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:
▆
- ├─openproblems.docs::render_task_readme_qmd(metadata)
- │ └─openproblems.docs:::.render_task_parts(task_metadata)
- │ └─purrr::map_chr(...)
- │ └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
- │ ├─purrr:::with_indexed_errors(...)
- │ │ └─base::withCallingHandlers(...)
- │ ├─purrr:::call_with_cleanup(...)
- │ └─openproblems.docs (local) .f(.x[[i]], ...)
- │ └─openproblems.docs::render_file_format(task_metadata$files[[file_name]])
- │ ├─openproblems.utils::strip_margin(glue("Format:\n |\n |:::{{.small}}\n |{paste(.render_file_format__example(spec), collapse = '\n')}\n |:::\n |\n |Data structure:\n |\n |:::{{.small}}\n |{paste(.render_file_format__table(spec), collapse = '\n')}\n |:::\n |"))
- │ │ └─base::gsub(paste0("(^|\n)[ \t]*", symbol), "\1", text)
- │ │ └─base::is.factor(x)
- │ ├─glue::glue("Format:\n |\n |:::{{.small}}\n |{paste(.render_file_format__example(spec), collapse = '\n')}\n |:::\n |\n |Data structure:\n |\n |:::{{.small}}\n |{paste(.render_file_format__table(spec), collapse = '\n')}\n |:::\n |")
- │ │ └─glue::glue_data(...)
- │ ├─base::paste(.render_file_format__example(spec), collapse = "\n")
- │ └─openproblems.docs:::.render_file_format__example(spec)
- │ ├─dplyr::summarise(...)
- │ └─dplyr:::summarise.data.frame(spec$expected_format, str = paste0("'", .data$name, "'", collapse = ", "))
- │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
- │ ├─base::withCallingHandlers(...)
- │ └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
- │ └─base::lapply(.x, .f, ...)
- │ └─dplyr (local) FUN(X[[i]], ...)
- │ └─mask$eval_all_summarise(quo)
- │ └─dplyr (local) eval()
- ├─glue (local)
<fn>("paste(.render_file_format__example(spec), collapse = '\n')")
- │ ├─.transformer(expr, env) %||% .null
- │ └─glue (local) .transformer(expr, env)
- │ ├─glue:::with_glue_error(...)
- │ │ └─base::withCallingHandlers(...)
- │ └─base::eval(expr, envir)
- │ └─base::eval(expr, envir)
- ├─base::paste0("'", .data$name, "'", collapse = ", ")
- ├─name
- ├─rlang:::
$.rlang_data_pronoun(.data, name)
- │ └─rlang:::data_pronoun_get(...)
- └─rlang:::abort_data_pronoun(x, call = y)
- └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
Execution halted
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Expected behavior
expect the README.md to be updated.
Describe the bug
After the PR that added the common submodule, the
common/scripts/create_task_readmescript fails in older tasks. Here attempting to run it for thetask_perturbation_predictionTo Reproduce
In
task_perturbation_prediction:❯ ./scripts/create_readme.sh
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Read task metadata
Looking for project root in
'/viash_automount/Users/arturszalata/perturbation_test/task_perturbation_prediction/src/api'
Project root found at
'/viash_automount/Users/arturszalata/perturbation_test/task_perturbation_prediction'
Reading project config
Reading component yamls
Reading file yamls
Generating task graph
Render README.qmd content
Warning message:
Component spec validation failed: 1 error validating api_component_spec object
from source
/viash_automount/Users/arturszalata/perturbation_test/task_perturbation_prediction/src/api/comp_method.yaml:
Render authors
Render task graph
Render task API parts
Error in
map_chr():ℹ In index: 5.
Caused by error:
! Failed to evaluate glue component {paste(.render_file_format__example(spec), collapse = '
')}
Caused by error in
summarise():ℹ In argument:
str = paste0("'", .data$name, "'", collapse = ", ").Caused by error in
.data$name:! Column
namenot found in.data.Backtrace:
▆
<fn>("paste(.render_file_format__example(spec), collapse = '\n')")$.rlang_data_pronoun(.data, name)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.