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create_task_readme fails for older tasks #924

@szalata

Description

@szalata

Describe the bug
After the PR that added the common submodule, the common/scripts/create_task_readme script fails in older tasks. Here attempting to run it for the task_perturbation_prediction

To Reproduce
In task_perturbation_prediction:

❯ ./scripts/create_readme.sh
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Read task metadata
Looking for project root in
'/viash_automount/Users/arturszalata/perturbation_test/task_perturbation_prediction/src/api'
Project root found at
'/viash_automount/Users/arturszalata/perturbation_test/task_perturbation_prediction'
Reading project config
Reading component yamls
Reading file yamls
Generating task graph
Render README.qmd content
Warning message:
Component spec validation failed: 1 error validating api_component_spec object
from source
/viash_automount/Users/arturszalata/perturbation_test/task_perturbation_prediction/src/api/comp_method.yaml:

  • (#/additionalProperties): must NOT have additional properties
    Render authors
    Render task graph
    Render task API parts
    Error in map_chr():
    ℹ In index: 5.
    Caused by error:
    ! Failed to evaluate glue component {paste(.render_file_format__example(spec), collapse = '
    ')}
    Caused by error in summarise():
    ℹ In argument: str = paste0("'", .data$name, "'", collapse = ", ").
    Caused by error in .data$name:
    ! Column name not found in .data.
    Backtrace:
    1. ├─openproblems.docs::render_task_readme_qmd(metadata)
    2. │ └─openproblems.docs:::.render_task_parts(task_metadata)
    3. │ └─purrr::map_chr(...)
    4. │ └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
    5. │ ├─purrr:::with_indexed_errors(...)
    6. │ │ └─base::withCallingHandlers(...)
    7. │ ├─purrr:::call_with_cleanup(...)
    8. │ └─openproblems.docs (local) .f(.x[[i]], ...)
    9. │ └─openproblems.docs::render_file_format(task_metadata$files[[file_name]])
  1. │ ├─openproblems.utils::strip_margin(glue("Format:\n |\n |:::{{.small}}\n |{paste(.render_file_format__example(spec), collapse = '\n')}\n |:::\n |\n |Data structure:\n |\n |:::{{.small}}\n |{paste(.render_file_format__table(spec), collapse = '\n')}\n |:::\n |"))
  2. │ │ └─base::gsub(paste0("(^|\n)[ \t]*", symbol), "\1", text)
  3. │ │ └─base::is.factor(x)
  4. │ ├─glue::glue("Format:\n |\n |:::{{.small}}\n |{paste(.render_file_format__example(spec), collapse = '\n')}\n |:::\n |\n |Data structure:\n |\n |:::{{.small}}\n |{paste(.render_file_format__table(spec), collapse = '\n')}\n |:::\n |")
  5. │ │ └─glue::glue_data(...)
  6. │ ├─base::paste(.render_file_format__example(spec), collapse = "\n")
  7. │ └─openproblems.docs:::.render_file_format__example(spec)
  8. │ ├─dplyr::summarise(...)
  9. │ └─dplyr:::summarise.data.frame(spec$expected_format, str = paste0("'", .data$name, "'", collapse = ", "))
  10. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
  11. │ ├─base::withCallingHandlers(...)
  12. │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
  13. │ └─base::lapply(.x, .f, ...)
  14. │ └─dplyr (local) FUN(X[[i]], ...)
  15. │ └─mask$eval_all_summarise(quo)
  16. │ └─dplyr (local) eval()
  17. ├─glue (local) <fn>("paste(.render_file_format__example(spec), collapse = '\n')")
  18. │ ├─.transformer(expr, env) %||% .null
  19. │ └─glue (local) .transformer(expr, env)
  20. │ ├─glue:::with_glue_error(...)
  21. │ │ └─base::withCallingHandlers(...)
  22. │ └─base::eval(expr, envir)
  23. │ └─base::eval(expr, envir)
  24. ├─base::paste0("'", .data$name, "'", collapse = ", ")
  25. ├─name
  26. ├─rlang:::$.rlang_data_pronoun(.data, name)
  27. │ └─rlang:::data_pronoun_get(...)
  28. └─rlang:::abort_data_pronoun(x, call = y)
  29. └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
    Execution halted
    WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

Expected behavior
expect the README.md to be updated.

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