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earnaud / MetaShARK-v2

MetaShARK (Metadata Shiny Automated Resource & Knowledge) is a R shiny app allowing the user to get information about Ecological Metadata Language and to fill in metadata for datasets according to this standard. This version of MetaShARK offers the user a R package to access the app.
MIT License
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1.7.2 "latest 31 08 version" bug when creating the EML #194

Open yvanlebras opened 2 years ago

yvanlebras commented 2 years ago

Testing this latest version digest dacb63f2c33d , with EAL testing files, I have a freeze when generating EML, with associated error message:

Warning: Argument issues found. Use issues() to see them.
Checking inputs
Warning: Template issues found. Use issues() to see them.
Making EML ...
<eml>
Warning: Missing 'package.id', assigning a UUID
  <dataset>
    <title>
    <creator>
    <pubDate>
    <abstract>
    <keywordSet>
    <additionalInfo>
    <intellectualRights>
    <coverage>
Warning: Geographic coverage is recommended.
        <temporalCoverage>
        <taxonomicCoverage>
    <maintenance>
    <contact>
    <methods>
    <dataTable> (datafile_1.tsv)
    <dataTable> (datafile_2.tsv)
</eml>
Writing EML (c0b87043-2046-47d3-bc1c-1ff14753c68c.xml)
Validating EML
  Validation passed :)
Done.
Called from: `<observer>`(...)
Browse[1]>
debug: valid <- EML::eml_validate(dir(main_env$save_variable$SelectDP$dp_eml_path,
    pattern = main_env$save_variable$SelectDP$dp_title, full.names = TRUE))
Warning: Error in if: argument is of length zero
  47: generalized_parser
  46: EML::eml_validate
  45: <observer>
   2: runApp
   1: MetaShARK::runMetashark

Furthermore, This latest version was generated to disable the "interactive table" function "manual editing of attributes" but the button is there and we can launch it ;) maybe the action done on the code to disable it was not done on the good place of the code and maybe is generating the error ?

yvanlebras commented 2 years ago

update: it seems the EML is generated (looking at local files). But impossible to load the created data package on MetaShARK (there is a freeze) with associated logs:

[Metric] Connected users at 2022-08-31 14:51:25: 1
[fill_module.R/navigation] save & template
[fill_module.R/navigation] set EAL variables
[fill_module.R/navigation] set local_rv
[setLocalRV] set variable 1
[fill_module.R/navigation] change pane
[fill_module.R/navigation] update UI
[fill_module.R/navigation] update history
[fill_module.R/navigation] save_variables change
[fill_module.R/navigation] display UI
[fill_module.R/navigation] ended
Browse[2]> Called from: `<observer>`(...)
Browse[1]> debug: valid <- EML::eml_validate(dir(main_env$save_variable$SelectDP$dp_eml_path,
    pattern = main_env$save_variable$SelectDP$dp_title, full.names = TRUE))
Warning: Error in if: argument is of length zero
  47: generalized_parser
  46: EML::eml_validate
  45: <observer>
   2: runApp
   1: MetaShARK::runMetashark
[fill_module.R/navigation] save & template
[fill_module.R/navigation] set EAL variables
[fill_module.R/navigation] set local_rv
[setLocalRV] set variable 9
[fill_module.R/navigation] change pane
[fill_module.R/navigation] update UI
[fill_updatePageUI.R] page 9
[fill_module.R/navigation] update history
[fill_module.R/navigation] save_variables change
[fill_module.R/navigation] display UI
[fill_module.R/navigation] ended
[fill_module.R/autosave] step: 9