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processor.py
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processor.py
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import pandas as pd
import re
import os
import numpy as np
from commons import CORDCommons
import json
from api.config import mongouser, mongopass, mongohost, doindex, cordversion
from pymongo import MongoClient
from elasticsearch import Elasticsearch
class CORDProcessor():
def __init__(self, df, directory):
self.df = df
self.directory = directory
self.mongoclient = MongoClient("mongodb://%s:%s@%s" % (mongouser, mongopass, mongohost))
self.db = self.mongoclient.get_database('cord19')
self.collection = self.db[cordversion]
def has_v15_metadata(self):
if self.directory:
jsfile = {}
self.papers = {}
for i in self.df.index:
self.metadata = {}
self.rows = []
doi = self.df.iloc[i].doi
relpath = self.df.iloc[i].pdf_json_files
section = (str(relpath) + "/") * 2
pmcid = self.df.iloc[i].pmcid
filename = self.directory + '/' + relpath
print("%s\n" % filename)
self.metadata['path'] = relpath
self.metadata['doi'] = doi
try:
with open(filename) as paperjs:
jsfile = json.load(paperjs)
except:
print("Problem with", self.df.iloc[i].cord_uid)
#continue
_id = self.df.iloc[i]["cord_uid"]
self.metadata['cord_uid'] = _id
#print(filename)
#print(jsfile)
if "title" in jsfile.keys():
self.rows.append(dict(cord_uid=_id, section="title", subsection=0, text=jsfile["title"]))
self.metadata['title'] = jsfile["title"]
else:
self.rows.append(dict(cord_uid=_id, section="title", subsection=0, text=self.df.iloc[i].title))
self.metadata['title'] = self.df.iloc[i].title
if "abstract" in jsfile.keys():
if len(jsfile["abstract"]) > 1:
for j in range(len(jsfile["abstract"])):
self.metadata['abstract'] = jsfile["abstract"]
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"][j]["text"]))
else:
self.metadata['abstract'] = jsfile["abstract"]
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"]))
elif "abstract" in jsfile["metadata"].keys():
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["metadata"]["abstract"]))
self.metadata['abstract'] = jsfile["metadata"]["abstract"]
else:
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=self.df.iloc[i].abstract))
self.metadata['abstract'] = self.df.iloc[i].abstract
sections = list(set([k["section"] for k in jsfile["body_text"]]))
for section in sections:
self.metadata['body_text'] = jsfile["body_text"]
for l in range(len(jsfile["body_text"])):
if jsfile["body_text"][l]["section"] == section:
if section == '':
section = "body_text"
self.rows.append(dict(cord_uid=_id, section=section,
subsection=l, text=jsfile["body_text"][l]["text"]))
c = CORDCommons(self.directory)
tables = c.extract_tables_from_json(jsfile)
self.metadata['tables'] = tables
for table in tables:
self.rows.append(dict(cord_uid=_id, section=table[0], subsection=table[1], text=table[2]))
self.metadata['body_rows'] = self.rows
if doindex == 'mongo':
try:
self.collection.insert_one(self.metadata)
except:
print("errors with doi %s" % doi)
else:
self.papers[doi] = self.metadata
return
def has_pmc_xml_parse(self):
if self.directory:
jsfile = {}
self.papers = {}
for i in self.df[self.df["has_pmc_xml_parse"] == 1].index:
self.metadata = {}
self.rows = []
doi = self.df.iloc[i].doi
section = (str(self.df.iloc[i].full_text_file) + "/") * 2
pmcid = self.df.iloc[i].pmcid
filename = self.directory + '/' + section + "pmc_json/" + pmcid + ".xml.json"
self.metadata['path'] = section + "pmc_json/" + pmcid + ".xml.json"
print(filename)
try:
with open(filename) as paperjs:
jsfile = json.load(paperjs)
except:
print("Problem with", self.df.iloc[i].cord_uid)
#continue
_id = self.df.iloc[i]["cord_uid"]
self.metadata['cord_uid'] = _id
#print(filename)
#print(jsfile)
if "title" in jsfile.keys():
self.rows.append(dict(cord_uid=_id, section="title", subsection=0, text=jsfile["title"]))
self.metadata['title'] = jsfile["title"]
else:
self.rows.append(dict(cord_uid=_id, section="title", subsection=0, text=self.df.iloc[i].title))
self.metadata['title'] = self.df.iloc[i].title
if "abstract" in jsfile.keys():
if len(jsfile["abstract"]) > 1:
for j in range(len(jsfile["abstract"])):
self.metadata['abstract'] = jsfile["abstract"]
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"][j]["text"]))
else:
self.metadata['abstract'] = jsfile["abstract"]
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"]))
elif "abstract" in jsfile["metadata"].keys():
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["metadata"]["abstract"]))
self.metadata['abstract'] = jsfile["metadata"]["abstract"]
else:
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=self.df.iloc[i].abstract))
self.metadata['abstract'] = self.df.iloc[i].abstract
sections = list(set([k["section"] for k in jsfile["body_text"]]))
for section in sections:
self.metadata['body_text'] = jsfile["body_text"]
for l in range(len(jsfile["body_text"])):
if jsfile["body_text"][l]["section"] == section:
if section == '':
section = "body_text"
self.rows.append(dict(cord_uid=_id, section=section,
subsection=l, text=jsfile["body_text"][l]["text"]))
c = CORDCommons(self.directory)
tables = c.extract_tables_from_json(jsfile)
self.metadata['tables'] = tables
for table in tables:
self.rows.append(dict(cord_uid=_id, section=table[0], subsection=table[1], text=table[2]))
self.metadata['body_rows'] = self.rows
self.papers[doi] = self.metadata
return
def has_no_pmc_xml_parse(self):
if self.directory:
self.papers = {}
jsfile = {}
self.df = self.df[self.df["has_pdf_parse"] == 1]
self.df = self.df[self.df["has_pmc_xml_parse"] == 0]
self.df = self.df[0:10]
print(self.df.index)
for i in self.df[(self.df["has_pmc_xml_parse"] == 0) & (self.df["has_pdf_parse"] == 1)].index:
self.metadata = {}
self.rows = []
section = (str(self.df.iloc[i].full_text_file) + "/") * 2
doi = self.df.iloc[i].doi
sha = self.df.iloc[i].sha
if len(sha.split("; ")) > 1:
sha = sha.split("; ")[0]
filename = self.directory + '/' + section + "pdf_json/" + sha + ".json"
self.metadata['path'] = section + "pdf_json/" + sha + ".json"
try:
with open(filename) as paperjs:
jsfile = json.load(paperjs)
except:
print("Problem with", self.df.iloc[i].cord_uid)
_id = self.df.iloc[i]["cord_uid"]
self.metadata['cord_uid'] = _id
if "title" in jsfile.keys():
self.metadata['title'] = jsfile["title"]
self.rows.append(dict(cord_uid=_id, section="title", subsection=0, text=jsfile["title"]))
else:
self.rows.append(dict(cord_uid=_id, section="title", subsection=0, text=self.df.iloc[i].title))
self.metadata['title'] = self.df.iloc[i].title
if "abstract" in jsfile.keys():
if len(jsfile["abstract"]) > 1:
for j in range(len(jsfile["abstract"])):
self.metadata['abstract'] = jsfile["abstract"]
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"][j]["text"]))
else:
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"]))
self.metadata['abstract'] = jsfile["abstract"]
elif "abstract" in jsfile["metadata"].keys():
self.metadata['abstract'] = jsfile["metadata"]["abstract"]
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["metadata"]["abstract"]))
else:
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=df.iloc[i].abstract))
self.metadata['abstract'] = self.df.iloc[i].abstract
self.metadata['body_text'] = jsfile["body_text"]
sections = list(set([k["section"] for k in jsfile["body_text"]]))
for section in sections:
for l in range(len(jsfile["body_text"])):
if jsfile["body_text"][l]["section"] == section:
if section == '':
section = "body_text"
self.rows.append(dict(cord_uid=_id, section=section,
subsection=l, text=jsfile["body_text"][l]["text"]))
c = CORDCommons(self.directory)
tables = c.extract_tables_from_json(jsfile)
self.metadata['tables'] = tables
for table in tables:
self.rows.append(dict(cord_uid=_id, section=table[0], subsection=table[1], text=table[2]))
self.papers[doi] = self.metadata
return
def has_no_pdf_parse(self):
self.papers = {}
if self.directory:
for i in self.df[(self.df["has_pmc_xml_parse"] == 0) & (self.df["has_pdf_parse"] == 0)].index:
self.metadata = {}
self.rows = []
section = (str(self.df.iloc[i].full_text_file) + "/") * 2
sha = self.df.iloc[i].sha
doi = self.df.iloc[i].doi
if len(sha.split("; ")) > 1:
sha = sha.split("; ")[0]
filename = self.directory + '/' + section + "pdf_json/" + sha + ".json"
self.metadata['path'] = section + "pdf_json/" + sha + ".json"
print(filename)
if len(sha) < 2:
bad_sha = True
try:
with open(directory + section + "pmc_json/" + df.iloc[i]["pmcid"] + ".xml.json") as paperjs:
jsfile = json.load(paperjs)
except:
pass
if bad_sha == True:
bad_sha = False
#continue
try:
with open(filename) as paperjs:
jsfile = json.load(paperjs)
except:
print("Problem with ", self.df.iloc[i].cord_uid)
#continue
_id = self.df.iloc[i]["cord_uid"]
self.metadata['cord_uid'] = _id
if "title" in jsfile.keys():
self.metadata['title'] = jsfile["title"]
rows.append(dict(cord_uid=_id, section="title", subsection=0, text=jsfile["title"]))
else:
rows.append(dict(cord_uid=_id, section="title", subsection=0, text=self.df.iloc[i].title))
self.metadata['title'] = self.df.iloc[i].title
if "abstract" in jsfile.keys():
if len(jsfile["abstract"]) > 1:
self.metadata['abstract'] = jsfile["abstract"]
for j in range(len(jsfile["abstract"])):
rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"][j]["text"]))
else:
self.metadata['abstract'] = jsfile["abstract"]
rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"]))
elif "abstract" in jsfile["metadata"].keys():
self.metadata['abstract'] = jsfile["metadata"]["abstract"]
rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["metadata"]["abstract"]))
else:
self.metadata['abstract'] = self.df.iloc[i].abstract
rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=self.df.iloc[i].abstract))
sections = list(set([k["section"] for k in jsfile["body_text"]]))
for section in sections:
self.metadata['body_text'] = jsfile["body_text"]
for l in range(len(jsfile["body_text"])):
if jsfile["body_text"][l]["section"] == section:
if section == '':
section = "body_text"
rows.append(dict(cord_uid=_id, section=section,
subsection=l, text=jsfile["body_text"][l]["text"]))
c = CORDCommons(self.directory)
tables = c.extract_tables_from_json(jsfile)
self.metadata['tables'] = tables
for table in tables:
rows.append(dict(cord_uid=_id, section=table[0], subsection=table[1], text=table[2]))
self.papers[doi] = self.metadata
return
def has_v22_parse(self):
self.papers = {}
if self.directory:
for i in self.df.index:
self.metadata = {}
self.rows = []
jsfile = ''
jsonfiles = re.split("( )", str(self.df.iloc[i].pdf_json_files))
jsonpath = jsonfiles
section = (jsonpath[0] + "/") * 2
sha = self.df.iloc[i].sha
doi = self.df.iloc[i].doi
# cord_uid,sha,source_x,title,doi,pmcid,pubmed_id,license,abstract,publish_time,authors,journal,mag_id,who_covidence_id,arxiv_id,pdf_json_files,pmc_json_files,url,s2_id
self.metadata['who_covidence_id'] = self.df.iloc[i].who_covidence_id
self.metadata['source_x'] = self.df.iloc[i].source_x
self.metadata['pmcid'] = self.df.iloc[i].pmcid
self.metadata['pubmed_id'] = self.df.iloc[i].pubmed_id
self.metadata['license'] = self.df.iloc[i].license
self.metadata['publish_time'] = self.df.iloc[i].publish_time
self.metadata['authors'] = self.df.iloc[i].authors
self.metadata['journal'] = self.df.iloc[i].journal
self.metadata['mag_id'] = self.df.iloc[i].mag_id
self.metadata['arxiv_id'] = self.df.iloc[i].arxiv_id
self.metadata['s2_id'] = self.df.iloc[i].s2_id
self.metadata['year'] = re.split('-', self.metadata['publish_time'])[0]
if len(sha.split("; ")) > 1:
sha = sha.split("; ")[0]
filename = self.directory + '/' + section + "pdf_json/" + sha + ".json"
self.metadata['path'] = section + "pdf_json/" + sha + ".json"
filename = self.directory + '/' + jsonpath[0]
bad_sha = False
if len(sha) < 2:
bad_sha = True
try:
with open(directory + section + "pmc_json/" + df.iloc[i]["pmcid"] + ".xml.json") as paperjs:
jsfile = json.load(paperjs)
except:
pass
if bad_sha == True:
bad_sha = False
#continue
print("Open file %s" % filename)
try:
with open(filename) as paperjs:
jsfile = json.load(paperjs)
except:
print("Problem with ", self.df.iloc[i].cord_uid)
continue
_id = self.df.iloc[i]["cord_uid"]
self.metadata['cord_uid'] = _id
if "title" in jsfile.keys():
self.metadata['title'] = jsfile["title"]
self.rows.append(dict(cord_uid=_id, section="title", subsection=0, text=jsfile["title"]))
else:
self.rows.append(dict(cord_uid=_id, section="title", subsection=0, text=self.df.iloc[i].title))
self.metadata['title'] = self.df.iloc[i].title
if "abstract" in jsfile.keys():
if len(jsfile["abstract"]) > 1:
self.metadata['abstract'] = jsfile["abstract"]
for j in range(len(jsfile["abstract"])):
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"][j]["text"]))
else:
self.metadata['abstract'] = jsfile["abstract"]
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["abstract"]))
elif "abstract" in jsfile["metadata"].keys():
self.metadata['abstract'] = jsfile["metadata"]["abstract"]
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=jsfile["metadata"]["abstract"]))
else:
self.metadata['abstract'] = self.df.iloc[i].abstract
self.rows.append(dict(cord_uid=_id, section="abstract", subsection=0, text=self.df.iloc[i].abstract))
sections = list(set([k["section"] for k in jsfile["body_text"]]))
for section in sections:
self.metadata['body_text'] = jsfile["body_text"]
for l in range(len(jsfile["body_text"])):
if jsfile["body_text"][l]["section"] == section:
if section == '':
section = "body_text"
self.rows.append(dict(cord_uid=_id, section=section,
subsection=l, text=jsfile["body_text"][l]["text"]))
c = CORDCommons(self.directory)
tables = c.extract_tables_from_json(jsfile)
self.metadata['tables'] = tables
for table in tables:
self.rows.append(dict(cord_uid=_id, section=table[0], subsection=table[1], text=table[2]))
#self.papers[doi] = self.metadata
self.metadata['body_rows'] = self.rows
if doindex == 'mongo':
try:
self.collection.insert_one(self.metadata)
except:
print("errors with doi %s" % doi)
else:
self.papers[doi] = self.metadata
return