-
Notifications
You must be signed in to change notification settings - Fork 0
/
managing-dataFiles.rst
374 lines (254 loc) · 16 KB
/
managing-dataFiles.rst
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
.. include:: cyverse_rst_defined_substitutions.txt
|CyVerse_logo|_
|Home_Icon|_
`Learning Center Home <http://learning.cyverse.org/>`_
===============================
Managing Data Files and Folders
===============================
The Data window contains both input data files that are used in analyses and output data files that are returned as the result of completed analyses.
Input data files can be uploaded or imported to your personal workspace from your desktop or from URL, as well as made available by other users in the Community Data folder and `shared <https://wiki.cyverse.org/wiki/display/DEmanual/Sharing+and+Unsharing+Data+Files+and+Folders+in+the+DE>`_ with others.
This section discusses how to organize and maneuver data files and folders in your Data window, including viewing and changing the file's info-type.
For information on using data files in your analyses, see `Submitting an Analysis <https://wiki.cyverse.org/wiki/display/DEmanual/Submitting+an+Analysis>`_.
You can access and manage data from outside the DE as well. For more information, see `Downloading and Uploading Data <https://wiki.cyverse.org/wiki/display/DS/Downloading+and+Uploading+Data>`_.
-----------------------
Opening the Data Window
-----------------------
Click the **Data** icon to open the Data window
------------
Window Icons
------------
.. |helpiconwindow| image:: img/de/HelpIconWindows.png
.. |WindowIcon-cascadeTile| image:: img/de/WindowIcon-CascadeTile.png
.. |WindowIcon-minMaxClose| image:: img/de/WindowIcon-MinMaxClose.png
.. list-table::
:header-rows: 0
* - |helpiconwindow|
- **Help:** Click to open the FAQs page for the current window.
* - |WindowIcon-cascadeTile|
- **Layout:** Resizes the window layout to half of the available available desktop space and positions it either to the left (**Snap Left**) or right side (**Snap Right**) of the window.
* - |WindowIcon-minMaxClose|
- Minimize, Maximize, or close the active window.
----------
Data Menus
----------
.. |datamenu| image:: img/de/DataMenu.jpg
The Data toolbar helps you `manage files and folders. <https://wiki.cyverse.org/wiki/display/DEmanual/Managing+Data+Files+and+Folders>`_.
|datamenu|
Upload menu
-----------
- `Upload (simple and bulk) and import <https://wiki.cyverse.org/wiki/display/DEmanual/Managing+Data+Files+and+Folders>`_ files and folders
File menu
---------
- `Open a new window in your home folder or at a selected location <https://wiki.cyverse.org/wiki/display/DEmanual/Opening+New+Data+Windows>`_
- `Create a new folder <https://wiki.cyverse.org/wiki/display/DEmanual/Creating+New+Files+and+Folders>`_
- `Create a new file <https://wiki.cyverse.org/wiki/display/DEmanual/Creating+New+Files+and+Folders>`_ including plain text files; tabular data files; R, Perl, Python, and Shell scripts; and Markdown files.
- `Move a file or folder to Trash <https://wiki.cyverse.org/wiki/pages/viewpage.action?pageId=11446737>`_
Edit menu
---------
- `Rename a file or folder <https://wiki.cyverse.org/wiki/display/DEmanual/Renaming+a+Data+File+or+Folder>`_
- `Edit files and folders <https://wiki.cyverse.org/wiki/display/DEmanual/Editing+Files+and+Folders>`_
- `Edit data comments <https://wiki.cyverse.org/wiki/display/DEmanual/Viewing%2C+Adding%2C+and+Retracting+Data+Comments>`_
- `Edit information type <https://wiki.cyverse.org/wiki/display/DEmanual/Editing+a+File%27s+Info-Type>`_
- `Move files and folders <https://wiki.cyverse.org/wiki/display/DEmanual/Moving+a+Data+File+or+Folder>`_
Dowload menu
------------
- `Download a file or folder using Simple or Bulk ownload <https://wiki.cyverse.org/wiki/display/DEmanual/Downloading+Files+and+Folders>`_
Share menu
----------
- `Share a file or folder with collaborators in the DE <https://wiki.cyverse.org/wiki/display/DEmanual/Sharing+and+Unsharing+Data+Files+and+Folders+in+the+DE>`_
- `Create a Public Link to a file <https://wiki.cyverse.org/wiki/display/DEmanual/Sharing+Data+Files+Via+Public+Links>`_
- `Share a folder location <https://wiki.cyverse.org/wiki/display/DEmanual/Creating+Shared+Path+Folder+Links>`_
- View genome files in `CoGe <https://wiki.cyverse.org/wiki/display/DEmanual/Viewing+Genome+Files+in+CoGe>`_ or `Ensembl <https://wiki.cyverse.org/wiki/display/DEmanual/Viewing+Genome+Files+in+a+Genome+Browser>`_, or Newick files in the `Tree Viewer <https://wiki.cyverse.org/wiki/display/DEmanual/Viewing+Newick+Files+in+the+Tree+Viewer>`_. These commands are also available for selected CoGe, Ensembl, or Newick files in the details pane.
Metadata
--------
- Use `metadata and metadata templates <https://wiki.cyverse.org/wiki/display/DEmanual/Using+Metadata+in+the+DE>`_, and `request a permanent identifier <https://wiki.cyverse.org/wiki/display/DC/Requesting+a+Permanent+Identifier+in+the+Data+Commons>`_ (DOI or ARK) to allow others to reuse your datasets
Refresh
-------
- Refresh the Data window if results are not updating as expected.
Search
------
- Search for a file using `basic or advanced search <https://wiki.cyverse.org/wiki/display/DEmanual/Searching+for+Data+Items>`_.
Trash
-----
- `Open, restore, empty the trash, or delete data items in the trash <https://wiki.cyverse.org/wiki/pages/viewpage.action?pageId=11446737>`_
-------------------
Using the Data list
-------------------
- Click in the search field, or paste the path, to search for a file or folder.
- Click a folder in the Navigation list to displays its contents (files and subfolders) in the middle column.
- Click a checkbox in the middle pane to view details about the item in the Details section in the right column.
--------------------------------------
Viewing and selecting files and folders
---------------------------------------
The navigation list in the left pane is where you navigate through data files and folders in your personal workspace.
.. list-table::
:header-rows: 0
* - Personal folder
- Click your username folder to `view the list of data items <https://wiki.cyverse.org/wiki/display/DEmanual/Viewing+and+Customizing+Data+Files>`_ you own.
* - Community Data
- View the list of data items that have been `shared <https://wiki.cyverse.org/wiki/display/DEmanual/Sharing+Data+Files+and+Folders>`_ by other CyVerse account users.
* - Shared With Me
- Click the `shared with me <https://wiki.cyverse.org/wiki/display/DEmanual/Sharing+Data+Files+and+Folders>`_ folder (does not show if no one has shared any items with you) to view data items that have been shared with you by other users.
* - Trash
- Click the `Trash <https://wiki.cyverse.org/wiki/pages/viewpage.action?pageId=11446737>`_ folder to view the list of deleted data items, empty the Trash folder to permanently delete all items in the folder, or delete selected items.
* - Saved filters
- If you `saved any search filters <https://wiki.cyverse.org/wiki/display/DEmanual/Searching+for+Data+Items#SearchingforDataItems-_savedSearchFilter>`_, the Saved filters folder is displayed below the Trash folder.
* - Favorites
- The list of your `favorite files and folders <https://wiki.cyverse.org/wiki/display/DEmanual/Using+Data+Favorites>`_.
-------------------------------------
Understanding inaccessible data items
-------------------------------------
Data items that are inaccessible are displayed in red italicized font.
.. image:: img/de/InaccessibleDataItem.gif
This may be due to special characters (' or ~) in the path or name, or system-level items, such as your iplant/home/shared folder or your home directory.
These data items cannot be opened, renamed, moved, deleted, or accessed in any way. For more information, see `Using Special Characters in the DE <https://wiki.cyverse.org/wiki/display/DEmanual/Using+Special+Characters+in+the+DE>`_.
----------------------------------------------------
Sorting, adding, and hiding columns in the Data list
----------------------------------------------------
You can sort on any column in the Data list, and hide or show columns to customize the look of your Data list.
1. Hover over the column header until a down arrow appears on the right side of the column, and then click the down arrow:
.. image:: img/de/ColumnDropdown.png
2. Click the setting to use
- To sort the column, click either **Sort Ascending** or **Sort Descending**.
- To hide or show a column, point to **Columns**, and then select or clear the checkbox for the column.
.. tip:: **Need to view the path?**
Show the **Path** column to help you determine which file or folder to use in search results.
----------------------------
Using the Data actions icons
----------------------------
.. |sharedpath| image:: img/de/DataActionsSharePathIcon.png
.. |publiclink| image:: img/de/Data_ShareViaPublicLinkIcon.png
.. |shareviade| image:: img/de/DataActionsShareViaDe.png
.. |metadataicon| image:: img/de/DataActionsMetadataIcon.jpg
.. |commentsicon| image:: img/de/DataActionsCommentsIcon.jpg
.. list-table::
:header-rows: 0
* - |sharedpath|
|publiclink|
- Create a `Shared Path Folder Link <https://wiki.cyverse.org/wiki/display/DEmanual/Creating+Shared+Path+Folder+Links>`_ (folders only)
*or*
Share the item `via Public Link <https://wiki.cyverse.org/wiki/display/DEmanual/Sharing+Data+Files+Via+Public+Links>`_ (files only)
* - |shareviade|
- Share the item `Via the Discovery Environment <https://wiki.cyverse.org/wiki/display/DEmanual/Sharing+and+Unsharing+Data+Files+and+Folders+in+the+DE>`_
* - Netadata
- Add or edit `metadata or select a metadate template <https://wiki.cyverse.org/wiki/display/DEmanual/Using+Metadata+in+the+DE>`_
* - |commentsicon|
- Add or retract `comments about a file or folder <https://wiki.cyverse.org/wiki/display/DEmanual/Viewing%2C+Adding%2C+and+Retracting+Data+Comments>`_
---------------
Viewing Details
---------------
Click the checkbox for a file or folder in the middle column to view information about it in the Details section on the right side of the Data window. The options that are available depend upon whether a file or a folder is selected.
.. list-table::
:header-rows: 1
* - **File Details**
- **Folder Details**
* - .. image:: img/de/Data_FileDetailsPane.jpg
- .. image:: img/de/Data_FolderDetailsPane.jpg
.. |check| image:: img/de/check.png
.. list-table::
:header-rows: 1
* - **Details Option**
- **Description**
- **File**
- **Folder**
* - Last Modified
- Date the item was last modified by the owner.
- |check|
- |check|
* - Date Submitted
- Date the owner `shared it publicly <https://wiki.cyverse.org/wiki/display/DEmanual/Sharing+your+App+or+Workflow+and+Editing+the+User+Manual>`_ with other CyVerse users.
- |check|
- |check|
* - Permissions
- `Permission level <https://wiki.cyverse.org/wiki/display/DEmanual/Changing+and+Viewing+Data+Permission+Levels+in+the+DE>`_ you have been granted for the item.
- |check|
- |check|
* - Share
- Displays whether the file or folder has been `shared <https://wiki.cyverse.org/wiki/display/DEmanual/Sharing+Data+Files+and+Folders>`_. If you are the owner, allows you to access the file or folder to share or change sharing permissions.
- |check|
- |check|
* - Size
- Size of the file.
- |check|
- |check|
* - Type
- File type for the file.
- |check|
-
* - Info-Type
- `Info-type <https://wiki.cyverse.org/wiki/display/DEmanual/Editing+a+File%27s+Info-Type>`_ for the file.
- |check|
-
* - md5 Checksum
- Useful for comparing files and verifying the integrity of the downloaded file.
- |check|
-
* - Send to
- CoGe, Ensemble, or Newick files only. Allows you to send a genome file to `CoGe <https://wiki.cyverse.org/wiki/display/DEmanual/Viewing+Genome+Files+in+CoGe>`_ or `Ensembl <https://wiki.cyverse.org/wiki/display/DEmanual/Viewing+Genome+Files+in+a+Genome+Browser>`_, or a Newick file to the `Tree Viewer <https://wiki.cyverse.org/wiki/display/DEmanual/Viewing+Newick+Files+in+the+Tree+Viewer>`_. These commands are also available in the share menu.
- |check|
-
* - File(s)/Folder(s)
- Number of files and subfolders contained in the folder.
-
- |check|
* - Tags
- Add or delete a `tag <https://wiki.cyverse.org/wiki/display/DEmanual/Using+Data+Tags+and+Tag+Descriptions>`_ for a file or folder, or enter a description about the tag or data item.
- |check|
- |check|
-------------
Basic process
-------------
To begin, you need the data files you want to use in your analysis. You can use any file in your personal, Community Data, or Shared With Me folder, or you can `upload or import a data file <https://wiki.cyverse.org/wiki/display/DEmanual/Changing+and+Viewing+Data+Permission+Levels+in+the+DE>`_ to your personal folder. Once the data file is in your workspace folder or in the Community Data folder, you can:
- `Use the file <https://wiki.cyverse.org/wiki/display/DEmanual/Submitting+an+Analysis>`_ in an analysis.
- `View the outputs <https://wiki.cyverse.org/wiki/display/DEmanual/Relaunching%2C+Canceling%2C+and+Deleting+Analyses%2C+Viewing+Analysis+Outputs+and+Info>`_ of a completed analysis.
- `Download <https://wiki.cyverse.org/wiki/display/DEmanual/Downloading+Files+and+Folders>`_ data files, output files, and folders.
- `Add or view metadata <https://wiki.cyverse.org/wiki/display/DEmanual/Using+Metadata+in+the+DE>`_ in files and folders.
- `Add tags and tag descriptions <https://wiki.cyverse.org/wiki/display/DEmanual/Using+Data+Tags+and+Tag+Descriptions>`_ to files and folders.
.. tip::
It is also possible to manage data outside of the Discovery Environment using other tools, as documented in `Downloading and Uploading Data <https://wiki.cyverse.org/wiki/display/DS/Downloading+and+Uploading+Data>`_.
-------------------------------------------------
Managing Data Files and Folders Table of contents
-------------------------------------------------
.. toctree::
:maxdepth: 9
managing-dataFileschildpages/uploading-importingData.rst
managing-dataFileschildpages/downloading-filesAndFolders.rst
managing-dataFileschildpages/searching-dataItems.rst
managing-dataFileschildpages/editing-filesAndFolders.rst
managing-dataFileschildpages/sharing-dataFilesandFolders.rst
managing-dataFileschildpages/using-metadataInDe.rst
managing-dataFileschildpages/using-dataTags.rst
managing-dataFileschildpages/opening-newDataWindows.rst
managing-dataFileschildpages/creating-newFiles.rst
----
**Fix or improve this documentation**
- Search for an answer:
|CyVerse Learning Center|
- Ask us for help:
click |Intercom| on the lower right-hand side of the page
- Report an issue or submit a change:
|Github Repo Link|
- Send feedback: `Tutorials@CyVerse.org <Tutorials@CyVerse.org>`_
- Live chat/help: Click on the |intercom| on the bottom-right of the page for questions on documentation
----
|Home_Icon|_
`Learning Center Home <http://learning.cyverse.org/>`_
.. Comment: Place Images Below This Line
use :width: to give a desired width for your image
use :height: to give a desired height for your image
replace the image name/location and URL if hyperlinked
.. |Clickable hyperlinked image| image:: ./img/IMAGENAME.png
:width: 500
:height: 100
.. _CyVerse logo: http://learning.cyverse.org/
.. |Static image| image:: ./img/IMAGENAME.png
:width: 25
:height: 25
.. Comment: Place URLS Below This Line
# Use this example to ensure that links open in new tabs, avoiding
# forcing users to leave the document, and making it easy to update links
# In a single place in this document
.. |Substitution| raw:: html # Place this anywhere in the text you want a hyperlink
<a href="REPLACE_THIS_WITH_URL" target="blank">Replace_with_text</a>
.. |Github Repo Link| raw:: html
<a href="FIX_FIX_FIX_FIX_FIX_FIX_FIX_FIX_FIX_FIX_FIX_FIX_FIX_FIX_FIX" target="blank">Github Repo Link</a>