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petermr / docanalysis

Semantic analysis of text documents including sentence and paragraph splitting
Apache License 2.0
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Errors: "cannot parse" when making dictionaries #15

Open EmanuelFaria opened 2 years ago

EmanuelFaria commented 2 years ago

Below I will copy two separate queries and their results. The "cannot parse" errors seem identical for both.

Last login: Thu Jun 16 10:47:57 on ttys016
emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % docanalysis --project_name terpene_10 --output entities.csv --make_ami_dict entities.xml
/usr/local/Cellar/python@3.10/3.10.4/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/_distutils_hack/__init__.py:36: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
 47%|█████████████████▍                   | 1067/2258 [00:00<00:00, 1326.29it/s]ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/12_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/14_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/3_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/2_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/13_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/4_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/5_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/1_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/10_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/9_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/0_ext-link.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/11_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/7_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/6_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/8_email.xml
 63%|███████████████████████▏             | 1416/2258 [00:01<00:00, 1538.14it/s]ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9165828/sections/1_front/1_article-meta/26_custom-meta-group/0_custom-meta/1_meta-value/0_xref.xml
100%|█████████████████████████████████████| 2258/2258 [00:01<00:00, 1281.98it/s]
INFO: Found 7134 sentences in the section(s).
/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py:351: FutureWarning: The default value of regex will change from True to False in a future version. In addition, single character regular expressions will *not* be treated as literal strings when regex=True.
  df[col] = df[col].astype(str).str.replace(
/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py:352: FutureWarning: The default value of regex will change from True to False in a future version. In addition, single character regular expressions will *not* be treated as literal strings when regex=True.
  "[", "").str.replace("]", "")
INFO: wrote output to /Users/emanuelfarruda/terpene_10/entities.csv
INFO: Wrote all the entities extracted to ami dict
Last login: Thu Jun 16 10:53:23 on ttys017
emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % docanalysis --project_name terpene_10 --output entities_202202019 --make_ami_dict entities_20220209

/usr/local/Cellar/python@3.10/3.10.4/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/_distutils_hack/__init__.py:36: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
 46%|█████████████████                    | 1044/2258 [00:00<00:00, 1363.29it/s]ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/12_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/14_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/3_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/2_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/13_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/4_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/5_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/1_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/10_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/9_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/0_ext-link.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/11_email.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/7_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/6_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9119530/sections/1_front/1_article-meta/24_custom-meta-group/0_custom-meta/1_meta-value/8_email.xml
 69%|█████████████████████████▋           | 1567/2258 [00:01<00:00, 1428.67it/s]ERROR: cannot parse /Users/emanuelfarruda/terpene_10/PMC9165828/sections/1_front/1_article-meta/26_custom-meta-group/0_custom-meta/1_meta-value/0_xref.xml
100%|█████████████████████████████████████| 2258/2258 [00:01<00:00, 1291.58it/s]
INFO: Found 7134 sentences in the section(s).
/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py:351: FutureWarning: The default value of regex will change from True to False in a future version. In addition, single character regular expressions will *not* be treated as literal strings when regex=True.
  df[col] = df[col].astype(str).str.replace(
/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py:352: FutureWarning: The default value of regex will change from True to False in a future version. In addition, single character regular expressions will *not* be treated as literal strings when regex=True.
  "[", "").str.replace("]", "")
INFO: wrote output to /Users/emanuelfarruda/terpene_10/entities_202202019
INFO: Wrote all the entities extracted to ami dict
EmanuelFaria commented 2 years ago

Here's another set of "cannot parse" errors, but in this query I used scispacy, and eded up the following new set of errors following "Traceback":

Traceback (most recent call last):
  File "/usr/local/bin/docanalysis", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/docanalysis/docanalysis.py", line 183, in main
    calldocanalysis.handlecli()
  File "/usr/local/lib/python3.10/site-packages/docanalysis/docanalysis.py", line 174, in handlecli
    self.entity_extraction.extract_entities_from_papers(args.project_name,args.dictionary,search_section=args.search_section,entities=args.entities,query=args.query,hits=args.hits,
  File "/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py", line 122, in extract_entities_from_papers
    self.run_spacy_over_sections(self.sentence_dictionary,entities)
  File "/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py", line 222, in run_spacy_over_sections
    doc = self.nlp(dict_with_parsed_xml[paragraph]['sentence'])
TypeError: 'NoneType' object is not callable

Here's the whole log:

emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % docanalysis --project_name /Users/emanuelfarruda/DAVEapps/getpapers/oil_100 --make_section --output scispacy.csv --spacy_model en_core_sci_scibert --entities PATHOLOGICAL_FORMATION --search_section ALL

/usr/local/Cellar/python@3.10/3.10.4/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/_distutils_hack/__init__.py:36: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622403/fulltext.xml
INFO: dict_keys: dict_keys(['abstract', 'acknowledge', 'affiliation', 'author', 'conclusion', 'discussion', 'ethics', 'fig_caption', 'front', 'introduction', 'jrnl_title', 'keyword', 'method', 'octree', 'pdfimage', 'pub_date', 'publisher', 'reference', 'results_discuss', 'search_results', 'sections', 'svg', 'table', 'title'])
WARNING: loading templates.json
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622403/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622403/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5203915/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5203915/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5203915/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5568258/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5568258/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5568258/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5603114/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5603114/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5603114/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5426739/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5426739/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5426739/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590070/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590070/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590070/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5597067/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5597067/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5597067/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5497343/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5497343/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5497343/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5486035/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5486035/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5486035/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5613177/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5613177/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5613177/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5702920/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5702920/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5702920/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750594/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750594/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750594/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5668225/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5668225/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5668225/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5393100/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5393100/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5393100/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5699893/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5699893/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5699893/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5641611/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5641611/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5641611/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5660901/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5660901/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5660901/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5746745/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5746745/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5746745/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5412227/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5412227/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5412227/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5237462/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5237462/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5237462/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5669080/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5669080/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5669080/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5717781/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5717781/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5717781/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5575638/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5575638/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5575638/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5364420/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5364420/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5364420/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5411863/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5411863/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5411863/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5748641/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5748641/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5748641/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5330108/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5330108/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5330108/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5788217/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5788217/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5788217/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5772139/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5772139/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5772139/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5761127/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5761127/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5761127/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5569441/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5569441/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5569441/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5778200/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5778200/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5778200/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5524814/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5524814/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5524814/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5282690/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5282690/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5282690/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5397855/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5397855/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5397855/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750605/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750605/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750605/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5535876/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5535876/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5535876/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590062/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590062/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590062/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590065/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590065/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590065/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5602841/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5602841/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5602841/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5592951/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5592951/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5592951/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5132230/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5132230/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5132230/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5324201/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5735349/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5423258/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590063/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5427463/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5674267/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5736702/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5615285/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622401/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5725564/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5485486/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5789316/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5615139/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5702407/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622382/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5080681/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5625792/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5543433/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5747963/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694875/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590060/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5669111/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590067/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694611/fulltext.xml
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 32%|██████████████████████████████████████████▋                                                                                            | 6212/19621 [00:07<00:16, 813.92it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5282690/sections/2_back/0_glossary/1_def-list/9_def-item/0_term/0_sup.xml
 49%|██████████████████████████████████████████████████████████████████▎                                                                    | 9640/19621 [00:12<00:12, 819.87it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5674267/sections/1_body/4_radioprotection_by_medicinal_a/1__/2_table-wrap/0_label/0_bold.xml
 54%|████████████████████████████████████████████████████████████████████████▋                                                             | 10650/19621 [00:13<00:13, 660.15it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/1_materials_and_methods/5_genetic_analysis_with_issr_mar/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/0_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/1_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/0_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/2_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/4_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/3_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/6_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/5_sup.xml
 69%|████████████████████████████████████████████████████████████████████████████████████████████▌                                         | 13546/19621 [00:17<00:06, 888.83it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5794096/sections/0_front/1_article-meta/21_funding-group/1_funding-statement/0_ext-link.xml
 83%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████▊                       | 16203/19621 [00:20<00:03, 1112.68it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5661929/sections/2_back/0_glossary/1_def-list/3_def-item/0_term/0_sub.xml
 92%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊           | 17976/19621 [00:23<00:02, 725.57it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5543433/sections/2_back/0_glossary/1_def-list/3_def-item/0_term/0_italic.xml
 99%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 19406/19621 [00:24<00:00, 895.63it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694611/sections/2_back/1_glossary/1_def-list/5_def-item/0_term/0_sub.xml
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 19621/19621 [00:24<00:00, 788.41it/s]
INFO: Found 57303 sentences in the section(s).
INFO: Loading en_core_sci_scibert
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Traceback (most recent call last):
  File "/usr/local/bin/docanalysis", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/docanalysis/docanalysis.py", line 183, in main
    calldocanalysis.handlecli()
  File "/usr/local/lib/python3.10/site-packages/docanalysis/docanalysis.py", line 174, in handlecli
    self.entity_extraction.extract_entities_from_papers(args.project_name,args.dictionary,search_section=args.search_section,entities=args.entities,query=args.query,hits=args.hits,
  File "/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py", line 122, in extract_entities_from_papers
    self.run_spacy_over_sections(self.sentence_dictionary,entities)
  File "/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py", line 222, in run_spacy_over_sections
    doc = self.nlp(dict_with_parsed_xml[paragraph]['sentence'])
emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % docanalysis --project_name /Users/emanuelfarruda/DAVEapps/getpapers/oil_100 --make_section --output scispacy.csv --spacy_model en_core_sci_scibert --entities PATHOLOGICAL_FORMATION --search_section ALL

  [Restored Jun 15, 2022 at 8:17:58 PM]
Last login: Wed Jun 15 20:17:58 on ttys000
Restored session: Wed 15 Jun 2022 20:14:54 -03
emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % 
  [Restored Jun 17, 2022 at 1:38:23 PM]
Last login: Fri Jun 17 13:38:23 on ttys000
Restored session: Fri 17 Jun 2022 13:18:29 -03
emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % 
  [Restored Jun 20, 2022 at 10:09:08 AM]
Last login: Fri Jun 17 13:38:25 on ttys019
Restored session: Fri 17 Jun 2022 17:17:06 -03
emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % docanalysis --project_name /Users/emanuelfarruda/DAVEapps/getpapers/oil_100 --make_section --output scispacy.csv --spacy_model en_core_sci_scibert --entities PATHOLOGICAL_FORMATION --search_section ALL

/usr/local/Cellar/python@3.10/3.10.4/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/_distutils_hack/__init__.py:36: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622403/fulltext.xml
INFO: dict_keys: dict_keys(['abstract', 'acknowledge', 'affiliation', 'author', 'conclusion', 'discussion', 'ethics', 'fig_caption', 'front', 'introduction', 'jrnl_title', 'keyword', 'method', 'octree', 'pdfimage', 'pub_date', 'publisher', 'reference', 'results_discuss', 'search_results', 'sections', 'svg', 'table', 'title'])
WARNING: loading templates.json
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622403/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622403/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5203915/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5203915/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5203915/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5568258/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5568258/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5568258/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5603114/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5603114/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5603114/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5426739/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5426739/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5426739/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590070/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590070/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590070/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5597067/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5597067/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5597067/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5497343/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5497343/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5497343/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5486035/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5486035/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5486035/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5613177/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5613177/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5613177/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5702920/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5702920/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5702920/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750594/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750594/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750594/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5668225/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5668225/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5668225/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5393100/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5393100/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5393100/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5699893/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5699893/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5699893/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5641611/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5641611/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5641611/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5660901/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5660901/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5660901/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5746745/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5746745/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5746745/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5412227/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5412227/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5412227/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5237462/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5237462/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5237462/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5669080/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5669080/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5669080/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5717781/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5717781/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5717781/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5575638/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5575638/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5575638/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5364420/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5364420/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5364420/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5411863/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5411863/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5411863/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5748641/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5748641/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5748641/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5330108/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5330108/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5330108/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5788217/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5788217/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5788217/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5772139/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5772139/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5772139/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5761127/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5761127/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5761127/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5569441/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5569441/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5569441/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5778200/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5778200/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5778200/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5524814/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5524814/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5524814/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5282690/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5282690/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5282690/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5397855/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5397855/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5397855/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750605/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750605/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750605/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5535876/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5535876/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5535876/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590062/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590062/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590062/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590065/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590065/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590065/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5602841/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5602841/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5602841/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5592951/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5592951/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5592951/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5132230/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5132230/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5132230/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5324201/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5324201/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5324201/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5735349/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5735349/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5735349/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5423258/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5423258/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5423258/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590063/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590063/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590063/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5427463/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5427463/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5427463/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5674267/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5674267/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5674267/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5736702/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5736702/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5736702/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5577677/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5577677/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5577677/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5620597/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5620597/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5620597/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5615285/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5615285/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5615285/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5751248/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5751248/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5751248/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5551175/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5551175/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5551175/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622401/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622401/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622401/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5742650/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5742650/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5742650/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5725564/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5725564/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5725564/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5485486/fulltext.xml
INFO: wrote XML sections for /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5485486/fulltext.xml /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5485486/sections
WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5789316/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5615139/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5702407/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622382/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5080681/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5625792/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5344628/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC4391421/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5794096/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694587/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5507808/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622397/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622390/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5750654/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694991/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5723952/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5622398/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5745743/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5651092/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5527698/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5307902/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5684592/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5448358/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5546729/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5454990/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5307246/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590066/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5602041/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5778779/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5543433/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5248495/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5747963/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694875/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5653886/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590060/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5669111/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5590067/fulltext.xml
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WARNING: Making sections in /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694611/fulltext.xml
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 32%|███████████████████████████████████████████████████████████████████████████████████████████████████                                                                                                                                                                                                                      | 6212/19621 [00:08<00:18, 714.84it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5282690/sections/2_back/0_glossary/1_def-list/9_def-item/0_term/0_sup.xml
 49%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████                                                                                                                                                               | 9661/19621 [00:13<00:11, 892.21it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5674267/sections/1_body/4_radioprotection_by_medicinal_a/1__/2_table-wrap/0_label/0_bold.xml
 54%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▎                                                                                                                                              | 10645/19621 [00:14<00:13, 658.58it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/1_materials_and_methods/5_genetic_analysis_with_issr_mar/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/0_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/1_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/0_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/2_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/4_xref.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/3_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/6_sup.xml
ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694497/sections/1_body/2_results/2_table-wrap/3_table-wrap-foot/0_attrib/0_italic/5_sup.xml
 69%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▍                                                                                                | 13552/19621 [00:18<00:06, 929.18it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5794096/sections/0_front/1_article-meta/21_funding-group/1_funding-statement/0_ext-link.xml
 83%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋                                                     | 16257/19621 [00:21<00:03, 1087.23it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5661929/sections/2_back/0_glossary/1_def-list/3_def-item/0_term/0_sub.xml
 92%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋                         | 18031/19621 [00:24<00:02, 739.66it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5543433/sections/2_back/0_glossary/1_def-list/3_def-item/0_term/0_italic.xml
 99%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌   | 19407/19621 [00:25<00:00, 889.12it/s]ERROR: cannot parse /Users/emanuelfarruda/DAVEapps/getpapers/oil_100/PMC5694611/sections/2_back/1_glossary/1_def-list/5_def-item/0_term/0_sub.xml
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 19621/19621 [00:25<00:00, 761.51it/s]
INFO: Found 57303 sentences in the section(s).
INFO: Loading en_core_sci_scibert
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Traceback (most recent call last):
  File "/usr/local/bin/docanalysis", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/docanalysis/docanalysis.py", line 183, in main
    calldocanalysis.handlecli()
  File "/usr/local/lib/python3.10/site-packages/docanalysis/docanalysis.py", line 174, in handlecli
    self.entity_extraction.extract_entities_from_papers(args.project_name,args.dictionary,search_section=args.search_section,entities=args.entities,query=args.query,hits=args.hits,
  File "/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py", line 122, in extract_entities_from_papers
    self.run_spacy_over_sections(self.sentence_dictionary,entities)
  File "/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py", line 222, in run_spacy_over_sections
    doc = self.nlp(dict_with_parsed_xml[paragraph]['sentence'])
TypeError: 'NoneType' object is not callable
emanuelfarruda@Mannys-MacBook-Pro-2021 ~ %
petermr commented 2 years ago

Please don't give the whole LOG file (the WARNING and INFO are normal) Chop them out and put [...] or similar. Just show the bug part, and only a few.

File "/usr/local/lib/python3.10/site-packages/docanalysis/entity_extraction.py", line 222, in run_spacy_over_sections

doc = self.nlp(dict_with_parsed_xml[paragraph]['sentence'])

TypeError: 'NoneType' object is not callable

PMR> This one looks like a rare document with errors (I hope) Please can you see if you can find which one . @Shweata will need to trap the line with try: except or test for null.

Message ID: @.***>

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK