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Small docs PR for building new OMOP CDM Versions

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Jacob S. Zelko 2023-07-18 08:41:23 -07:00 committed by GitHub
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@ -91,10 +91,14 @@ For **changes to the model structure**, rename the table level and field level i
For **squashing bugs** make the necessary changes in the csv file corresponding to the major.minor version you are fixing. For example, if you are working on fixes to v5.3.3 you would make changes in the v5.3 files. (skip to step 2)
### Step 1.2
The csv files can now be updated with the changes and additions for the new CDM version. If a new table should be added, add a line to the *Table_Level.csv* with the table name and description and list it as part of the CDM schema. The remaining columns are quality checks that can be run. Details [here](https://ohdsi.github.io/DataQualityDashboard/index.html) on what those are. After adding any tables, make any changes or additions to CDM fields in the *Field_Level.csv*. The columns are meant to mimic how a DDL is structured, which is how it will eventually be generated. A yes in the field *isRequired* indicates a NOT NULL constraint and the datatype field should be filled in exactly how it would look in the DDL. Any additions or changes should also be reflected in the userGuidance and etlConventions fields, which are the basis for the documentation. **DO NOT MAKE ANY CHANGES IN THE DDL ITSELF**. The structure is set up in such a way that the csv files are the ground truth. If changes are made in the DDL instead of the csv files then the DDL will be out of sync with the documentation and the DQD.
The csv files can now be updated with the changes and additions for the new CDM version. If a new table should be added, add a line to the *Table_Level.csv* with the table name and description and list it as part of the CDM schema. The remaining columns are quality checks that can be run. Details [here](https://ohdsi.github.io/DataQualityDashboard/index.html) on what those are. After adding any tables, make any changes or additions to CDM fields in the *Field_Level.csv*. The columns are meant to mimic how a DDL is structured, which is how it will eventually be generated. A yes in the field *isRequired* indicates a NOT NULL constraint and the datatype field should be filled in exactly how it would look in the DDL. Any additions or changes should also be reflected in the userGuidance and etlConventions fields, which are the basis for the documentation. **DO NOT MAKE ANY CHANGES IN THE DDL ITSELF**. The structure is set up in such a way that the csv files are the ground truth. If changes are made in the DDL instead of the csv files then the DDL will be out of sync with the documentation and the DQD.
### Step 1.3
Within `R/listSupportedVersions.R`, modify the `listSupportedVersions` function to have the value associated with your newly created CSVs. For example, if you created CSVs named "OMOP_CDMv5.9_Field_Level.csv" and "OMOP_CDMv5.9_Table_Level.csv", you would need to add the value `"5.9"` to the `supportedVersions` variable within the function. Save this function after you have updated it.
## Step 2
Once all changes are made the csvs, rebuild the package and then open `extras/codeToRun.R`. To make sure that your new version is recognized by the package run the function `listSupportedVersions()`. If you do not see it, make sure your new csv files are in inst/csv and that you have rebuilt the package. Once you have confirmed that the package recognizes your new version, run the function `buildRelease()`. You should now see a file in inst/ddl for your new version.
Once all changes are made to the csvs and package as needed, rebuild the package and then open `extras/codeToRun.R`. To make sure that your new version is recognized by the package run the function `listSupportedVersions()`. If you do not see it, make sure your new csv files are in inst/csv and that you have rebuilt the package. Once you have confirmed that the package recognizes your new version, run the function `buildRelease()`. You should now see a file in inst/ddl for your new version.
**NOTE ABOUT CDM v6.0**
====================