Error in seq.int(0, to0 - from, by) : 'to' must be a finite number

[faubele]

Problem Description

Shortly after downloading all the necessary FHIR resources, the script stops working and throws an error. The error message is shown below.

Execution Informations

• blaze_update branch
• Execution with docker-compose

Error Message

...
[1] "Data selection done"
Warning messages:
1: `fhir_style()` was deprecated in fhircrackr 2.0.0.
ℹ Please code style elements directly in fhir_table_description().
2: The `style` argument of `fhir_table_description()` is deprecated as of
fhircrackr 2.0.0.
ℹ Please code style elements directly in the table description. Overwriting
  fhir_table_descriptions arguments for now.
3: In crack_bundles_to_one_table(bundles = bundles, table_description = table_description,  :
  The resource type or columns you are looking for don't seem to be present in the bundles.
 Returning an empty table.
4: In crack_bundles_to_one_table(bundles = bundles, table_description = table_description,  :
  The resource type or columns you are looking for don't seem to be present in the bundles.
 Returning an empty table.
5: In crack_bundles_to_one_table(bundles = bundles, table_description = table_description,  :
  The resource type or columns you are looking for don't seem to be present in the bundles.
 Returning an empty table.
[1] "loading stroke cohort"
[1] "extracting lat and long based on PLZ"
[1] "stroke daily counts - three different outputs"
Error in seq.int(0, to0 - from, by) : 'to' must be a finite number
Calls: source -> withVisible -> eval -> eval -> seq -> seq.Date
Execution halted

Hint

In other projects we had problems with our encounter resources, because there are a lot of resources that have no end-date set. So in the data table 'stroke_cohort.csv the admission_date and discharge_date are 'NA' for some rows.
Maybe this is unexpected and causing problems.

[NandhiniS08]

Hi, Thanks for raising the issue and providing a hint about the possible cause of the issue. I have added a logic to handle this before creating the different data frames. I hope this clears the error I have also added some new updates from the master branch to the blaze branch as well. This requires a change in config.yml to add a new parameter (max_bundles). Please copy the config_default.yml and update it.

[faubele]

Hi, thank you for providing such a quick fix.
I will pull the new changes and check if everything works fine. The download of the FHIR resources just takes a while, but I will update you as soon as possible.

[faubele]

I pulled the new changes, adjusted the config.yml file and started the docker container again, but sadly the error still appears.

[NandhiniS08]

Can you tell me what its printing with the message?

• "Missing dates count after coalesce:"
• Stroke cohort rows after removing missing dates:"

[NandhiniS08]

Solved in the commit for fix #17