Make JoinKeys related changes due to refactor

[gogonzo]

Open over #75 to implement improved JoinKeys API

Also closes #95

Fixed apps:

• basic-teal
• exploratory
• safety
• efficacy
• patient-profile
• early-dev
• longitudinal
• RNA-seq
• python

Full installation

staged.dependencies::dependency_table(
  project = "insightsengineering/teal.data@https://github.com",
  project_type = "repo@host",
  ref = "591-migrate-to-teal_data@78_simplify_joinkeys@main",
  verbose = 1
) |> staged.dependencies::install_deps(install_direction = "all")

[m7pr]

Hey, overall looks good and simplifies the code redundancy. I noticed few places where we can substitute data@join_keys with join_keys(data)

[vedhav]

Have switched the target to dev because for now, we can only have successful deployments with multiple branches. Soon, we plan to see if there is something better we can do about this.

[vedhav]

After the teal_data_module is created in the teal PR #957 and the new python_dataset_connector is created the python app will be fixed.

[kartikeyakirar]

should we exclude ADSLPCA since it is not present in the default_cdisc_join_keys. Instead, we should simply use c("ADSL", "ADRS", "ADLB").to enhance clarity in the subsequent step ?

[gogonzo]

Makes sense to default_cdisc_join_keys[c("ADSL", "ADRS", "ADLB")] # no ADLBPCA defaults

[vedhav]

I think it's just a matter of DRY here. We already store the datanames in a variable so it's convenient to do a subset like this. Now it's okay, previously we used to get a join key set for ADLB with NULL.

[kartikeyakirar]

@averissimo @gogonzo what about datanames not present in default_cdisc_join_keys ?

> join_keys(data)
A join_keys object containing foreign keys between 9 datasets:
ADSL: [STUDYID, USUBJID]
  <-- ADAE: [STUDYID, USUBJID]
  <-- ADCM: [STUDYID, USUBJID]
  <-- ADEX: [STUDYID, USUBJID]
  <-- ADLB: [STUDYID, USUBJID]
  <-- ADRS: [STUDYID, USUBJID]
  <-> ADTR: [STUDYID, USUBJID]
  <-> ADTRWF: [STUDYID, USUBJID]
  <-> ADRSSWIM: [STUDYID, USUBJID]
ADAE: [STUDYID, USUBJID, ASTDTM, AETERM, AESEQ]
  --> ADSL: [STUDYID, USUBJID]
  --* (implicit via parent with): ADCM, ADEX, ADLB, ADRS
ADCM: [STUDYID, USUBJID, ASTDTM, CMSEQ, ATC1CD, ATC2CD, ATC3CD, ATC4CD]
  --> ADSL: [STUDYID, USUBJID]
  --* (implicit via parent with): ADAE, ADEX, ADLB, ADRS
ADEX: [STUDYID, USUBJID, PARCAT1, PARAMCD, AVISITN, ASTDTM, EXSEQ]
  --> ADSL: [STUDYID, USUBJID]
  --* (implicit via parent with): ADAE, ADCM, ADLB, ADRS
ADLB: [STUDYID, USUBJID, PARAMCD, AVISIT]
  --> ADSL: [STUDYID, USUBJID]
  --* (implicit via parent with): ADAE, ADCM, ADEX, ADRS
ADRS: [STUDYID, USUBJID, PARAMCD, AVISIT]
  --> ADSL: [STUDYID, USUBJID]
  --* (implicit via parent with): ADAE, ADCM, ADEX, ADLB
ADTR: [STUDYID, USUBJID, PARAMCD, AVISIT]
  <-> ADSL: [STUDYID, USUBJID]
ADTRWF: [STUDYID, USUBJID, PARAMCD, AVISIT]
  <-> ADSL: [STUDYID, USUBJID]
ADRSSWIM: [STUDYID, USUBJID, PARAMCD, AVISIT]
  <-> ADSL: [STUDYID, USUBJID] 

> old_key$get_join_keys()
A join_keys object containing foreign keys between 9 datasets:
ADSL: [STUDYID, USUBJID]
  <-- ADAE: [STUDYID, USUBJID]
  <-- ADEX: [STUDYID, USUBJID]
  <-- ADCM: [STUDYID, USUBJID]
  <-- ADTR: [STUDYID, USUBJID]
  <-- ADTRWF: [STUDYID, USUBJID]
  <-- ADRS: [STUDYID, USUBJID]
  <-- ADRSSWIM: [STUDYID, USUBJID]
  <-- ADLB: [STUDYID, USUBJID]
ADAE: [STUDYID, USUBJID, AETERM, AESEQ]
  --> ADSL: [STUDYID, USUBJID]
  <-> ADEX: [STUDYID, USUBJID]
  <-> ADCM: [STUDYID, USUBJID]
  <-> ADTR: [STUDYID, USUBJID]
  <-> ADTRWF: [STUDYID, USUBJID]
  <-> ADRS: [STUDYID, USUBJID]
  <-> ADRSSWIM: [STUDYID, USUBJID]
  <-> ADLB: [STUDYID, USUBJID]
ADEX: [STUDYID, USUBJID, PARCAT1, PARAMCD, AVISITN, ASTDTM, EXSEQ]
  --> ADSL: [STUDYID, USUBJID]
  <-> ADAE: [STUDYID, USUBJID]
  <-> ADCM: [STUDYID, USUBJID]
  <-> ADTR: [STUDYID, USUBJID]
  <-> ADTRWF: [STUDYID, USUBJID]
  <-> ADRS: [STUDYID, USUBJID]
  <-> ADRSSWIM: [STUDYID, USUBJID]
  <-> ADLB: [STUDYID, USUBJID]
ADCM: [STUDYID, USUBJID, ASTDTM, CMSEQ, ATC1CD, ATC2CD, ATC3CD, ATC4CD]
  --> ADSL: [STUDYID, USUBJID]
  <-> ADAE: [STUDYID, USUBJID]
  <-> ADEX: [STUDYID, USUBJID]
  <-> ADTR: [STUDYID, USUBJID]
  <-> ADTRWF: [STUDYID, USUBJID]
  <-> ADRS: [STUDYID, USUBJID]
  <-> ADRSSWIM: [STUDYID, USUBJID]
  <-> ADLB: [STUDYID, USUBJID]
ADTR: [STUDYID, USUBJID, PARAMCD, AVISIT]
  --> ADSL: [STUDYID, USUBJID]
  <-> ADAE: [STUDYID, USUBJID]
  <-> ADEX: [STUDYID, USUBJID]
  <-> ADCM: [STUDYID, USUBJID]
  <-> ADTRWF: [STUDYID, USUBJID]
  <-> ADRS: [STUDYID, USUBJID]
  <-> ADRSSWIM: [STUDYID, USUBJID]
  <-> ADLB: [STUDYID, USUBJID]
ADTRWF: [STUDYID, USUBJID, PARAMCD, AVISIT]
  --> ADSL: [STUDYID, USUBJID]
  <-> ADAE: [STUDYID, USUBJID]
  <-> ADEX: [STUDYID, USUBJID]
  <-> ADCM: [STUDYID, USUBJID]
  <-> ADTR: [STUDYID, USUBJID]
  <-> ADRS: [STUDYID, USUBJID]
  <-> ADRSSWIM: [STUDYID, USUBJID]
  <-> ADLB: [STUDYID, USUBJID]
ADRS: [STUDYID, USUBJID, PARAMCD, AVISIT]
  --> ADSL: [STUDYID, USUBJID]
  <-> ADAE: [STUDYID, USUBJID]
  <-> ADEX: [STUDYID, USUBJID]
  <-> ADCM: [STUDYID, USUBJID]
  <-> ADTR: [STUDYID, USUBJID]
  <-> ADTRWF: [STUDYID, USUBJID]
  <-> ADRSSWIM: [STUDYID, USUBJID]
  <-> ADLB: [STUDYID, USUBJID]
ADRSSWIM: [STUDYID, USUBJID, PARAMCD, AVISIT]
  --> ADSL: [STUDYID, USUBJID]
  <-> ADAE: [STUDYID, USUBJID]
  <-> ADEX: [STUDYID, USUBJID]
  <-> ADCM: [STUDYID, USUBJID]
  <-> ADTR: [STUDYID, USUBJID]
  <-> ADTRWF: [STUDYID, USUBJID]
  <-> ADRS: [STUDYID, USUBJID]
  <-> ADLB: [STUDYID, USUBJID]
ADLB: [STUDYID, USUBJID, PARAMCD, AVISIT]
  --> ADSL: [STUDYID, USUBJID]
  <-> ADAE: [STUDYID, USUBJID]
  <-> ADEX: [STUDYID, USUBJID]
  <-> ADCM: [STUDYID, USUBJID]
  <-> ADTR: [STUDYID, USUBJID]
  <-> ADTRWF: [STUDYID, USUBJID]
  <-> ADRS: [STUDYID, USUBJID]
  <-> ADRSSWIM: [STUDYID, USUBJID] 

[gogonzo]

Thanks @kartikeyakirar
The second is the old class which will be removed next week. In old classes update_keys_given_parent are run in a different moment so the keys are hardcoded in a list.
Both lists will work as expected, where the second one won't be here anymore.

[kartikeyakirar]

Got it!

[vedhav]

Please merge this PR #96 and merge the main into dev before merging this PR targeting thedev branch.

[kartikeyakirar]

I've tested all the applications, and none of them have encountered any failures in any module.