Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

run conversion on 500 article sample #73

Open
tcatapano opened this issue Mar 12, 2024 · 4 comments
Open

run conversion on 500 article sample #73

tcatapano opened this issue Mar 12, 2024 · 4 comments
Assignees
@tcatapano @gsautter
Labels
bug Something isn't working conversion gg markup invalid This doesn't seem right

Comments

@tcatapano
Copy link
Member

of latest 500 processed articles
@tcatapano tcatapano self-assigned this Mar 12, 2024
@tcatapano
Copy link
Member Author

tcatapano commented Mar 12, 2024 •
edited
Loading

Removed 1 large (100M+) file.

Errors in 63 of 499 articles. 12.6%

@tcatapano
Copy link
Member Author

tcatapano commented Mar 12, 2024 •
edited
Loading

top errs by frequency:

1480  Unexpected element "tp:material-citation". The content of the parent element type must match "(named-content|tp
 133  Unexpected element "tp:material-citation". The content of the parent element type must match "(tp
  18  Unexpected character data "
  13  Unexpected element "p". The content of the parent element type must match "(email|ext-link|uri|inline-supplementary-material|related-article|related-object|address|alternatives|answer|answer-set|array|block-alternatives|boxed-text|chem-struct-wrap|code|explanation|fig|fig-group|graphic|media|preformat|question|question-wrap|question-wrap-group|supplementary-material|table-wrap|table-wrap-group|disp-formula|disp-formula-group|citation-alternatives|element-citation|mixed-citation|nlm-citation|bold|fixed-case|italic|monospace|overline|roman|sans-serif|sc|strike|underline|ruby|award-id|funding-source|open-access|chem-struct|inline-formula|inline-graphic|inline-media|private-char|def-list|list|tex-math|mml:math|abbrev|milestone-end|milestone-start|named-content|styled-content|tp
  11  The content of element type "kwd-group" is incomplete, it must match "(label?,title?,(kwd|compound-kwd|nested-kwd)+)".
   9  Unexpected element "title". The content of the parent element type must match "(sec-meta?,((label,title?)|title),(address|alternatives|answer|answer-set|array|block-alternatives|boxed-text|chem-struct-wrap|code|explanation|fig|fig-group|graphic|media|preformat|question|question-wrap|question-wrap-group|supplementary-material|table-wrap|table-wrap-group|disp-formula|disp-formula-group|def-list|list|tex-math|mml:math|p|related-article|related-object|disp-quote|speech|statement|verse-group)*,(sec|tp
   9  The markup in the document following the root element must be well-formed.
   9  Attribute "xmlns:tp" is not allowed to appear in element "journal-meta".
   7  Unexpected element "sec". The content of the parent element type must match "(sec-meta?,label?,title?,(address|alternatives|answer|answer-set|array|block-alternatives|boxed-text|chem-struct-wrap|code|explanation|fig|fig-group|graphic|media|preformat|question|question-wrap|question-wrap-group|supplementary-material|table-wrap|table-wrap-group|disp-formula|disp-formula-group|def-list|list|tex-math|mml:math|p|related-article|related-object|disp-quote|speech|statement|verse-group)*,tp
   5  Unexpected element "tp:treatment-sec". The content of the parent element type must match "((address|alternatives|answer|answer-set|array|block-alternatives|boxed-text|chem-struct-wrap|code|explanation|fig|fig-group|graphic|media|preformat|question|question-wrap|question-wrap-group|supplementary-material|table-wrap|table-wrap-group|disp-formula|disp-formula-group|def-list|list|tex-math|mml

tcatapano added a commit that referenced this issue Mar 12, 2024
@tcatapano
#73: convert 500 article sample
dd62e2a
@tcatapano
Copy link
Member Author

tcatapano commented Mar 12, 2024 •
edited
Loading

top errs per file:

See: https://github.com/plazi/ggxml2taxpub/blob/dd62e2ade37250a1a28cd586415d28bea4bc01ec/errs/sample_500_errors_20240312_per-article.txt

620 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/BiodivDatJour_12__e117362_tp.xml
 540 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/BiodivDatJour_12__e115051_tp.xml
 319 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/BiodivDatJour_12__e120292_tp.xml
  42 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/LinzerbiolBeitr.55.2.455-494.pdf_tp.xml
  19 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/SoilOrg.92.1.15-86.pdf_tp.xml
  17 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/LinzerbiolBeitr.55.1.9-35.pdf_tp.xml
  16 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/AmMusNovit.2024.4009.1-47.pdf_tp.xml
  12 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/SoilOrg.91.1.7-32.pdf_tp.xml
   9 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/InsectaMundi.2024.1036.1-31.pdf_tp.xml
   8 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/ZoolAnz.56.264-281.imf_tp.xml
   8 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/SoilOrg.95.1.23-73.pdf_tp.xml
   8 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/InsectaMundi.2024.1037.1-16.pdf_tp.xml
   7 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/LinzerbiolBeitr.55.1.307-349.pdf_tp.xml
   6 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/SoilOrg.90.2.57-70.pdf_tp.xml
   6 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/LinzerbiolBeitr.55.1.47-60.pdf_tp.xml
   4 System ID: /Users/thc4/Github/ggxml2taxpub/level1/articles/sample_500/PakistanJNematol.37.2.171-243.pdf.imf_tp.xml

@tcatapano tcatapano added bug Something isn't working invalid This doesn't seem right gg markup conversion labels Mar 12, 2024
@tcatapano
Copy link
Member Author

sample contains several small files which are likely
metadata only:

8.0K	/Users/thc4/working/articles_sample_500/phytotaxa.637.3.10.pdf.xml
8.0K	/Users/thc4/working/articles_sample_500/CheckList_20_2___444-449.xml
8.0K	/Users/thc4/working/articles_sample_500/CheckList_20_2___279-443.xml
8.0K	/Users/thc4/working/articles_sample_500/CheckList_20_2___268-278.xml
8.0K	/Users/thc4/working/articles_sample_500/CheckList_20_2___258-267.xml
8.0K	/Users/thc4/working/articles_sample_500/CheckList_20_2___249-257.xml
8.0K	/Users/thc4/working/articles_sample_500/CheckList_20_1___242-248.xml
8.0K	/Users/thc4/working/articles_sample_500/CheckList_20_1___233-241.xml
8.0K	/Users/thc4/working/articles_sample_500/CheckList_20_1___227-232.xml
4.0K	/Users/thc4/working/articles_sample_500/EJT.2024.923.1-119.pdf.imf.xml

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@tcatapano tcatapano

@gsautter gsautter

Labels
bug Something isn't working conversion gg markup invalid This doesn't seem right
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@tcatapano @gsautter