wip
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parent
ce1c4f88f3
commit
4cc72067e4
1 changed files with 67 additions and 32 deletions
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@ -9,10 +9,8 @@ fake = Faker()
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# pip install faker pymongo
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# TODO: number on publicationDetails (random)
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# TODO: figures (fake)
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# TODO: inject (fake) figures and references in content
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# TODO: references are a dictionary
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# - article doi or JSON filename can be used as paper id
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# - no author id, authors are equal based on name for lack of info
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@ -73,14 +71,6 @@ def getProp(obj: dict, props: str, default = None):
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target = target[prop]
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return target
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def setProp(obj: dict, props: str, toSave: any):
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target = obj
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for prop in props.split("."):
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if prop not in target:
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target[prop] = {}
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target = target[prop]
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target[prop] = toSave
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def save_sentence(body: dict, parents: [dict], sentence: str):
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target = body
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for p in parents:
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@ -156,21 +146,33 @@ def json_to_paper(filename: str, jsonObj: dict) -> dict:
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publicationDetails["journal"] = journal["name"]
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publicationDetails["volume"] = volume
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publicationDetails["number"] = random.randint(1, 99)
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publicationDetails["date"] = date.isoformat()
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publicationDetails["pages"] = {
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"start": getProp(jsonObj, "metadata.firstpage"),
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"end": getProp(jsonObj, "metadata.lastpage")
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}
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paper["publicationDetails"] = publicationDetails
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references = {}
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figures = []
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for i in range(0, random.randint(3, 15)):
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figures.push({
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"page": random.randint(1, 10),
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"label": "fig" + str(i),
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"caption": fake.paragraph(nb_sentences=1),
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"imageURL": fake.image_url()
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})
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paper["figures"] = figures
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i = 0
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references = []
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for key, value in getProp(jsonObj, "bib_entries", {}).items():
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i += 1
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if value is None:
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continue
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references[key] = {
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ref = {
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"referenceNumber": i,
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"doi": getProp(value, "doi"),
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"title": getProp(value, "title"),
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"authors": [],
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@ -180,7 +182,8 @@ def json_to_paper(filename: str, jsonObj: dict) -> dict:
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}
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for author in getProp(value, "authors", []):
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references[key]["authors"].append({ "name": get_author_name(author) })
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ref["authors"].append({ "name": get_author_name(author) })
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references.append(ref)
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paper["references"] = references
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body = {
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@ -231,20 +234,28 @@ def main():
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paper_ids[paper["doi"]] = x.inserted_id
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i += 1
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if i % 20 == 0:
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print("Papers processed: " + i)
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if i == 10: # TODO: remove
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if i % 100 == 0:
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print("Papers processed: ", i)
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if i == 1000: # TODO: remove
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break
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i = 0
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for name, author in authors.items():
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x = db["authors"].insert_one(author)
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author_ids[name] = x.inserted_id
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i += 1
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if i % 1000 == 0:
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print("Authors processed: ", i)
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i = 0
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for issn, journal in journals.items():
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x = db["journals"].insert_one(journal)
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journal_ids[issn] = x.inserted_id
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i += 1
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if i % 100 == 0:
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print("Journals processed: ", i)
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i = 0
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for paper in db["papers"].find():
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mongo_filter = { "_id": paper["_id"] }
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update = {}
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@ -252,30 +263,54 @@ def main():
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issn = getProp(paper, "publicationDetails.issn", "")
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if issn in journal_ids:
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setProp(update, "publicationDetails.journalRef", journal_ids[issn])
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for key, ref in getProp(paper, "references", {}).items():
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update["publicationDetails.journalRef"] = journal_ids[issn]
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references = getProp(paper, "references", [])
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for ref in references:
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if ref["doi"] in paper_ids:
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setProp(update, "references." + key + ".paperId", paper_ids[ref["doi"]])
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ref["paperId"] = paper_ids[ref["doi"]]
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authors_loc = getProp(ref, "authors", [])
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for author in authors_loc:
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for author in ref["authors"]:
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name = author["name"]
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if name in author_ids:
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author["authorId"] = author_ids[name]
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setProp(update, "references." + key + ".authors", authors_loc)
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issn = getProp(ref, "issn", "")
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if issn in journal_ids:
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setProp(update, "references." + key + ".journalId", journal_ids[issn])
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if ref["issn"] in journal_ids:
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ref["journalId"] = journal_ids[issn]
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update["references"] = references
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authors_loc = getProp(paper, "authors", [])
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for author in authors_loc:
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name = author["name"]
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if name in author_ids:
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author["authorId"] = author_ids[name]
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setProp(update, "authors", authors_loc)
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print(mongo_update)
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update["authors"] = authors_loc
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db["papers"].update_one(mongo_filter, mongo_update)
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i += 1
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if i % 100 == 0:
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print("Papers updated with refs: ", i)
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i = 0
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for journal in db["journals"].find():
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mongo_filter = { "_id": journal["_id"] }
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update = {}
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mongo_update = { "$set": update }
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volumes = getProp(journal, "volumes", [])
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for volume in volumes:
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v_papers = []
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for p in volume["papers"]:
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v_papers.append(paper_ids[p])
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volume["papers"] = v_papers
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update["volumes"] = volumes
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db["journals"].update_one(mongo_filter, mongo_update)
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i += 1
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if i % 100 == 0:
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print("Journals updated with refs: ", i)
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if __name__ == "__main__":
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