From 21268bb25f0ef8a70c7822d36b540e114c3c114b Mon Sep 17 00:00:00 2001 From: Joe Ziminski <55797454+JoeZiminski@users.noreply.github.com> Date: Tue, 3 Oct 2023 22:56:43 +0100 Subject: [PATCH] Change data-type to datatype in docs. --- docs/source/pages/documentation.md | 40 +++++++++++++++--------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/docs/source/pages/documentation.md b/docs/source/pages/documentation.md index 4187831f..5339377f 100644 --- a/docs/source/pages/documentation.md +++ b/docs/source/pages/documentation.md @@ -58,7 +58,7 @@ The _configurations_ tell DataShuttle: - The paths to the *local* and *central* folders that contain the project. - How to connect to the _central_ machine. - The settings that specify how data is transferred. -- The *data-types* that will be used in the project, e.g. *behaviour* (`behav`) or *electrophysiology* (`ephys`). +- The *datatypes* that will be used in the project, e.g. *behaviour* (`behav`) or *electrophysiology* (`ephys`). The command `make-config-file` is used for the initial setup of the project. The **required arguments** are: @@ -68,7 +68,7 @@ The command `make-config-file` is used for the initial setup of the project. The `connection_method`: `local_filesystem` or `ssh`. Local filesystem can be used if the *central* storage is mounted to the local machine. Otherwise `ssh` can be used. -Finally, the *data-type* flags `--use_ephys`, `--use_funcimg`, `--use_histology`, `--use_behav` set the types of data required for the project on the local machine. While individual flags are optional, at least one must be chosen when initialising the project. +Finally, the *datatype* flags `--use_ephys`, `--use_funcimg`, `--use_histology`, `--use_behav` set the types of data required for the project on the local machine. While individual flags are optional, at least one must be chosen when initialising the project. ### Optional Arguments @@ -137,7 +137,7 @@ my_first_project \ make-sub-folders -sub 001@TO@003 -ses 010_@TIME@ -dt all ``` -When the `all` argument is used for `--data_type` (`-dt`), the folders created depend on the *data-types* specified during *configuration* setup. For example, if +When the `all` argument is used for `--data_type` (`-dt`), the folders created depend on the *datatypes* specified during *configuration* setup. For example, if `--use_behav`, `--use_funcimg`, `--use_histology` were set during *configuration* setup, the folder tree from the above command (assuming the time is `4.02.48 PM`), would look like: ``` @@ -161,7 +161,7 @@ When the `all` argument is used for `--data_type` (`-dt`), the folders created d ### Data Types Folders -In [SWC-Blueprint](https://swc-blueprint.neuroinformatics.dev/specification.html), *data-types* specify where acquired experimental data of currently supported types (`behav`, `ephys`, `funcimg` and `histology`) is stored. See the [*data-types* section of the SWC-Blueprint for more details](https://swc-blueprint.neuroinformatics.dev/specification.html#datatype). +In [SWC-Blueprint](https://swc-blueprint.neuroinformatics.dev/specification.html), *datatypes* specify where acquired experimental data of currently supported types (`behav`, `ephys`, `funcimg` and `histology`) is stored. See the [*datatypes* section of the SWC-Blueprint for more details](https://swc-blueprint.neuroinformatics.dev/specification.html#datatype). At present, `histology` is saved to the `sub-` level, as it is assumed `histology` is conducted *ex vivo* and so session will be possible. Please don't hesitate to get into contact if you have an alternative use case. @@ -182,7 +182,7 @@ upload \ Will *upload* (from *local* to *central* ) _behavioural_ _sessions_ 5 and 6, collected at any date, for _subjects_ 1 to 3. -The keyword `all` can be input in place of a `-sub`, `-ses` or _data-type_ argument `dt` to transfer all available subject, sessions or data types available. For example: +The keyword `all` can be input in place of a `-sub`, `-ses` or _datatype_ argument `-dt` to transfer all available subject, sessions or data types available. For example: ``` datashuttle \ @@ -249,9 +249,9 @@ run on the folder tree: will transfer all data in both the `rawdata` and `derivatives` folders from the *local* machine to the *central* machine. -### Transferring files that are not within data-type folders +### Transferring files that are not within datatype folders -In some cases, files related to metadata may be stored outside of *data-type* folders. When the `all` flag is used, files outside of folders at the *top-level folder* (for `-sub`), *subject* level (for `-ses`) and *session* level (`for -dt`) will also be transferred. However, if specific subject, session or data-type are selected, files outside of these will not be transferred. +In some cases, files related to metadata may be stored outside of *datatype* folders. When the `all` flag is used, files outside of folders at the *top-level folder* (for `-sub`), *subject* level (for `-ses`) and *session* level (`for -dt`) will also be transferred. However, if specific subject, session or datatype are selected, files outside of these will not be transferred. The example below exemplifies how the `all` argument works during data transfer. For example, given the project folder: @@ -281,13 +281,13 @@ upload \ will move: -- The file `a_project_file.json` (and any other files at this level) and search all *subjects* for the specified *sessions* */ data-types*. +- The file `a_project_file.json` (and any other files at this level) and search all *subjects* for the specified *sessions* */ datatypes*. - Only *sessions* called `001`, but not any other files or folders at this level (i.e. `sub-001_ses-001_extrafile-ses.json` will not be transferred). -- All *data-types* and non-*data-types* at the session level. For example, `behav` and `sub-001_ses-001_extrafile-dtype.json` (that reside in *session* folders called `ses-001`) will be transferred. +- All *datatypes* and non-*datatypes* at the session level. For example, `behav` and `sub-001_ses-001_extrafile-dtype.json` (that reside in *session* folders called `ses-001`) will be transferred. -For convenience, it is suggested to keep all files within *data-type* level folders. However, the `all` argument, as well as the additional available arguments: `all_sub` and `all_non_sub` (for `-sub`), `all_ses` and `all_non_ses` (for `-ses`) and `-all_ses_level_non_data_type` are available, as [detailed below](#flexible-transfers-with-keyword-arguments) +For convenience, it is suggested to keep all files within *datatype* level folders. However, the `all` argument, as well as the additional available arguments: `all_sub` and `all_non_sub` (for `-sub`), `all_ses` and `all_non_ses` (for `-ses`) and `-all_ses_level_non_data_type` are available, as [detailed below](#flexible-transfers-with-keyword-arguments) ### Transferring a specific file or folder @@ -492,7 +492,7 @@ To change this behaviour, the configuration `overwrite_old_files` can be set to ### Flexible transfers with keyword arguments -DataShuttle provides a number of keyword arguments to allow separate handling of files that are not found in *data-type* folders. +DataShuttle provides a number of keyword arguments to allow separate handling of files that are not found in *datatype* folders. #### For use with the `-sub` / `--sub-names` flag @@ -510,14 +510,14 @@ DataShuttle provides a number of keyword arguments to allow separate handling of `all_non_ses` : All files and folders that are not prefixed with `-sub` will be transferred. Any folders prefixed with `-ses` will not be transferred. -#### For use with the `-dt` / `--data-type` flag +#### For use with the `-dt` / `--datatype` flag -`all` : All *data-type* folders at the *subject* or *session* folder level will be transferred, as well as all files and folders within selected *session* folders. +`all` : All *datatype* folders at the *subject* or *session* folder level will be transferred, as well as all files and folders within selected *session* folders. -`all_data_type` : All *data-type* folders (i.e. folders with the pre-determined name: `behav`, `ephys`, `funcimg`, `histology`) residing at either the *subject* or *session* level will be -transferred. Non-*data-type* folders at the *session* level will not be transferred +`all_data_type` : All *datatype* folders (i.e. folders with the pre-determined name: `behav`, `ephys`, `funcimg`, `histology`) residing at either the *subject* or *session* level will be +transferred. Non-*datatype* folders at the *session* level will not be transferred -`all_ses_level_non_data_type` : Non *-data-type* folders at the *session* level will not be transferred +`all_ses_level_non_data_type` : Non *datatype* folders at the *session* level will not be transferred Below, a number of examples are given to exemplify how these arguments effect data transfer. Given the *local* project folder: @@ -544,7 +544,7 @@ Below, a number of examples are given to exemplify how these arguments effect da └── ... ``` -1) The first example indicates the effect of selectively transferring non-*data-type* sessions. The command: +1) The first example indicates the effect of selectively transferring non-*datatype* sessions. The command: ``` datashuttle \ @@ -559,7 +559,7 @@ Would upload: - All non-*subject* files in the *top-level* folder (`rawdata`) - The `sub-001_extra_file.json` and `sub-002_extra_file.json` -- For `sub-001`, the file `ses-001_extra_file.json`. For `sub-002`, no other files are transferred because there is no non-*data-type* files at the *session* level. +- For `sub-001`, the file `ses-001_extra_file.json`. For `sub-002`, no other files are transferred because there is no non-*datatype* files at the *session* level. 2) The next two examples show the effect of selecting `-dt all` vs. `-dt all_data_type`. The command: @@ -577,7 +577,7 @@ Would upload: - Contents residing in the `sub-001` folder only. - The file `sub-001_extra-file.json` -- All *data-type* folder contents (`histology`, `behav`, `ephys`) +- All *datatype* folder contents (`histology`, `behav`, `ephys`) The command: @@ -593,7 +593,7 @@ upload Would upload: - Contents residing in the `sub-001` folder only. -- All *data-type* folder contents (`histology`, `behav`, `ephys`) +- All *datatype* folder contents (`histology`, `behav`, `ephys`) 3) The final example shows the effect of transferring `all_non_sub` files only. The command: