Last modified by Dennis Segebarth on 2026/02/26 10:27
From version 23.1
edited by Dennis Segebarth
on 2024/08/16 09:02
Change comment: Deleted image "Projects Request Copy to Core v2.1.2 2023-01-18.png"
To version 29.1
edited by Dennis Segebarth
on 2026/02/26 10:22
Change comment: There is no comment for this version

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10 10  
11 11  All files uploaded to the platform land in the //Green Room//. In this isolated storage area, the only people who can view and download the files you have uploaded are you and the Project Administrator(s). Project Administrators can verify that the data are compliant with the Project’s data management plan before being copied to the //Core //where all other Project members (except Project Contributors, see //Managing HDC Projects > Project Roles//) can view and access the file.
12 12  
13 -[[image:Project File Upload v2.0.10 2023-01-17.png||height="8%" width="50%"]]
13 +[[image:1723802592552-117.png||height="139" width="859"]]
14 14  
15 15  == Prerequisites ==
16 16  
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50 50  * //Moving and renaming files and folders~://** **Once a file or folder is uploaded it cannot be moved or renamed in the Green Room File Explorer. Instead, you can re-upload the file or folder with a different name or destination, or copy the file or folder to the Core and use the Workspace tools to organize the Project files.
51 51  * //Uploading duplicate files: //Duplicate files cannot be uploaded to the same destination folder. If you attempt to upload a file that already exists in the destination folder with the same filename, an error message is returned. Instead, you can either upload the file with a different filename, or create a new Green Room folder and upload the file to the new folder.
52 52  
53 +----
54 +
53 53  = Checking File Status =
54 54  
55 55  You can check the progress and completion status (success or failure) of Project files uploaded, downloaded, and deleted during the current login session using the File Status panel. Click the **File Status icon** in the Main Menu to open the File Status panel then browse the activity tabs (**In Progress**, **Uploaded**, **Downloaded**, **Trash Bin**).
56 56  
57 -[[image:Project File Status v2.0.10 2023-01-16.png||height="20%" width="50%"]]
59 +[[image:1723802613048-462.png||height="474" width="864"]]
58 58  
59 59  To view the complete history of all Project files uploaded, downloaded and deleted, not just activities in the current login session, use the File Stream Advanced Search.
60 60  
61 -[[image:Project Recent File Stream Advanced Search v2.2.6 2023-04-14.png||height="21%" width="50%"]]
63 +[[image:1723802630131-211.png||height="358" width="870"]]
62 62  
63 63  1. Navigate to the Project Canvas and locate the Recent File Stream panel.
64 64  1. Click **Advanced Search** to open the File Stream Advanced Search.
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70 70  
71 71  The Portal provides the ability to resume a file upload already in progress so you don’t have to restart the upload from the beginning.
72 72  
73 -[[image:Resume File Upload v2.2.6 2023-04-13 1815.png||height="19%" width="50%"]]
75 +[[image:1723802641609-122.png||height="324" width="871"]]
74 74  
75 75  To resume a file upload after a failure:
76 76  
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78 78  1. Open the **File Status panel** and check the **In Progress** tab for the failed file. Click **Re-upload file** and select the same file from your local source folder.
79 79  1. The upload resumes as shown by the progress bar and successful completion is indicated in the **File Status panel**.
80 80  
83 +----
84 +
81 81  = Viewing File Properties =
82 82  
83 83  The File Properties panel displays detailed metadata about Project files to help find them and facilitate their appropriate use.
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96 96  
97 97  For a detailed description of other information available in the File Properties menu, see sections //Adding and Modifying File Tags//, //Adding and Modifying File Attributes,// and //Data Lineage Graph.//
98 98  
103 +----
104 +
99 99  = Previewing Files =
100 100  
101 101  The File Previewer can be used to check the inner folder structure of uploaded file archives. Supported types include:
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105 105  * 7zip: .7z
106 106  * RAR: .rar
107 107  
108 -[[image:Projects File Previewer v2.2.3 2023-05-03.png||height="29%" width="50%"]]
114 +[[image:1723802657065-379.png||height="506" width="868"]]
109 109  
110 110  1. Locate the file in the File Explorer.
111 111  1. Click the **Action icon** (three dots) beside the file and select **Preview** (only visible for archive file listed above).
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114 114  
115 115  To unzip the file, use one of the available workspace tools such as a Jupyter notebook in **JupyterHub **(see //Using HDC Workspace Tools//).
116 116  
123 +----
124 +
117 117  = Adding and Modifying File Tags =
118 118  
119 119  File Tags are keywords assigned to files and/or folders to help describe them and allow them to be found. Two types of tags can be associated with Project files:
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148 148  
149 149  Recommended for bulk tagging of files and folders.
150 150  
151 -[[image:Project Customized Tags v2.0.10 2023-01-17.png||height="8%" width="50%"]]
159 +[[image:1723802673774-424.png||height="141" width="868"]]
152 152  
153 153  1. Navigate to the Project File Explorer (Green Room or Core).
154 154  1. Select one or more files and/or folders by clicking the checkbox beside each one, then click **Add/Remove Tags** in File Explorer menu.
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170 170  * In the Green Room, Customized Tags can only be added or edited by the Project Member who uploaded the file, or the Project Administrator.  In the Core, Collaborators and Project Administrators can edit Customized tags of files in any folder.
171 171  * Tags can also be attached to Projects and Datasets.
172 172  
181 +----
182 +
173 173  = Adding and Modifying File Attributes =
174 174  
175 175  It may be important to annotate your uploaded Project files with descriptive metadata that conform with your own defined categories, formats, or values to make the files more readily searchable and machine readable. For example, when uploading a file containing test scores you wish to specify metadata on the research site that performed the test, or on a DICOM imaging file you wish to specify the MRI scanner manufacturer. File Attributes enable this enriched metadata capture on files.
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180 180  
181 181  Use this method to add Project-specific metadata annotations to your files on upload.
182 182  
183 -[[image:Projects File Attributes v2.1.2 2023-01-18.png||height="46%" width="40%"]]
193 +[[image:1723802688075-223.png||height="456" width="394"]]
184 184  
185 185  1. Begin a File upload (see //Uploading Files//)
186 186  1. Select a File Attribute template from the dropdown menu (only visible if the Project Administrator has configured File Attributes) and enter the requested information.  File Attributes can be either required or optional on upload depending on how the Project Administrator has configured them. 
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189 189  
190 190  == Method 2: from the Project File Explorer ==
191 191  
192 -[[image:Projects File Attributes from File Explorer v2.1.2 2023-01-18.png||height="8%" width="50%"]]
202 +[[image:1723802709785-695.png||height="139" width="856"]]
193 193  
194 194  1. Navigate to the Project File Explorer Green Room or Core.
195 195  1. Select one or more files and/or folders by clicking the checkbox beside each one, then click **Add Attributes** in File Explorer menu.
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197 197  
198 198  File Attributes added to a file or folder are visible in its Properties menu in the File Explorer. Additionally, you can search all Project Files for specific File Attributes by using the Project Search tool (see //Projects Interface > Search //in the article //HDC Portal Navigation//).
199 199  
210 +----
211 +
200 200  = Requesting File Copy from the Green Room to the Core =
201 201  
202 202  The Core is the storage area where Project members can access each others’ Project files, create file collections, and use the workspace tools to open files and perform analyses.
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205 205  
206 206  To submit a request to copy data from the Green Room to the Core (requires Collaborator role),
207 207  
208 -[[image:Projects Request Copy to Core v2.1.2 2023-01-18.png||height="9%" width="50%"]]
220 +[[image:1723802723363-498.png||height="157" width="867"]]
209 209  
210 210  1. Navigate to the Project File Explorer Green Room
211 211  1. Select one or more files and/or folders to be copied by clicking the checkbox beside each one. The Request to Core option becomes visible in the File Explorer menu.
... ... @@ -217,11 +217,13 @@
217 217  
218 218  To view your submitted and approved requests:
219 219  
220 -[[image:Projects Requests Left Menu v2.3.3 2023-04-26.png||height="27%" width="50%"]]
232 +[[image:1723802735878-454.png||height="317" width="587"]]
221 221  
222 222  1. Click the Requests icon from the Project left menu bar.
223 223  1. Click **New** to view your new requests that have not been fulfilled, or **Completed **to view requests that the Project Administrator has fulfilled. Requests are identified by the username and the date/time stamp when the request was submitted.
224 224  
237 +----
238 +
225 225  = Viewing Data Lineage =
226 226  
227 227  When you copy data from one location to another, execute a pipeline, or perform other actions on a file, the platform data lineage service captures the points in the file’s journey and displays them in the File Properties Data Lineage graph.
... ... @@ -240,13 +240,15 @@
240 240  * //Upstream lineage// displays the points in a file's journey up to its current state. For example, a file newly uploaded to the Green Room has only one upstream point, the Green Room File node, representing the point when the file was introduced the the platform.
241 241  * //Downstream lineage// displays points in a file’s journey from a specific state forward. For example, when viewing the lineage of a file stored in the Green Room that was later copied to the Core, the downstream lineage displays the Green Room File node, the copy Pipeline, and the Core File node.
242 242  
243 -[[image:Project File Lineage v2.1.3 2023-01-19.png||height="25%" width="50%"]]
257 +[[image:1723802879104-591.png||height="397" width="802"]]
244 244  
259 +----
260 +
245 245  = Downloading Files =
246 246  
247 247  ​Files can be downloaded individually or in bulk directly from the File Explorer.
248 248  
249 -[[image:Projects File Download v2.1.3 2023-01-19.png||height="9%" width="50%"]]
265 +[[image:1723802890566-839.png||height="164" width="868"]]
250 250  
251 251  1. Before downloading a file, check your browser settings and ensure that pop-up windows are enabled.
252 252  1. (((
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264 264  * Download performance may be impacted by your internet connection.
265 265  * Ensure pop-ups are enabled in your browser.
266 266  
267 -= Deleting Files =
283 +----
268 268  
269 -Project members can delete files that are no longer needed in the Green Room or Core. When you delete a file, it is moved to a Trash Bin where it can be permanently deleted later, or restored in case of accidental deletion.
285 += Deleting Files and Folders =
270 270  
271 -[[image:Projects File Delete v2.1.3 2023-01-19.png||height="9%" width="50%"]]
287 +== Moving Items to the Trash Bin ==
272 272  
289 +Project members can move files or folders that are no longer needed in the Green Room or Core to the Trash Bin. Items in the Trash Bin can be marked for permanent deletion (see below), or restored back to the original location in Green Room or Core.
290 +
291 +[[image:1772032907007-375.png]]
292 +
273 273  1. Navigate to the Project File Explorer Green Room or Core.
274 -1. Select one or more files and/or folders by clicking the checkbox beside each one (or use the select all checkbox), then click **Delete **in File Explorer menu//.//
294 +1. Select one or more files and/or folders by clicking the checkbox beside each one (or use the select all checkbox), then click **Move to Trash Bin **in File Explorer menu//.//
275 275  1. A popup window prompts you to confirm the file deletion. Click **OK** or cancel to exit without deleting.
276 276  1. The file is moved to the Trash Bin.
277 277  
278 -Open the File Status panel to check the status of the single file deletion, or open the Trash Bin in the left menu of the File Explorer to view all files in your Trash Bin. Files can be permanently deleted by a Platform Administrator.
298 +Open the File Status panel to check the status of the single file deletion, or open the Trash Bin in the left menu of the File Explorer to view items in the Project`s Trash Bin (your role in the Project governs what items are visible to you).
279 279  
300 +{{info}}
301 +**Note:** Items in the Trash Bin are not yet deleted. You can imagine it like the "Recycle Bin" in Windows OS. Thus, if you want to permanently delete a file or folder, check the following sections on //Mark Items for Deletion// and //Deleting Items immediately//. Please note that these actions are available only to members that hold the Project Administrator role.
302 +{{/info}}
303 +
304 +== Restoring Items from the Trash Bin ==
305 +
306 +All Project members can restore items visible to them in the Trash Bin back to their original location in the Green Room or Core. For this:
307 +
308 +1. Navigate to the Project File Explorer Trash Bin.
309 +1. Use the Actions Menu (three dots) in the row of the respective item you´d like to restore to open the Actions drop down menu.
310 +1. In the Actions drop down menu, click **Restore** to restore the item to its original source location in the Green Room or Core.
311 +
312 +[[image:Restore_from_Trash_Bin.png||height="251" width="868"]]
313 +
314 +== Mark Items for Deletion ==
315 +
316 +Items in the Trash Bin will not be deleted automatically and continue to consume your Project´s available resources. As a Project Administrator, you can go to the Trash Bin and mark files and folders for permanent deletion. For this:
317 +
318 +1. Navigate to the Project File Explorer Trash Bin.
319 +1. Use the Actions Menu (three dots) in the row of the respective item you´d like to mark for permanent deletion to open the Actions drop down menu.
320 +1. In the Actions drop down menu, click **Delete **to mark the item for permanent deletion.
321 +
322 +[[image:Mark_for_deletion_in_Trash_Bin.png||height="249" width="857"]]
323 +
324 +{{info}}
325 +**Note: **Once marked for deletion, an item is scheduled for permanent deletion after a grace period of 30 days has expired. Until end of this grace period, the Project Administrator that marked the item for deletion can revoke this action and restore the item back to the Trash Bin, or delete it immediately, skipping the grace period (see following sections).
326 +{{/info}}
327 +
328 +== Restore Items before Grace Period Expiration ==
329 +
330 +Once an item has been marked for permanent deletion, it can still be restored until a grace period of 30 days has expired. This action can be performed only by the Project Administrator who marked the item for deletion. For this:
331 +
332 +1. Go to your User Account page by clicking on your username in the upper right corner and then click on **Account**.
333 +1. In the lower right section, you´ll find the //Recently Deleted// table that provides an overview of all items you´ve marked for deletion and for which the grace period of 30 days has not expired yet. It also denotes for each item to which Project it belongs, and when it was marked for deletion.
334 +1. Click on the **Restore** button to restore the item back to the Trash Bin, from where you can restore it back to it´s original source location in the Project (see //Restoring Items from the Trash Bin//).  
335 +
336 +[[image:Restore_items_before_grace_period_expiration.png||height="269" width="869"]]
337 +
338 +== Deleting Items immediately ==
339 +
340 +Once an item has been marked for permanent deletion, you can also issue its immediate deletion, terminating the grace period early. This action can be performed only by the Project Administrator who marked the item for deletion. For this:
341 +
342 +1. Go to your User Account page by clicking on your username in the upper right corner and then click on **Account**.
343 +1. In the lower right section, you´ll find the //Recently Deleted// table that provides an overview of all items you´ve marked for deletion and for which the grace period of 30 days has not expired yet. It also denotes for each item to which Project it belongs, and when it was marked for deletion.
344 +1. Click on the **Delete **button to delete the item - you will be prompted to confirm this action, as it cannot be undone.
345 +1. A pop-up will prompt you to confirm the immediate and permanent deletion of the corresponding item. To confirm, click **Delete**. To abort, click **Cancel**.
346 +
347 + [[image:Delete_items_immediately.png||height="225" width="1199"]]
348 +
349 +{{info}}
350 +**Note:** For forensic and compliance purposes, standard retention policies continue to apply to basic metadata (e.g., unique file/folder identifiers) and audit logs after permanent deletion of files and folders in Pilot-HDC.
351 +{{/info}}
352 +
280 280  == Considerations ==
281 281  
282 -* Delete permission is role-based - any Project member can delete files that they uploaded in the Green Room, Collaborators can delete files from any folder in the Core, and Project Administrators can delete any file from any location.
283 -* Deleted files are moved to a Trash Bin but are not permanently removed from the platform until requested.
284 284  * Files that have been copied to a Dataset will remain in the Dataset even if the original version has been deleted from the Core.
285 285  
357 +----
358 +
286 286  = Creating File Collections =
287 287  
288 288  When working with Project files in the Core, it can be useful to organize them in temporary or permanent views to help find them more easily. A Collection gives Project members the flexibility to create their own virtual groups of Project files from any number of Core folder locations. Similar to a music playlist, a Collection establishes a reference to the file(s) without moving or copying the actual files themselves. Adding a Collection to your Favourites gives you quick access to it from your Dashboard page.
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291 291  
292 292  == Create an empty Collection ==
293 293  
294 -[[image:Projects Core Create Collection v2.1.5 2023-01-20 1130.png||height="27%" width="40%"]]
367 +[[image:1723802914607-379.png||height="328" width="490"]]
295 295  
296 296  1. Navigate to the Project’s Core File Explorer .
297 297  1. From the Left navigation menu, click **Create Collection**.
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300 300  
301 301  == Add files to a Collection ==
302 302  
303 -[[image:Projects Core Add to Collection v2.1.3 2023-01-19.png||height="10%" width="50%"]]
376 +[[image:1723802928478-851.png||height="178" width="869"]]
304 304  
305 305  1. Navigate to the Project’s Core File Explorer .
306 306  1. Select one or more files and/or folders by clicking the checkbox beside each one (or use the select all checkbox), then click **Add to Collection **in File Explorer menu//.//
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313 313  
314 314  == Remove files from a Collection ==
315 315  
316 -[[image:Projects Core Remove File from Collection v2.1.5 2023-01-20.png||height="10%" width="50%"]]
389 +[[image:1723802939784-600.png||height="179" width="879"]]
317 317  
318 318  1. Click the name of the Collection in the left File Explorer navigation menu to open it.
319 319  1. Click the checkbox beside the file(s) to be removed, then click **Remove from Collection** in the File Explorer menu.
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322 322  
323 323  == Deleting or renaming a Collection ==
324 324  
325 -[[image:Projects Core Delete Rename Collection v2.1.5 2023-01-20.png||height="12%" width="50%"]]
398 +[[image:1723802950421-299.png||height="200" width="862"]]
326 326  
327 327  1. Click the name of the Collection in the left File Explorer navigation menu to open it.
328 328  1. Click either the Delete or Rename tool in the File Explorer menu.
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336 336  * A file can be added to one or more Collection(s).
337 337  * Adding or removing files in a Collection does not change the file's storage location or data lineage.
338 338  
412 +----
413 +
339 339  = Adding Files and Collections to Favourites =
340 340  
341 341  File and Collections from your Project can be “starred” to add them as Favourites and make them quickly accessible in the Favourites panel in the Dashboard
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345 345  
346 346  ----
347 347  
348 -Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
423 +Copyright © 2023-2026 [[Indoc Systems>>url:https://www.indocsystems.com]].
349 349  
350 350  HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
351 -
352 -
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