... | ... | @@ -45,12 +45,46 @@ Once data has been stored in PEP, it can be downloaded by [authorized](Access-co |
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/app/pepcli pull -p POM162733743006 -c Holter.Visit1
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```
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The `pepcli pull` puts the downloaded data into a file system structure:
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Data for multiple participants and/or columns can be downloaded in one fell swoop by specifying more of the corresponding switches. E.g.:
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- A top level directory for this download. By default the directory is named `pulled-data`, but the name and/or location can be changed by means of the `-o` switch. Within the top level directory:
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- One subdirectory per participant, named after the participant's [local pseudonym](Pseudonymization#identifiers-in-pep). Within the participant subdirectory:
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```
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/app/pepcli pull -p POM162733743006 -p POM390792184872 -p 834735705658 -c Holter.Visit1 -c Holter.Visit2 -c IsTestParticipant
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```
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The command also allows participant groups (as opposed to individual participant IDs) and column groups (as opposed to individual column names) to be specified. Group-denoting switches have uppercase letters, can also be specified multiple times, and can be combined with individual specifications. E.g.:
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```
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/app/pepcli pull -P all-pit -P all-denovo -C DeNovoWatchData -C Castor -c IsTestParticipant
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```
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Whatever data is downloaded, the `pepcli pull` command writes it to a directory tree with the following structure:
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- A top level directory for this download, containing:
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- One subdirectory per participant (named after the participant's [local pseudonym](Pseudonymization#identifiers-in-pep)), containing:
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- One file per cell downloaded for this participant. The file is named after the column.
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By default the top level directory is named `pulled-data` and placed into the current working directory. This behavior can be overridden by means of the `-o` switch, e.g.:
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```
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/app/pepcli pull -o ~/analyze/todays-data -P all-pit -P all-denovo -C DeNovoWatchData -C Castor -c IsTestParticipant
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```
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Once users have downloaded data, they can use the `--update` switch to update their directory to the current data set stored in PEP (e.g. adding files that have since been uploaded by some other user). Note that no column(group)s or participant(group)s must be specified when using the `--update` switch. The data will be updated for the original download's participants and columns, e.g.:
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```
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/app/pepcli pull -o ~/analyze/todays-data --update
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```
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To prevent data loss, the `pepcli pull` command will be aborted if
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- the output directory already exists when performing a regular (initial) download.
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- file contents have been altered when performing an update.
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Use the `--force` switch to have the command (discard local data and) proceed anyway.
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## `List`ing and `get`ting files manually
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@@@ more here @@@
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## 2. List data from PEP e.g. to retrieve a short pseudonym
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... | ... | |