... | ... | @@ -7,7 +7,15 @@ The `pepcli` utility is documented extensively on a [separate page](Using-pepcli |
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- [uploading data](#uploading-data) using the `pepcli store` command, and
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- [downloading data](#downloading-data) using the `pepcli pull` command.
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The documentation on this page assumes that the user is familiar with the `pepcli` utility's [general usage](Using-pepcli#general-usage) principles. In particular, the user should be able to [ensure that they are enrolled](Using-pepcli#enrollment) with the PEP system. The examples on this page are based on use of a Unix-like environment.
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The documentation on this page assumes that the user is familiar with PEP's [data structure](Data-structure). The examples on this page assume use of a Unix-like environment; users of different platforms should adapt their command lines accordingly. Additionally, users are expected to pass command line switches [appropriate to their situation](Using-pepcli#general-usage), and to [ensure that they are enrolled](Using-pepcli#enrollment) with the PEP system. For brevity, the examples on this page do not include such switches.
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## Limitations
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PEP can only store a single file in any given cell. If multiple files are to be distributed together (e.g. because one is unusable without another), they should be stored in multiple columns, and all those columns should be made available to downloaders. Alternatively, uploaders could package files into an archive (e.g. using the `tar` utility) and upload the archive to a single PEP column. Downloaders would then need to unpack the archive before they can analyze the original file contents.
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Additionally, PEP does not (by default) perform any processing on the data it stores. The consequence is that downloaders will receive the exact same data that the uploader stored. Uploaders should therefore ensure that their data is stripped of information unsuitable for dissemination. This includes any fixed identifiers that the data may contain, since those could be used to blend the downloads from different access groups.
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PEP eases some of these limitations with its built-in support for some [data formats](#data-format-processing).
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# Uploading data
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... | ... | @@ -84,17 +92,9 @@ Use the `--force` switch to have the command (discard/overwrite local data and) |
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Like its `pull` command, the `pepcli` utility's `list` and `get` commands allow data to be downloaded from PEP. But although they provide more fine-grained control over the download process, they do not provide PEP's built-in support for [data format processing](#data-format-processing), making them unusable for certain types of data. **Use of these commands is therefore strongly discouraged.** They are retained only for backward compatibility purposes, and may be removed from future versions of PEP.
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# Limitations
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PEP can only store a single file in any given cell. If multiple files are to be distributed together (e.g. because one is unusable without another), they should be stored in multiple columns, and all those columns should be made available to downloaders. Alternatively, uploaders could package files into an archive (e.g. using the `tar` utility) and upload the archive to a single PEP column. Downloaders would then need to unpack the archive before they can analyze the original file contents.
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Additionally, PEP does not (by default) perform any processing on the data it stores. The consequence is that downloaders will receive the exact same data that the uploader stored. Uploaders should therefore ensure that their data is stripped of information unsuitable for dissemination. This includes any fixed identifiers that the data may contain, since those could be used to blend the downloads from different access groups.
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With proper configuration, PEP can ease some of these limitations for some [supported data formats](#data-format-processing).
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# Data format processing
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PEP has the ability to perform special processing for some data formats that would otherwise be cumbersome to distribute. Support for these data formats requires proper configuration of affected columns.
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PEP has the ability to perform special processing for some data formats that would otherwise be cumbersome to distribute. Support for these data formats must be properly configured for appropriate columns.
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## MRI data in the BIDS format
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