Add one or more vignettes

[schuemie]

For example just walking through the test code here

[gowthamrao]

Add to vignette https://github.com/OHDSI/ROhdsiWebApi/issues/37#issuecomment-618177373

[schuemie]

@gowthamrao: When you have time, would you mind drafting the vignette?

[gowthamrao]

Add insights from this discussion to Vignette https://github.com/OHDSI/ROhdsiWebApi/issues/60

[gowthamrao]

Model Vignette (in terms of length and style) based on http://ohdsi.github.io/DatabaseConnector/articles/UsingDatabaseConnector.html

[ablack3]

Can we change the vignette so that it can be knitted without requiring access to a webapi server provided it has not changed since the last time it was knitted? Maybe we can use the cache = TRUE option to cache the chunks and not rerun them unless the vignette actually changes.

[gowthamrao]

Thank you @ablack3 Would you be able to make the initial attempt and do a PR?

[ablack3]

I'm getting hung up on the post example in the vignette. @gowthamrao Are you able to successfully run the code below?

library(ROhdsiWebApi)
baseUrl <- 'http://api.ohdsi.org:80/WebAPI'

jsonExpression <- '{
  "items": [
    {
      "concept": {
        "CONCEPT_ID": 81097,
        "CONCEPT_NAME": "Feltys syndrome",
        "STANDARD_CONCEPT": "S",
        "STANDARD_CONCEPT_CAPTION": "Standard",
        "INVALID_REASON": "V",
        "INVALID_REASON_CAPTION": "Valid",
        "CONCEPT_CODE": "57160007",
        "DOMAIN_ID": "Condition",
        "VOCABULARY_ID": "SNOMED",
        "CONCEPT_CLASS_ID": "Clinical Finding"
      },
      "isExcluded": true,
      "includeDescendants": false,
      "includeMapped": false
    },
    {
      "concept": {
        "CONCEPT_ID": 80809,
        "CONCEPT_NAME": "Rheumatoid arthritis",
        "STANDARD_CONCEPT": "S",
        "STANDARD_CONCEPT_CAPTION": "Standard",
        "INVALID_REASON": "V",
        "INVALID_REASON_CAPTION": "Valid",
        "CONCEPT_CODE": "69896004",
        "DOMAIN_ID": "Condition",
        "VOCABULARY_ID": "SNOMED",
        "CONCEPT_CLASS_ID": "Clinical Finding"
      },
      "isExcluded": false,
      "includeDescendants": true,
      "includeMapped": false
    },
    {
      "concept": {
        "CONCEPT_ID": 4035611,
        "CONCEPT_NAME": "Seropositive rheumatoid arthritis",
        "STANDARD_CONCEPT": "S",
        "STANDARD_CONCEPT_CAPTION": "Standard",
        "INVALID_REASON": "V",
        "INVALID_REASON_CAPTION": "Valid",
        "CONCEPT_CODE": "239791005",
        "DOMAIN_ID": "Condition",
        "VOCABULARY_ID": "SNOMED",
        "CONCEPT_CLASS_ID": "Clinical Finding"
      },
      "isExcluded": false,
      "includeDescendants": true,
      "includeMapped": false
    }
  ]
}'
rExpression <- RJSONIO::fromJSON(jsonExpression)
conceptSetName <- '[ROhdsiWebApi Vignette] Rheumatoid Arthritis concept set'
ROhdsiWebApi::postConceptSetDefinition(baseUrl = baseUrl, 
                                       conceptSetDefinition = rExpression, 
                                       name = conceptSetName)
#> Error in postDefinition(name = name, baseUrl = baseUrl, category = "conceptSet", :

^{Created on 2020-07-14 by the reprex package (v0.3.0)}

[gowthamrao]

tagging @azimov as he experienced similar issue

[azimov]

I removed the execution of posts in the vignette is #180, whoever produces the package documentation for github should

1) Set a good web api endpoint before generating the pdf doc that gets uploaded to github 2) Set eval= TRUE for the parts of the vignette that requires a conseptset/cohort to be posted to WebApi 3) Make sure the posted definitions are cleaned up from the webapi instance 4) Run the package maintenance script to remove the old pdf and create the new docs 5) Commit and push the new pdf.

The issue with posting concept sets should have also been fixed in #179

[gowthamrao]

Thank you @azimov !