ERROR: section papers using --run_sectioning before search

[Kaartik7]

When I run the following command in terminal on my mac - docanalysis --run_pygetpapers -q "terpene" -k 10 --project_name terpene_10, I run into the above mentioned error. Kindly help me with it

[Kaartik7]

Although it does install the papers and makes Cproject, but I get this error message after the command finishes executing

[Kaartik7]

Additional info that might help understand the issue : I get this error message "docanalysis: error: unrecognized arguments: --run_sectioning" when I try to section the papers

[petermr]

I have just run this: pm286macbook:awena-wikidata-crawler pm286$ docanalysis --help /opt/anaconda3/lib/python3.8/site-packages/_distutils_hack/__init__.py:36: UserWarning: Setuptools is replacing distutils. warnings.warn("Setuptools is replacing distutils.") usage: docanalysis [-h] [--run_pygetpapers] [--run_sectioning] [-q QUERY] [-k HITS] [--project_name PROJECT_NAME] [-d DICTIONARY] [-o OUTPUT] [--make_ami_dict MAKE_AMI_DICT] [-l LOGLEVEL] [-f LOGFILE] [--section [SECTION [SECTION ...]]] [--entities [ENTITIES [ENTITIES ...]]] [--spacy_model SPACY_MODEL] [--html HTML] Welcome to Docanalysis version 0.0.7. -h or --help for help optional arguments: -h, --help show this help message and exit

…

--run_pygetpapers queries EuropePMC via pygetpapers

--run_sectioning make sections -q QUERY, --query QUERY query to pygetpapers -k HITS, --hits HITS numbers of papers to download from pygetpapers

--project_name PROJECT_NAME name of CProject folder -d DICTIONARY, --dictionary DICTIONARY Ami Dictionary to tag sentences and support supervised entity extraction -o OUTPUT, --output OUTPUT Output CSV file [default=entities.csv]

--make_ami_dict MAKE_AMI_DICT if provided will make ami dict with given title -l LOGLEVEL, --loglevel LOGLEVEL [All] Provide logging level. Example --log warning <<info,warning,debug,error,critical>>, default='info' -f LOGFILE, --logfile LOGFILE [All] save log to specified file in output directory as well as printing to terminal

--section [SECTION [SECTION ...]] Which section to get

--entities [ENTITIES [ENTITIES ...]] Which entities to get. Default(ALL)

--spacy_model SPACY_MODEL Optional. (spacy, scispacy). Default(spacy)

--html HTML Saves output in html format to given path [...] (base) pm286macbook:projects pm286$ docanalysis -q "lantana" -k 5 --run_pygetpapers --run_sectioning /opt/anaconda3/lib/python3.8/site-packages/_distutils_hack/__init__.py:36: UserWarning: Setuptools is replacing distutils. warnings.warn("Setuptools is replacing distutils.") *INFO:* making project/searching lantana for 5 hits into /Users/pm286/projects/2022_05_29_09_04_26 *INFO:* Total Hits are 2174 1it [00:00, 323.31it/s] *INFO:* Saving XML files to /Users/pm286/projects/2022_05_29_09_04_26/*/fulltext.xml 100%|█████████████████████████████████████████████████████████████| 5/5 [00:01<00:00, 3.79it/s] *WARNING:* Making sections in /Users/pm286/projects/2022_05_29_09_04_26/PMC9095257/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/pm286/projects/2022_05_29_09_04_26/PMC9095257/fulltext.xml /Users/pm286/projects/2022_05_29_09_04_26/PMC9095257/sections *WARNING:* Making sections in /Users/pm286/projects/2022_05_29_09_04_26/PMC8933013/fulltext.xml *INFO:* wrote XML sections for /Users/pm286/projects/2022_05_29_09_04_26/PMC8933013/fulltext.xml /Users/pm286/projects/2022_05_29_09_04_26/PMC8933013/sections *WARNING:* Making sections in /Users/pm286/projects/2022_05_29_09_04_26/PMC8879267/fulltext.xml *INFO:* wrote XML sections for /Users/pm286/projects/2022_05_29_09_04_26/PMC8879267/fulltext.xml /Users/pm286/projects/2022_05_29_09_04_26/PMC8879267/sections *WARNING:* Making sections in /Users/pm286/projects/2022_05_29_09_04_26/PMC8593682/fulltext.xml *INFO:* wrote XML sections for /Users/pm286/projects/2022_05_29_09_04_26/PMC8593682/fulltext.xml /Users/pm286/projects/2022_05_29_09_04_26/PMC8593682/sections *WARNING:* Making sections in /Users/pm286/projects/2022_05_29_09_04_26/PMC8896935/fulltext.xml *INFO:* wrote XML sections for /Users/pm286/projects/2022_05_29_09_04_26/PMC8896935/fulltext.xml /Users/pm286/projects/2022_05_29_09_04_26/PMC8896935/sections *INFO:* starting tokenization on 1 paragraphs 100%|████████████████████████████████████████████████████████| 847/847 [00:01<00:00, 716.46it/s] *INFO:* Found 2610 sentences *INFO:* getting terms from/to False *INFO:* Loading spacy 100%|██████████████████████████████████████████████████████| 2610/2610 [00:14<00:00, 175.90it/s] /opt/anaconda3/lib/python3.8/site-packages/docanalysis/entity_extraction.py:257: 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( *INFO:* wrote output to /Users/pm286/projects/2022_05_29_09_04_26/entities.csv (base) pm286macbook:projects pm286$ ls -lt | more total 88200 drwxr-xr-x 9 pm286 staff 288 29 May 10:04 2022_05_29_09_04_26 drwxr-xr-x 21 pm286 staff 672 22 May 18:29 presentations [...] (base) pm286macbook:projects pm286$ tree 2022_05_29_09_04_26/ | more 2022_05_29_09_04_26/ ├── PMC8593682 │ ├── eupmc_result.json │ ├── fulltext.xml │ └── sections │ ├── 0_processing-meta │ │ └── 0_restricted-by.xml │ ├── 1_front │ │ ├── 0_journal-meta │ │ │ ├── 0_journal-id.xml │ │ │ ├── 1_journal-id.xml │ │ │ ├── 2_journal-id.xml │ │ │ ├── 3_journal-title-group.xml │ │ │ ├── 4_issn.xml │ │ │ └── 5_publisher.xml │ │ └── 1_article-meta │ │ ├── 0_article-id.xml │ │ ├── 10_pub-date.xml │ │ ├── 11_pub-date.xml │ │ ├── 12_pub-date.xml │ │ ├── 13_volume.xml │ │ ├── 14_issue.xml │ │ ├── 15_elocation-id.xml │ │ ├── 16_history.xml │ │ ├── 17_permissions.xml │ │ ├── 18_self-uri.xml │ │ ├── 19_abstract.xml │ │ ├── 1_article-id.xml │ │ ├── 20_kwd-group.xml │ │ ├── 21_funding-group │ │ │ ├── 0_award-group │ │ │ │ ├── 0_funding-source │ │ │ │ │ └── 0_institution-wrap │ │ │ │ │ ├── 0_institution.xml │ │ │ │ │ └── 1_institution-id.xml │ │ │ │ ├── 1_award-id.xml │ │ │ │ ├── 2_principal-award-recipient │ │ │ │ │ └── 0_name.xml │ │ │ │ ├── 3_principal-award-recipient │ │ │ │ │ └── 0_name.xml │ │ │ │ ├── 4_principal-award-recipient │ │ │ │ │ └── 0_name.xml │ │ │ │ ├── 5_principal-award-recipient │ │ │ │ │ └── 0_name.xml │ │ │ │ ├── 6_principal-award-recipient │ │ │ │ │ └── 0_name.xml │ │ │ │ ├── 7_principal-award-recipient │ │ │ │ │ └── 0_name.xml │ │ │ │ └── 8_principal-award-recipient │ │ │ │ └── 0_name.xml │ │ │ ├── 1_award-group [...] So it works for me , although pip install seems to give version 0.0.7 Shweata, any thoughts? P.

On Sun, May 29, 2022 at 9:21 AM Kaartik7 ***@***.***> wrote: Additional info that might help understand the issue : I get this error message "docanalysis: error: unrecognized arguments: --run_sectioning" when I try to section the papers — Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAFTCS4JHHVUA6IWRABUHYDVMMSHPANCNFSM5XHZYWGQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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