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import io
import sys
import sqlite3
import argparse
from typing import List, Dict, Optional, Any
import requests
import internetarchive
from fatcat_scholar.djvu import djvu_extract_leaf_texts
from fatcat_scholar.issue_db import IssueDB
from fatcat_scholar.schema import (
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_item: str, pub_collection: str) -> 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_item)
pub_meta = self.ia_client.get_metadata(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_obj = self.ia_client.get_item(issue_item)
issue_item_djvu = issue_item_obj.get_file(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)
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_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 full_issue_to_pages(self, full_issue: dict) -> List[IntermediateBundle]:
pages = []
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"],
),
)
pages.append(bundle)
return pages
def run_issue_db(self, limit: int = None) -> 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["issue_item"], row["pub_collection"]
)
except requests.exceptions.ConnectionError as e:
print(str(e), file=sys.stderr)
continue
except requests.exceptions.ReadTimeout as e:
print(str(e), file=sys.stderr)
continue
if not full_issue:
continue
pages = self.full_issue_to_pages(full_issue)
for bundle in pages:
print(bundle.json(exclude_none=True, sort_keys=True))
count += 1
if limit is not None and count >= limit:
break
if limit is not None and count >= limit:
break
def main() -> None:
"""
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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