References from migration shows HTML tags in abstracts and notes

Created on 11 April 2024, 3 months ago
Updated 16 April 2024, 2 months ago

After a migration using the bibcite_migrate module, I retrieved my 2700+ references from a D7 site and the Bibliography module.

Unfortunately, all abstracts and notes have retrieved the HTML tags and nothing is decoded.

I tried to manage the default display and table mode but I can only choose "Default" or "Trimmed" and the html tags are still visible.

When trying to display my references with Views, it's the same thing, I can't choose a text format that will decode the HTML tags (even with rewrite results and strip HTML tags options).

In the bibcite_reference table, all values contain HTML tags. I have tried to add "basic_html" for one reference (column bibcite_abst_e__format) but I see no changes.

How can I decode these HTML tags to cleanly display my abstracts and reference notes?

Thanks for any tip here.

🐛 Bug report
Status

Active

Version

2.0

Component

Code

Created by

🇫🇷France Toki Caen, Normandy

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  • Issue created by @Toki
  • 🇫🇷France Toki Caen, Normandy
  • 🇫🇷France Toki Caen, Normandy

    I have just tried to save one bibcite reference from UI and the abstract is now HTML tags free. The bibcite_abs_e__format column in the bibcite_reference table is now filled (filtered_html). So I guess if I save all references again they will apply the default text format from Abstract field? For Notes, this workaround will not work, the bibcite field is not formatted (raw text). Is there a way to edit the field type for bibcite_notes or to format values in Views?

  • 🇫🇷France Toki Caen, Normandy

    For any purpose, this is what I have for one example on target (D10 Bibcite) in the database (html tags on abstracts and notes). Views displays what you can see on screenshot "ref-bibcite-views-d10.png".

    INSERT INTO `bibcite_reference` (`id`, `revision_id`, `type`, `uuid`, `langcode`, `status`, `title`, `uid`, `bibcite_abst_e__value`, `bibcite_abst_e__format`, `bibcite_abst_f__value`, `bibcite_abst_f__format`, `bibcite_notes`, `bibcite_custom1`, `bibcite_custom2`, `bibcite_custom3`, `bibcite_custom4`, `bibcite_custom5`, `bibcite_custom6`, `bibcite_custom7`, `bibcite_auth_address`, `bibcite_year`, `bibcite_secondary_title`, `bibcite_volume`, `bibcite_edition`, `bibcite_section`, `bibcite_issue`, `bibcite_number_of_volumes`, `bibcite_number`, `bibcite_pages`, `bibcite_date`, `bibcite_type_of_work`, `bibcite_lang`, `bibcite_reprint_edition`, `bibcite_publisher`, `bibcite_place_published`, `bibcite_issn`, `bibcite_isbn`, `bibcite_accession_number`, `bibcite_call_number`, `bibcite_other_number`, `bibcite_url`, `bibcite_doi`, `bibcite_research_notes`, `bibcite_tertiary_title`, `bibcite_short_title`, `bibcite_alternate_title`, `bibcite_translated_title`, `bibcite_original_publication`, `bibcite_other_author_affiliations`, `bibcite_remote_db_name`, `bibcite_remote_db_provider`, `bibcite_label`, `bibcite_access_date`, `bibcite_refereed`, `bibcite_pmid`, `created`, `changed`)
    VALUES
    	(1, 1, 'journal_article', '480303b4-8cc6-47bb-bb23-bcab863965ad', 'fr', 1, 'Updated checklist of the freshwater and estuarine fishes of French Guiana', 0, '<p>The fish fauna of French Guiana is among the best known of South America. Various fieldwork campaigns have been conducted since the publication of the “Atlas des poissons d’eau douce” de Guyane, particularly in poorly surveyed areas, leading to the discovery of new taxa, and numerous scientific publications have provided new insights concerning this fauna. An updated checklist of the fishes of French Guiana, including all of this new information, is therefore desirable. The list contains 416 species, 367 of which are strictly freshwater. Fish diversity is strongly correlated with catchment size and is, on average, higher in French Guiana than in Suriname. The largest groups are the Characiformes (41{%}), Siluriformes (33{%}) and Perciformes (13{%}). The relative abundance of taxonomic groups differs between catchments, probably reflecting the ecological character of the rivers. Eighty seven species, around a quarter of the ichthyofauna, are listed as endemic, but this may be an underestimate because a rather strict definition of endemism is used. The rate of endemism is strongly correlated with catchment size, with some families showing higher than average rates. Comparison of the number of species shared by the different catchments suggests a highly complex pattern of dispersal as a function of the catchment size, topography, and species. The Oyapock River seems to belong to a relatively distinct biogeographic zone influenced by the Amazon basin, but it is not possible to show a broader trend. These results provide an additional tool for environmental managers and decision makers.</p>\r\n', NULL, NULL, NULL, '<p><strong>How to cite</strong>:&nbsp;Le Bail, P.-Y., Covain, R., Jégu, M., Fisch-Muller, S., Vigouroux, R., &amp; Keith, P. (2012). Updated checklist of the freshwater and estuarine fishes of French Guiana. <em>Cybium</em>, 36(1): 293-319. https://doi.org/10.26028/CYBIUM/2012-361-016</p>\r\n', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 2012, 'Cybium', '36', NULL, NULL, NULL, NULL, '1', '293-319', NULL, NULL, 'eng', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'https://doi.org/10.26028/cybium/2012-361-016', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 1695376428, 1712854272);

    And this is the same example in the source (D7 Biblio). Views displays screenshot "ref-biblio-views-d7.png"

    INSERT INTO `biblio` (`nid`, `vid`, `biblio_type`, `biblio_number`, `biblio_other_number`, `biblio_sort_title`, `biblio_secondary_title`, `biblio_tertiary_title`, `biblio_edition`, `biblio_publisher`, `biblio_place_published`, `biblio_year`, `biblio_volume`, `biblio_pages`, `biblio_date`, `biblio_isbn`, `biblio_lang`, `biblio_abst_e`, `biblio_abst_f`, `biblio_full_text`, `biblio_url`, `biblio_issue`, `biblio_type_of_work`, `biblio_accession_number`, `biblio_call_number`, `biblio_notes`, `biblio_custom1`, `biblio_custom2`, `biblio_custom3`, `biblio_custom4`, `biblio_custom5`, `biblio_custom6`, `biblio_custom7`, `biblio_research_notes`, `biblio_number_of_volumes`, `biblio_short_title`, `biblio_alternate_title`, `biblio_original_publication`, `biblio_reprint_edition`, `biblio_translated_title`, `biblio_section`, `biblio_citekey`, `biblio_coins`, `biblio_doi`, `biblio_issn`, `biblio_auth_address`, `biblio_remote_db_name`, `biblio_remote_db_provider`, `biblio_label`, `biblio_access_date`, `biblio_refereed`, `biblio_md5`, `biblio_formats`)
    VALUES
    	(63, 63, 102, '1', '', 'Updated checklist of the freshwater and estuarine fishes of Fren', 'Cybium', NULL, NULL, '', NULL, 2012, '36', '293-319', NULL, '', 'eng', '<p>The fish fauna of French Guiana is among the best known of South America. Various fieldwork campaigns have been conducted since the publication of the “Atlas des poissons d’eau douce” de Guyane, particularly in poorly surveyed areas, leading to the discovery of new taxa, and numerous scientific publications have provided new insights concerning this fauna. An updated checklist of the fishes of French Guiana, including all of this new information, is therefore desirable. The list contains 416 species, 367 of which are strictly freshwater. Fish diversity is strongly correlated with catchment size and is, on average, higher in French Guiana than in Suriname. The largest groups are the Characiformes (41{%}), Siluriformes (33{%}) and Perciformes (13{%}). The relative abundance of taxonomic groups differs between catchments, probably reflecting the ecological character of the rivers. Eighty seven species, around a quarter of the ichthyofauna, are listed as endemic, but this may be an underestimate because a rather strict definition of endemism is used. The rate of endemism is strongly correlated with catchment size, with some families showing higher than average rates. Comparison of the number of species shared by the different catchments suggests a highly complex pattern of dispersal as a function of the catchment size, topography, and species. The Oyapock River seems to belong to a relatively distinct biogeographic zone influenced by the Amazon basin, but it is not possible to show a broader trend. These results provide an additional tool for environmental managers and decision makers.</p>\r\n', '', 0, '', NULL, '', '', '', '<p><strong>How to cite</strong>:&nbsp;Le Bail, P.-Y., Covain, R., Jégu, M., Fisch-Muller, S., Vigouroux, R., &amp; Keith, P. (2012). Updated checklist of the freshwater and estuarine fishes of French Guiana. <em>Cybium</em>, 36(1): 293-319. https://doi.org/10.26028/CYBIUM/2012-361-016</p>\r\n', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'LeBailP.Y.2012', '<span class=\"Z3988\" title=\"ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Updated+checklist+of+the+freshwater+and+estuarine+fishes+of+French+Guiana&amp;rft.title=Cybium&amp;rft.date=2012&amp;rft.volume=36&amp;rft.spage=293&amp;rft.epage=319&amp;rft.aulast=Le+Bail&amp;rft.aufirst=Pierre-Yves&amp;rft.au=Covain%2C+Rapha%C3%ABl&amp;rft.au=J%C3%A9gu%2C+Michel&amp;rft.au=Fisch-Muller%2C+Sonia&amp;rft.au=Vigouroux%2C+R%C3%A9gis&amp;rft.au=Keith%2C+Philippe&amp;rft_id=info%3Adoi%2Fhttps%3A%2F%2Fdoi.org%2F10.26028%2Fcybium%2F2012-361-016\"></span>', 'https://doi.org/10.26028/cybium/2012-361-016', NULL, NULL, NULL, NULL, NULL, NULL, NULL, '2bd1c12018875082b2bb47823104a07c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
  • 🇫🇷France Toki Caen, Normandy
  • 🇫🇷France Toki Caen, Normandy

    It seems there is no difference between database abstract values from Biblio D7 and Bibcite D10. But in bibcite, format is defined in a second column (bibcite_abst_e__format) and NULL values are displayed after migration. If I save the bibcite reference from UI, text format is detected and NULL value disappears.
    So I guess one line is missing in the migration process about format?
    Anyway, for the moment, as a workaround for abstracts, I will save references just after migration to force the format column to be filled.

    Concerning bibcite_notes, in Bibcite, this is a Longtext field without any format whereas it's a formatted text in Biblio.
    For the moment, I will use Feeds to import these notes from Biblio inside a custom field with formatted text type so HTML tags will be displayed properly as my client needs.
    Perhaps in the future this bibcite_notes field could be updated to accept format?

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