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Repository Operations


This section contains a list of basic operations that are available for items in the Repository.

Different operations are available depending on the type and number of items selected.

Context Menu

Most operations can be performed via a context menu. This menu is accessed by right-clicking on an item in the Folder Listing (or one of the currently selected items when using Multi-Select). The same menu can be accessed by clicking the Down Arrow button next to the item's name in the right-hand panel. You may need to click on the Collapsed button if the panel is collapsed.

Depending on your Permissions and addons some operations may not be available.
Move

Move opens the Move Item dialog, allowing you to move the item (or items) to any accessible folder.

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Move

  3. In the popup dialog, select the destination folder from the available list

  4. Click on the Move to Folder button

Copy

Copy opens the Copy Item dialog, allowing you to make a copy of the item (or items) in another folder.

When copying entries in the Repository, the underlying files are not duplicated (i.e. copies are linked to the same underlying file) and thus do not consume additional storage. However, the metadata associated with the copied entries, such as annotations, snapshots, and custom fields, are duplicated when an entry in the Repository is copied (i.e. duplicated entries will retain an independent copy of the original metadata).

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Copy

  3. In the popup dialog, select the destination folder from the available list

  4. Click on the Copy to Folder button

View Image(s) (images only)

View Images opens the select item (or items) in the Viewer.

Only images can be opened in the Viewer.
Retry Type Detection (attachments only)

Retry Type Detection attempts to force the system to detect this attachment as an image again. This can be useful if an image uploaded completely, but for whatever reason is not being recognised by PathcoreFlow as an image. If this still does not work you may need to contact Pathcore Support.

This operation only applies to attachments.
Rename (single item only)

Rename allows you to change the name of the item. While all entries in the Repository have names, names do not have to be unique because each entry has a unique ID, see Names and IDs.

It’s not possible to rename multiple items at the same time.

  1. Right-click on the item to bring up the context menu

  2. Click Rename

  3. In the popup dialog, type a new name for the folder

  4. Click on the Rename button or press the Enter key to save. To discard your changes, click on the Cancel button or press the Escape key

Edit Metadata

Edit Metadata opens a dialog where you can add, change, or remove Metadata fields for the item (or items).

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Edit Metadata

  3. The popup dialog allows you to add or remove metadata System Fields, Custom Fields, and/or Field Sets. See the Metadata section for more details

Share (single item only)

Share opens the Share Links dialog, which allows you to add and manage share links for the item.

It’s not possible to share multiple items at a time. However it is possible to share a folder of items.

  1. Right-click on the item to bring up the context menu

  2. Click Share

  3. The popup dialog allows you to add and manage share links. See Managing Share Links for more details

Mark as Read / Mark as Unread

An item can be marked as "read" (name in plain text) or "unread" (name in bold) depending on whether or not you have previously viewed it.

See Read Status for more details.

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Mark as Read to enable the read status, or

  3. Click Mark as Unread to clear the read status

Favorite / Unfavorite

Favorite tags the item (or items) as Starred. Items tagged this way are quickly and easily accessible from the Starred Items List. Unfavorite removes this tag. See Favorite Status for more details.

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Favorite to add the Starred tag, or

  3. Click Unfavorite to remove the tag

Download

Download opens the Download dialog, allowing you to save items and metadata locally.

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Download

  3. In the popup dialog, select what you would like to download (files and/or metadata). See Downloading for more details

  4. Click on the Download button

Open in VIS [addon]

Open in VIS allows you to open the item (or items) in Visiopharm.

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Open in VIS

  3. In the popup dialog, select your options. See Visiopharm Integration for more details

  4. Click on the Open button

Open in HALO [addon]

Open in HALO allows you to open the item (or items) in Indica Labs's HALO software.

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Open in HALO

  3. A SIS file will download

  4. Open the SIS file in HALO. See HALO Integration for more details

Audit [addon]

Audit opens the Audit Report dialog, which can generate a CSV file of changes made to the folder over a specified period of time.

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Audit

  3. In the popup dialog, select the start date from which you wish to see the audit data

  4. Click on the Download Audit button to download a CSV file

Delete

Delete allows you to remove the folder and all of its contents from the Repository.

Deleted items cannot be recovered. Be careful with this action.

  1. Right-click on the item (or items) to bring up the context menu

  2. Click Delete

  3. Click on the Yes button to confirm if you are sure you wish to remove the item. To cancel the delete action, click on the Cancel button or press the Escape key

Description

Every item in the Repository has a user editable multi-line description. By default, an item's description is empty. Use the description to record a finding about an image, folder or file.

To edit an item's description

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the left-hand sidebar then navigate to a folder)

  2. Select a single item in a folder

  3. Click on the Edit Description button (or Add Description button if no description yet exists) in the Metadata tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the Collapsed button if the panel is collapsed

  4. Type the description in the text area that appears

  5. Click on the Save button to save the changes. To discard your changes, click on the Cancel button

Read Status

The names of items (files and folders) in the Repository are in bold to indicate an item is “unread”. Once an item has been “read”, plain text font is used for the name of the item. New items are always unread and are automatically marked as read once they have been opened, viewed or downloaded by a user. The following actions will cause the status of an item to be marked as “read”:

  • Clicking on an image file causing the viewer to launch
  • Clicking on any other item causing it open in the browser or be downloaded

The read status is unique for each user and can be toggled at any time, making it useful for tracking items that require further attention.

The “read” status can be changed manually from the Context Menu for an item.

Favorite Status

Each Repository item has a favorite status, which can be toggled by clicking on the Empty Star button adjacent to the item’s name. A solid star indicates an item has been marked as a favorite while a hollow star (default) status indicates the item is not a favorite.

The favorite status is unique for each user and can be toggled at any time, making it useful for tracking items that require further attention.

To view a list of all favorited items
  1. Click on the Star Starred button in the TAGS section of the left-hand sidebar
To toggle favorite status

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the left-hand sidebar then navigate to a folder)

  2. Toggle the Empty Star button next to the item to indicate the status

Downloading

In general, one or more files or folders can be downloaded from the Repository. When downloading a single file, the download operation will be initiated in the normal way. When downloading multiple files and/or folders (or if you include any metadata), the download operation will be initiated in the normal way after the files/folders have been combined into an archive file.

Certain item types cannot be combined into a single download. For example, a Figure cannot be downloaded with any other item (including another Figure) because it has a unique export workflow.

Some browsers may require your permission before downloading files.
Download dialog options

The following options are available when downloading:

  • Files: Toggle to include the selected files and folders
  • Metadata: Toggle to include metadata about the selected files and folders. You can further customize the additional metadata to include:
    • Annotations: Toggle to include your private annotations as well as shared annotations by others
    • Snapshot Coordinates: Toggle to include snapshot coordinates and properties
    • Fields: Toggle to include System Fields, Custom Fields, and Field Sets. See the Metadata section for more details
    • Tags: Toggle to include tags you have assigned to the items
    • Overlays: Toggle to include overlay images added to images in the selected items
    • VIS Results: Toggle to include analysis results imported from Visiopharm. This option is only available if you have the Visiopharm Integration addon
    • HALO Results: Toggle to include analysis results imported from HALO. This option is only available if you have the HALO Integration addon
  • Download as JSON / Download as CSV: choose the file format of the selected metadata. These options can only be selected if metadata is included in the download
  • .tar / .tar.gz / .zip: This dropdown lets you select the archive format when more than one item and/or metadata are included

When the selection contains a single item, such as an image file, attachment, or report, the file itself will be downloaded. In other cases, such as for a single saved Figure item, the download will trigger an export and preview window. When there are multiple items or a folder selected, a downloadable archive will be generated in the chosen format with the option to include metadata.

Multi-Select

One or more files can be selected from the folder listing page in order to perform bulk operations such as download, copy or move.

To select more than one file

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the left-hand sidebar then navigate to a folder)

  2. Click on an item from the file listing

  3. While holding the Ctrl key (on Windows) or Command key (on macOS) select another file

  4. Repeat step 3 as necessary

To select more than one file in a continuous range

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the left-hand sidebar then navigate to a folder)

  2. Click on the first item in the range from the file listing

  3. While holding the Shift key, select the last file in the range