Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

User Story #1797 (new)

Opened 10 years ago

Last modified 4 years ago

User-specified annotations on Import

Reported by: cxallan Owned by:
Priority: critical Milestone: Metadata
Component: Import Keywords: paris2011
Cc: fs@…, ux@…, h.perrett@… Story Points: n.a.
Sprint: n.a. Importance: n.a.
Total Remaining Time: n.a. Estimated Remaining Time: n.a.

Description (last modified by jmoore)

The importer should be able to handle user specified annotations, linking them to all images in a given import run.

Admins or Group leaders should be able to specify an annotation "template", like an OMERO.editor file that has to be filled out by users when importing images. This could include 'required' vv optional fields.

http://www.openmicroscopy.org/community/viewtopic.php?f=6&t=753

Would be nice to allow population of OMERO.tables with this data, to support some of the features of Batch Annotation #4271.

Questions / Answers:

  • When users import, do you want to give them a choice of templates they fill out?
    • If possible this would be great. We had thought of just using a very broard set of fields that would cover all the gaps from all the file types but, (if I understand correctly) if a user could select their template, say one for an AxioVision? file import, and or another for a SPOT RT file import that would be much nicer.
  • Would there be anyway to restrict who has permissions to create a template, so that only adamins can?
  • How complex is the template? E.g. Simple list of attributes (like column headers in a table)? Or "fully featured" like OMERO.editor, with a "type" for each parameter (boolean, String, integer etc), options for some fields, default values, "required" vv optional parameters etc.
    • Fully featured would be great, as there are some fields that are required and others optional, some fields will need to have a set list of options (e.g. checkboxes, radio buttons), and others just open text. A webform like template. A simple list of attributes isn't really sophisticated enough as we would like to ensure the naming of the fields is consistent and all relevant metadata is captured correctly for the publishing and discoverability component.
  • If I'm importing 100 images with 10 fields each, when do I fill these out? E.g. after I hit "Import" (before importing starts), after import is finished (but how to enforce this) or before Import. E.g. Create an Excel table of images (identified by name) and fill out the values, then pick this file on import.
    • Again ideally.... A) If I select multiple images (or a folder? not sure if this is possible?) at once from my local directory then hit 'import' to go to get ready for download to OMERO, a pop-up box would come up and ask for extra metadata to apply to that SET of images (i.e. all images selected will get the same extra metadata added) B) If I select a single image from my local directory then hit 'import', a pop-up box would come up and ask for the extra metadata to apply to that file.

Comments:

  • It would also be good if the files would automatically upload to the appropriate folder/s based on the extra metadata added, such as Proejct name or Chief Investigator.
  • Can we ensure that users importing images HAVE to specify the missing metadata before any import is successful?

Change History (18)

comment:1 Changed 10 years ago by cxallan

  • Owner changed from bwzloranger to cxallan

comment:2 Changed 10 years ago by cxallan

r6081: Added capability to handle text annotations

comment:3 Changed 10 years ago by cxallan

  • Owner changed from cxallan to bwzloranger

Date/Time?, boolean, long and double annotations should be added to the command line importer.

comment:4 Changed 10 years ago by bwzloranger

  • Milestone changed from OMERO-Beta4.2 to Unscheduled

comment:5 Changed 10 years ago by cxallan

(In [8274]) Added text annotation linkages to the command line importer. (See #1797)

comment:6 Changed 9 years ago by cxallan <cxallan@…>

(In [1208a2da7848b7830b105f82053aec9458a5f849/ome.git]on branches 4_1, dev_4_1, dev_4_1_custom) Added text annotation linkages to the command line importer. (See #1797)

git-svn-id: file:///home/svn/omero/branches/Beta4.1@8274 05709c45-44f0-0310-885b-81a1db45b4a6

comment:7 Changed 9 years ago by jmoore <josh@…>

(In [0ed10cb9b92a9fd02ad7c28a2267f1026d3a36d2/ome.git] on branch dev_4_1_custom) Merge remote branch 'origin/dev_4_1' into dev_4_1_custom

Conflicts:

.classpath
components/tools/OmeroImporter/src/ome/formats/importer/ImportLibrary.java
components/tools/OmeroImporter/src/ome/formats/importer/cli/CommandLineImporter.java
etc/omero.properties
lib/repository/bio-formats-9071a01.jar
lib/repository/jai_imageio-9071a01.jar
lib/repository/loci-common-9071a01.jar
lib/repository/mdbtools-java-9071a01.jar
lib/repository/ome-xml-9071a01.jar
lib/repository/poi-loci-9071a01.jar

comment:8 Changed 9 years ago by cxallan <cxallan@…>

(In [1208a2da7848b7830b105f82053aec9458a5f849/ome.git]on branches 4_1, 4_1_custom, dev_4_1, dev_4_1_custom, josh/4.1-web-backport) Added text annotation linkages to the command line importer. (See #1797)

git-svn-id: file:///home/svn/omero/branches/Beta4.1@8274 05709c45-44f0-0310-885b-81a1db45b4a6

comment:9 Changed 9 years ago by jmoore <josh@…>

(In [0ed10cb9b92a9fd02ad7c28a2267f1026d3a36d2/ome.git]on branches 4_1_custom, dev_4_1_custom, josh/4.1-web-backport) Merge remote branch 'origin/dev_4_1' into dev_4_1_custom

Conflicts:

.classpath
components/tools/OmeroImporter/src/ome/formats/importer/ImportLibrary.java
components/tools/OmeroImporter/src/ome/formats/importer/cli/CommandLineImporter.java
etc/omero.properties
lib/repository/bio-formats-9071a01.jar
lib/repository/jai_imageio-9071a01.jar
lib/repository/loci-common-9071a01.jar
lib/repository/mdbtools-java-9071a01.jar
lib/repository/ome-xml-9071a01.jar
lib/repository/poi-loci-9071a01.jar

comment:10 Changed 9 years ago by wmoore

  • Cc jburel wmoore added
  • Description modified (diff)
  • Summary changed from Add ability to handle user specified annotations to User-specified annotations on Import

comment:11 Changed 9 years ago by wmoore

  • Description modified (diff)

comment:12 Changed 9 years ago by jmoore

  • Cc jmoore added
  • Keywords paris2011 added
  • Priority changed from major to critical

comment:13 Changed 9 years ago by jmoore

  • Description modified (diff)

comment:14 Changed 9 years ago by jmoore

  • Cc h.perrett@… added

comment:15 Changed 9 years ago by jburel

  • Cc saloynton added
  • Owner bwzloranger deleted

comment:16 Changed 9 years ago by jmoore

This quite likely a great candidate for the usability backlog.

comment:17 Changed 7 years ago by jamoore

  • Cc fs@… ux@… added; saloynton jburel wmoore jamoore removed
  • Milestone changed from Unscheduled to 5.0.0

Moving to 5.0.0 for review as a general "import" issue.

comment:18 Changed 4 years ago by jamoore

  • Milestone changed from 5.x to Metadata
Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.180017 sec.)

We're Hiring!