import re
import os
import gzip
import glob
import simplejson as json
import click
import math
import string
from util import *

PDF_DIR = 'datasets/s2/pdf'

@click.command()
def report_first_pages():
  rows = []
  institution_names = []
  institutions = []
  no_institutions = []
  for fn in glob.iglob('{}/**/*.txt'.format(PDF_DIR), recursive=True):
    data = process_paper(fn)
    rows.append(data['first_pages'])
    if data['institutions']:
      for institution in data['institutions']:
        institutions.append(institution)
        institution_names.append(institution[1])
    if data['no_institutions']:
      no_institutions.append(data['no_institutions'])
  deduped_institutions = dedupe(institution_names)

  write_report('reports/first_pages.html', title='First pages', keys=None, rows=rows)
  write_report('reports/institutions.html', title='Institutions', keys=None, rows=sorted(institutions, key=lambda x: x[1]))
  write_report('reports/institutions_missing.html', title='Institutions', keys=None, rows=no_institutions)
  write_csv('reports/institution_names_extracted.csv', keys=None, rows=[(name,) for name in deduped_institutions])
  print("{} deduped institutions".format(len(deduped_institutions)))

def dedupe(a):
  p = {}
  for s in a:
    p[s] = None
  ss = sorted(p.keys())
  return ss

def process_paper(fn):
  paper_id = fn.replace(PDF_DIR, '').split('/')[2]
  paper = load_paper(paper_id)
  if paper is None:
    print("{} no paper found!".format(paper_id))
    return None
  with open(fn, 'r') as f:
    lines = []
    emails = []
    institutions = []
    authors = [ (a[0], a[1], a[1].lower(),) for a in paper.authors ]
    journal = paper.journal.lower()
    found_authors = []
    for line in f.readlines():
      l = line.lower()
      if 'abstract' in l:
        break
      if len(line) < 3:
        continue
      if journal and journal in l:
        continue
      if '@' in line:
        # print('email {}'.format(line))
        emails.append(line)
        continue
      names = [s.strip() for s in re.split(',| and ', l)]
      was_found = False
      for name in names:
        found = find_authors(authors, name)
        if found:
          was_found = True
          # print("found {}".format(found[1]))
          if found[0]:
            found_authors.append(found)
      if was_found:
        # lines.append(NameLine(line))
        continue

      if 'university' in l or 'universiteit' in l or 'research center' in l or 'research lab' in l or 'college' in l or ', inc' in l or 'institute' in l:
        inst = re.sub(r'^[\W\d]+', '', line)
        inst = re.sub(r'[\W\d]+$', '', inst)
        inst = re.sub(r'\s+', ' ', inst)
        inst = re.sub(r'Dept.', 'Department ', inst)
        if len(inst) < 160:
          inst = inst.replace('&', 'and')
          inst_parts = []
          department = ''
          for inst_part in inst.split(','):
            inst_part = inst_part.strip()
            inst_low = inst_part.lower()
            if 'prof' in inst_low:
              continue
            if 'article ' in inst_low:
              continue
            if 'department' in inst_low:
              department = inst_part
            else:
              inst_parts.append(inst_part)
          inst = ', '.join(inst_parts)
          if inst:
            inst = ''.join([i if ord(i) < 128 else ' ' for i in inst]).strip()
            institutions.append([ paper_id, inst, department ])
        lines.append(BoldLine(inst))
        continue
      lines.append(line)
    write_json('{}/{}'.format(paper_path(paper_id), 'institutions.json'), { 'institutions': institutions })
    return {
      'first_pages': [
        paper_id,
        lines,
        found_authors,
        emails,
      ],
      'institutions': None if not len(institutions) else institutions,
      'no_institutions': None if len(institutions) else [
        paper_id,
        lines,
      ],
    }

def find_authors(authors, line):
  for a in authors:
    if a[2] in line:
      return a
  return None

def paper_path(paper_id):
  return '{}/{}/{}'.format(PDF_DIR, paper_id[0:2], paper_id)
  
if __name__ == '__main__':
  report_first_pages()