Rspacer cannot replace files when the template contains a missing field

[hleegwater]

I cannot replace a document using the Rspace API if there are missing numbers in the columnIndex, which is a parameter within fields. I tried replacing documents with other templates and it is fine if they have for example the LACDR-ISA - Study v1.0.0 template, but the Assay template does not work.

Screenshot of the error:

Code that you can use to see that the columnIndex is missing some numbers.

library(rspacer)
template_id <- "SD260025" # LACDR-ISA - Assay (General) v1.0.0
template_file <- rspacer:::doc_get_fields(template_id) |> 
  relocate(columnIndex)
head(template_file)

gives:

Using the field id instead, as described on https://community.researchspace.com/public/apiDocs > Documents > PUT did not solve the issue. I do not know why this error occurs and think that we should contact the people at Rspace.

[hleegwater]

Some additional clarification: the API user manual from Rspace says that one can replace a specific field. I noticed, while trying this, that this is sometimes a problem when replacing one field and no changes are made. That is not a very big problem, but there is another problem as well, described above. Somehow, a subset of our templates could not be replaced with a new version. LACDR-ISA - Investigation v1.0.0 and LACDR-ISA - Study v1.0.0 work very well, but I could not replace individual fields, or entire versions of documents that were built using LACDR-ISA - Assay (General) v1.0.0.

After looking at it for a long time, I noticed that there is a column columnIndex that has gaps, fields 6 and 7 are missing, which results in a total of 7 rows (7 fields). The Rspace API expects 10 rows, I do not know why. Defining the id, which should work, did not work.

• not all templates have the problem. It is only the Assay
• It doesn't matter whether I try to make changes from html, excel, or directly by concatenating some strings. All give the same error, which is why it is on the Rspace API side.
• Making new documents with the Assay template still works. It is really in the replacing part.

[hleegwater]

Code to use to test and recreate the problem:

1. Install the LACDR-ISA templates from GitHub remotes::install_github("LACDR/LACDR.ISA")
2. Create a new LACDR-ISA - Assay (General) v1.0.0 and save it as .qmd. Render it to html. For this: File > R markdown > From Template > LACDR-ISA - Assay (General) v1.0.0. Fill in some stuff. Save as .qmd file. Render to html. Save as test1.html
3. Repeat by making some changes, so that you have a second file. Save as test2.html
4. Use the following chunk to upload, and replace the upload with your second file:

# Test upload

library(rspacer)
template_id <- "SD260025" # LACDR-ISA - Assay (General) v1.0.0
# Create new document
new_doc <- document_create_from_html(
  path = "test1.html",
  template_id = template_id
)
# Replace document - which fails
new_doc$id
new_doc$globalId

new_doc <- document_create_from_html(
  path = "test2.html",
  tags = "updated",
  existing_document_id = new_doc$globalId
)

# Look at the missing column number
template_file <- rspacer:::doc_get_fields(template_id) |> 
  relocate(columnIndex)
head(template_file)