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PathcoreFlow User Manual

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.

On a mobile device, tap and hold on an item to display the context menu. Alternatively, you may tap on an item to select it and then tap on the 1 Selected dropdown menu at the top of the item list, next to the search box.

Depending on your Permissions and add-ons 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. Bring up the context menu for the item (or items)

  2. Click Move

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

  4. Click on the Move to Folder button

If you attempt to move an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.
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. Bring up the context menu for the item (or items)

  2. Click Copy

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

  4. Click on the Copy to Folder button

The new file or folder will be named "Copy of item name".
Copy URL (single item only)

Copy URL copies the URL of the item to the clipboard.

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 recognized 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. Bring up the context menu for the item

  2. Click Rename

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

  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

If you attempt to rename an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.
Edit Metadata

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

See the Metadata section for more details.

  1. Bring up the context menu for the item (or items)

  2. Click Edit Metadata

  3. The popup dialog allows you to add or remove metadata System Fields, Custom Fields, and/or Field Sets

If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.
Share (single item only)

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

See Managing Share Links for more details.

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

  1. Bring up the context menu for the item

  2. Click Share

  3. The popup dialog allows you to add and manage share links

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. Bring up the context menu for the item (or items)

  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. Bring up the context menu for the item (or items)

  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.

See Downloading for more details.

  1. Bring up the context menu for the item (or items)

  2. Click Download

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

  4. Click on the Download button

Open in VIS [add-on]

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

See Visiopharm Integration for more details.

  1. Bring up the context menu for the item (or items)

  2. Click Open in VIS

  3. In the popup dialog, select your options

  4. Click on the Open button

When opening multiple images in Visiopharm, they must all be in the same folder. Also, no images in in Unsorted Uploads can be opened in Visiopharm.
Open in HALO [add-on]

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

See HALO Integration for more details.

  1. Bring up the context menu for the item (or items)

  2. Click Open in HALO

  3. A SIS file will download

  4. Open the SIS file in HALO

Export Activities (single item only) [add-on]

Export Activities opens the Export Activities dialog, which can generate a CSV file of changes made to the item over a specified period of time.

See Activity Logs for more details.

  1. Bring up the context menu for the item

  2. Click Export Activities

  3. (Optional) In the popup dialog, select the start date from the Since field

  4. (Optional) Select the desired output timezone from the Timezone dropdown menu

  5. Click on the Export CSV button to download a CSV file

Delete

Delete allows you to remove the item and all of its contents (in the case of a folder) from the Repository.

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

  1. Bring up the context menu for the item (or items)

  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

If you attempt to delete an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.

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 Navigation Menu 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. You may need to click on the Expand 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

If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.

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 Navigation Menu
To toggle favorite status

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the Navigation Menu 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. Depending on the type and number of items downloaded, or the options selected in the download dialog, an archive file may need to be generated before the download can begin. The following will cause this to occur:

  • Selecting multiple items, or a folder of items, for download
  • Including metadata options in the download dialog
  • Downloading a multi-file image format, such as MRXS

When this is the case, the download dialog will include a dropdown menu to select an archive file format.

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 web 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 add-on
    • HALO Results: Toggle to include analysis results imported from HALO. This option is only available if you have the HALO Integration add-on

  • 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: This dropdown menu lets you select the archive format when more than one item and/or metadata are included

    The .tar.gz and .zip archive formats are not available by default in this release. If you require these formats, you may need to contact Pathcore Support.

    .tar archives are natively supported by Microsoft Windows 11, macOS, and all major Linux distributions. For users running Windows 10 or prior, we recommend a third-party archive manager such as [7-Zip](https://www.7-zip.org/).

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.

Most downloads can be paused and resumed later (e.g., in the event of a network interruption).

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 Navigation Menu 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 Navigation Menu 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