djvu_bytes.close = lambda: None # type: ignore
assert issue_item_djvu.download(fileobj=djvu_bytes) == True
djvu_bytes.seek(0)
djvu_xml = io.StringIO(djvu_bytes.read().decode("UTF-8"))
del(djvu_bytes)
leaf_dict = djvu_extract_leaf_texts(djvu_xml)
for leaf_num, raw_text in leaf_dict.items():
page_texts.append(dict(page_num=leaf_index.get(leaf_num), leaf_num=leaf_num, raw_text=raw_text))
return dict(
issue_item=issue_db_row['issue_item'],
pages=None,
page_texts=page_texts,
release_ident=None,
pub_item_metadata=truncate_pub_meta(pub_meta),
issue_item_metadata=truncate_issue_meta(issue_meta),
)
def run_issue_db(self, limit: int = None):
count = 0
self.issue_db.db.row_factory = sqlite3.Row
cur = self.issue_db.db.cursor()
for row in cur.execute('SELECT * FROM sim_issue LEFT JOIN sim_pub ON sim_issue.sim_pubid = sim_pub.sim_pubid WHERE sim_issue.release_count < 3'):
# filter out "contents" and "index" items
# TODO: more filters; also redundant with IssueDB code?
if row['issue_item'].endswith('_contents') or row['issue_item'].endswith('_index'):
continue
try:
full_issue = self.fetch_sim_issue(row)
except requests.exceptions.ReadTimeout as e:
print(str(e), file=sys.stderr)
continue
if not full_issue:
continue
for leaf in full_issue['page_texts']:
bundle = IntermediateBundle(
doc_type=DocType.sim_page,
releases=[],
biblio_release_ident=None,
grobid_fulltext=None,
pdftotext_fulltext=None,
sim_fulltext=dict(
issue_item=full_issue['issue_item'],
pages=str(leaf['page_num']),
page_texts=[leaf],
release_ident=None,
pub_item_metadata=full_issue['pub_item_metadata'],
issue_item_metadata=full_issue['issue_item_metadata'],
)
)
print(bundle.json())
count += 1
if limit is not None and count >= limit:
break
if limit is not None and count >= limit:
break
def main():
"""
Run this command like:
python -m fatcat_scholar.sim_pipeline
"""
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
subparsers = parser.add_subparsers()
parser.add_argument("--issue-db-file",
help="sqlite3 database file to open",
default='data/issue_db.sqlite',
type=str)
sub = subparsers.add_parser('run_issue_db',
help="iterates through entire IssueDB")
sub.set_defaults(func='run_issue_db')
sub.add_argument("--limit",
help="maximum number of pages to index",
type=int)
args = parser.parse_args()
if not args.__dict__.get("func"):
print("tell me what to do! (try --help)")
sys.exit(-1)
sp = SimPipeline(issue_db=IssueDB(args.issue_db_file))
if args.func == 'run_issue_db':
sp.run_issue_db(limit=args.limit)
else:
func = getattr(sp, args.func)
func()
if __name__=="__main__":
main()
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