wip
This commit is contained in:
parent
ce1c4f88f3
commit
4cc72067e4
|
|
@ -9,10 +9,8 @@ fake = Faker()
|
|||
|
||||
# pip install faker pymongo
|
||||
|
||||
# TODO: number on publicationDetails (random)
|
||||
# TODO: figures (fake)
|
||||
# TODO: inject (fake) figures and references in content
|
||||
# TODO: references are a dictionary
|
||||
|
||||
# - article doi or JSON filename can be used as paper id
|
||||
# - no author id, authors are equal based on name for lack of info
|
||||
|
|
@ -73,14 +71,6 @@ def getProp(obj: dict, props: str, default = None):
|
|||
target = target[prop]
|
||||
return target
|
||||
|
||||
def setProp(obj: dict, props: str, toSave: any):
|
||||
target = obj
|
||||
for prop in props.split("."):
|
||||
if prop not in target:
|
||||
target[prop] = {}
|
||||
target = target[prop]
|
||||
target[prop] = toSave
|
||||
|
||||
def save_sentence(body: dict, parents: [dict], sentence: str):
|
||||
target = body
|
||||
for p in parents:
|
||||
|
|
@ -156,21 +146,33 @@ def json_to_paper(filename: str, jsonObj: dict) -> dict:
|
|||
|
||||
publicationDetails["journal"] = journal["name"]
|
||||
publicationDetails["volume"] = volume
|
||||
|
||||
publicationDetails["number"] = random.randint(1, 99)
|
||||
publicationDetails["date"] = date.isoformat()
|
||||
|
||||
publicationDetails["pages"] = {
|
||||
"start": getProp(jsonObj, "metadata.firstpage"),
|
||||
"end": getProp(jsonObj, "metadata.lastpage")
|
||||
}
|
||||
paper["publicationDetails"] = publicationDetails
|
||||
|
||||
references = {}
|
||||
figures = []
|
||||
for i in range(0, random.randint(3, 15)):
|
||||
figures.push({
|
||||
"page": random.randint(1, 10),
|
||||
"label": "fig" + str(i),
|
||||
"caption": fake.paragraph(nb_sentences=1),
|
||||
"imageURL": fake.image_url()
|
||||
})
|
||||
paper["figures"] = figures
|
||||
|
||||
i = 0
|
||||
references = []
|
||||
for key, value in getProp(jsonObj, "bib_entries", {}).items():
|
||||
i += 1
|
||||
if value is None:
|
||||
continue
|
||||
|
||||
references[key] = {
|
||||
ref = {
|
||||
"referenceNumber": i,
|
||||
"doi": getProp(value, "doi"),
|
||||
"title": getProp(value, "title"),
|
||||
"authors": [],
|
||||
|
|
@ -180,7 +182,8 @@ def json_to_paper(filename: str, jsonObj: dict) -> dict:
|
|||
}
|
||||
|
||||
for author in getProp(value, "authors", []):
|
||||
references[key]["authors"].append({ "name": get_author_name(author) })
|
||||
ref["authors"].append({ "name": get_author_name(author) })
|
||||
references.append(ref)
|
||||
paper["references"] = references
|
||||
|
||||
body = {
|
||||
|
|
@ -231,20 +234,28 @@ def main():
|
|||
paper_ids[paper["doi"]] = x.inserted_id
|
||||
|
||||
i += 1
|
||||
if i % 20 == 0:
|
||||
print("Papers processed: " + i)
|
||||
if i == 10: # TODO: remove
|
||||
if i % 100 == 0:
|
||||
print("Papers processed: ", i)
|
||||
if i == 1000: # TODO: remove
|
||||
break
|
||||
|
||||
i = 0
|
||||
for name, author in authors.items():
|
||||
x = db["authors"].insert_one(author)
|
||||
author_ids[name] = x.inserted_id
|
||||
|
||||
i += 1
|
||||
if i % 1000 == 0:
|
||||
print("Authors processed: ", i)
|
||||
|
||||
i = 0
|
||||
for issn, journal in journals.items():
|
||||
x = db["journals"].insert_one(journal)
|
||||
journal_ids[issn] = x.inserted_id
|
||||
i += 1
|
||||
if i % 100 == 0:
|
||||
print("Journals processed: ", i)
|
||||
|
||||
i = 0
|
||||
for paper in db["papers"].find():
|
||||
mongo_filter = { "_id": paper["_id"] }
|
||||
update = {}
|
||||
|
|
@ -252,30 +263,54 @@ def main():
|
|||
|
||||
issn = getProp(paper, "publicationDetails.issn", "")
|
||||
if issn in journal_ids:
|
||||
setProp(update, "publicationDetails.journalRef", journal_ids[issn])
|
||||
|
||||
for key, ref in getProp(paper, "references", {}).items():
|
||||
update["publicationDetails.journalRef"] = journal_ids[issn]
|
||||
|
||||
references = getProp(paper, "references", [])
|
||||
for ref in references:
|
||||
if ref["doi"] in paper_ids:
|
||||
setProp(update, "references." + key + ".paperId", paper_ids[ref["doi"]])
|
||||
ref["paperId"] = paper_ids[ref["doi"]]
|
||||
|
||||
authors_loc = getProp(ref, "authors", [])
|
||||
for author in authors_loc:
|
||||
for author in ref["authors"]:
|
||||
name = author["name"]
|
||||
if name in author_ids:
|
||||
author["authorId"] = author_ids[name]
|
||||
setProp(update, "references." + key + ".authors", authors_loc)
|
||||
|
||||
issn = getProp(ref, "issn", "")
|
||||
if issn in journal_ids:
|
||||
setProp(update, "references." + key + ".journalId", journal_ids[issn])
|
||||
if ref["issn"] in journal_ids:
|
||||
ref["journalId"] = journal_ids[issn]
|
||||
update["references"] = references
|
||||
|
||||
authors_loc = getProp(paper, "authors", [])
|
||||
for author in authors_loc:
|
||||
name = author["name"]
|
||||
if name in author_ids:
|
||||
author["authorId"] = author_ids[name]
|
||||
setProp(update, "authors", authors_loc)
|
||||
|
||||
print(mongo_update)
|
||||
update["authors"] = authors_loc
|
||||
|
||||
db["papers"].update_one(mongo_filter, mongo_update)
|
||||
|
||||
i += 1
|
||||
if i % 100 == 0:
|
||||
print("Papers updated with refs: ", i)
|
||||
|
||||
i = 0
|
||||
for journal in db["journals"].find():
|
||||
mongo_filter = { "_id": journal["_id"] }
|
||||
update = {}
|
||||
mongo_update = { "$set": update }
|
||||
|
||||
volumes = getProp(journal, "volumes", [])
|
||||
for volume in volumes:
|
||||
v_papers = []
|
||||
for p in volume["papers"]:
|
||||
v_papers.append(paper_ids[p])
|
||||
volume["papers"] = v_papers
|
||||
update["volumes"] = volumes
|
||||
|
||||
db["journals"].update_one(mongo_filter, mongo_update)
|
||||
i += 1
|
||||
if i % 100 == 0:
|
||||
print("Journals updated with refs: ", i)
|
||||
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
|
|
|||
Reference in New Issue