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- For users enrolled as an `Access Administrator`:
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- [`ama cgar`](ama-cgar) can be used to manage the type(s) of access that access groups have to column groups.
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- [`castor`](#castor) provides subcommands to perform administrative tasks related to (the import of) data from the Castor EDC system.
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- [`castor`](#castor) provides subcommands to perform administrative tasks related to PEP's [Castor integration](Castor-integration) functionality.
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- [`castor export`](#castor-export) @@@ TODO @@@
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- [`castor list-sp-columns`](#castor-list-sp-columns) @@@ TODO @@@
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- [`castor list-import-columns`](#castor-list-import-columns) @@@ TODO @@@
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- [`castor create-import-columns`](#castor-create-import-columns) @@@ TODO @@@
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- [`castor column-name-mapping`](#castor-column-name-mapping) @@@ TODO @@@
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## `ama`
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... | ... | @@ -166,25 +171,10 @@ The output lists |
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The `castor` command's various sub-commands are used to interact with PEP's [Castor integration](https://gitlab.pep.cs.ru.nl/pep-public/user-docs/-/wikis/Castor-integration) functionality. Most commands are intended for (and restricted to) use by Data Administrator to configure the system for the [import of Castor data](https://gitlab.pep.cs.ru.nl/pep-public/user-docs/-/wikis/Castor-integration#import).
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### `castor export`
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### `castor column-name-mapping`
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@@@ more here @@@
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### `castor list-import-columns`
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This command lists the columns that are needed when the specified Castor data are [imported into PEP](https://gitlab.pep.cs.ru.nl/pep-public/user-docs/-/wikis/Castor-integration#import). Since the import process cannot create columns itself, Data Administrator must create required columns beforehand. (S)he then uses this command to find out which columns are needed. The command must be invoked with the `--sp-column` switch, specifying the column containing short pseudonym values that correspond with the Castor study's record IDs. E.g.:
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```
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pepcli castor list-import-columns --sp-column ShortPseudonym.Visit1.Castor.HomeQuestionnaires`
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```
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While the output lists the columns that will be needed by the import process, missing columns are not created by this command. Use the [`castor create-import-columns` command](#castor-create-import-columns) instead to have the columns created instead of just listed. Alternatively, Data Administrator can `castor list` the columns, then invoke [`ama column`](#ama-column)'s `create` and `addTo` commands manually to create the columns and group them into the `Castor` column group.
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The `castor list-import-columns` command accepts two optional switches:
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- the `--xml-structure-file` switch can be used to work around a Castor bug that prevents `pepcli` from being able to list import columns when PEP is configured to import Castor survey data, and there are survey packages containing more than 10 surveys. For such situations, the Castor administrator should [export](https://helpdesk.castoredc.com/article/170-export-and-import-the-form-structure) the survey package structures from the Castor Web interface, which yields an XML file. The path to this XML file must then be passed to the `--xml-structure-file` switch to allow import columns to be listed.
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- the `--answer-set-count` is used for Castor studies containing surveys that are answered multiple times by participants. PEP imports such survey data into [numbered columns](https://gitlab.pep.cs.ru.nl/pep-public/user-docs/-/wikis/Castor-integration#column-naming), and the switch indicates the number of answer sets to expect. For example, if participants will answer a survey a maximum of 10 times, specify `--answer-set-count 10` to have the command list sufficient column names for all survey answers to be imported.
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### `castor create-import-columns`
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This command ensures that all columns exist that will be needed when the specified Castor data are [imported into PEP](https://gitlab.pep.cs.ru.nl/pep-public/user-docs/-/wikis/Castor-integration#import). Since the import process cannot create columns itself, Data Administrator can use this command to create them beforehand. When invoked without further parameters, the command creates missing columns for all Castor data that will be imported. Each created column is also automatically added to the `Castor` column group, ensuring that the column is writable to the import process:
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pepcli castor create-import-columns --sp-column ShortPseudonym.Covid.Castor.CovidQuestionnaires --answer-set-count 30 --xml-structure-file C:\Users\Gonk\Desktop\CastorExport.xml
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```
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### `castor export`
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@@@ more here @@@
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### `castor list-import-columns`
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This command lists the columns that are needed when the specified Castor data are [imported into PEP](https://gitlab.pep.cs.ru.nl/pep-public/user-docs/-/wikis/Castor-integration#import). Since the import process cannot create columns itself, Data Administrator must create required columns beforehand. (S)he then uses this command to find out which columns are needed. The command must be invoked with the `--sp-column` switch, specifying the column containing short pseudonym values that correspond with the Castor study's record IDs. E.g.:
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```
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pepcli castor list-import-columns --sp-column ShortPseudonym.Visit1.Castor.HomeQuestionnaires`
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```
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While the output lists the columns that will be needed by the import process, missing columns are not created by this command. Use the [`castor create-import-columns` command](#castor-create-import-columns) instead to have the columns created instead of just listed. Alternatively, Data Administrator can `castor list` the columns, then invoke [`ama column`](#ama-column)'s `create` and `addTo` commands manually to create the columns and group them into the `Castor` column group.
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The `castor list-import-columns` command accepts two optional switches:
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- the `--xml-structure-file` switch can be used to work around a Castor bug that prevents `pepcli` from being able to list import columns when PEP is configured to import Castor survey data, and there are survey packages containing more than 10 surveys. For such situations, the Castor administrator should [export](https://helpdesk.castoredc.com/article/170-export-and-import-the-form-structure) the survey package structures from the Castor Web interface, which yields an XML file. The path to this XML file must then be passed to the `--xml-structure-file` switch to allow import columns to be listed.
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- the `--answer-set-count` is used for Castor studies containing surveys that are answered multiple times by participants. PEP imports such survey data into [numbered columns](https://gitlab.pep.cs.ru.nl/pep-public/user-docs/-/wikis/Castor-integration#column-naming), and the switch indicates the number of answer sets to expect. For example, if participants will answer a survey a maximum of 10 times, specify `--answer-set-count 10` to have the command list sufficient column names for all survey answers to be imported.
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### `castor list-sp-columns`
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When invoked without further parameters, this command lists the names of all short pseudonym columns that refer to a Castor study. This means that the values in the listed columns are the Castor record IDs for the corresponding participant.
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The command accepts an optional `--imported-only` switch. If specified, the command outputs only those columns that are processed when importing data from Castor into PEP. These are the column names that can be passed to the `--sp-column` switch of the [`castor list-import-columns`](#castor-list-import-columns) and [`castor create-import-columns`](castor-create-import-columns) subcommands.
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### `castor column-name-mapping`
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@@@ more here @@@
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## `get`
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After you have [`list`](#list)ed data, depending on whether data was inlined or not, you have IDs for data entries. You can retrieve the data as follows:
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