Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Critical
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.0.2 Minor Release
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Labels:
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Story Points:0.5
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Sprint:Summer 2018 Part 2
Description
An IGB App developer asks:
"Can I select a region/part of my data and get the location, or maybe even values for different lines, of it as an output? For example, I have peaks from ChIP-seq analysis and I want to know exact location/values of those which are selected in IGB."
Investigate how this could be done and add comments here.
- How does an App find out what items are currently selected in IGB?
- How does an App gain access to attributes of the currently selected items?
Tips:
- Look at how ProtAnnot does it.
- Look at Development plug-ins that perform operations on single annotation Glyph objects
- Look at IgbService
- Look at how API services are implemented in general
Attachments
Issue Links
- relates to
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IGBF-1355 Make a new IGB "demo" App that shows how Apps can get access to track data
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Ann Loraine [ aloraine ] |
| Summary | how does an App get access to currently selected items in IGB | Document how Apps get access to currently selected items in IGB |
| Rank | Ranked higher |
| Description |
An IGB App developer asks:
"Can I select a region/part of my data and get the location, or maybe even values for different lines, of it as an output? For example, I have peaks from ChIP-seq analysis and I want to know exact location/values of those which are selected in IGB." Investigate how this could be done and add comments here. * How does an App find out what items are currently selected in IGB? * How does an App gain access to attributes of the currently selected items? |
An IGB App developer asks:
"Can I select a region/part of my data and get the location, or maybe even values for different lines, of it as an output? For example, I have peaks from ChIP-seq analysis and I want to know exact location/values of those which are selected in IGB." Investigate how this could be done and add comments here. * How does an App find out what items are currently selected in IGB? * How does an App gain access to attributes of the currently selected items? Tips: * Look at how ProtAnnot does it. * Look at Development plug-ins that perform operations on single annotation Glyph objects |
| Description |
An IGB App developer asks:
"Can I select a region/part of my data and get the location, or maybe even values for different lines, of it as an output? For example, I have peaks from ChIP-seq analysis and I want to know exact location/values of those which are selected in IGB." Investigate how this could be done and add comments here. * How does an App find out what items are currently selected in IGB? * How does an App gain access to attributes of the currently selected items? Tips: * Look at how ProtAnnot does it. * Look at Development plug-ins that perform operations on single annotation Glyph objects |
An IGB App developer asks:
"Can I select a region/part of my data and get the location, or maybe even values for different lines, of it as an output? For example, I have peaks from ChIP-seq analysis and I want to know exact location/values of those which are selected in IGB." Investigate how this could be done and add comments here. * How does an App find out what items are currently selected in IGB? * How does an App gain access to attributes of the currently selected items? Tips: * Look at how ProtAnnot does it. * Look at Development plug-ins that perform operations on single annotation Glyph objects * Look at IgbService * Look at how API services are implemented in general |
| Rank | Ranked higher |
| Assignee | Ivory Blakley [ ieclabau ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | In Progress [ 3 ] |
Notes on terminology and language:
- "App" instead of "plugin"
- upper-case "A"
- Apps are active
- IGB is a platform that offers services Apps can use
- present tense
Example verbiage)
"The ScatterPlot App opens an interactive scatter plot that compares two selected Graph tracks."
"When you use the App Manager to install the ProtAnnot App, it adds a menu item to the IGB Tools menu."
"The Get Extra Details App obtains information about selected items from IGB and then displays a summary."
"The Summarize Graph App access all loaded data for a selected graph track and displays summary statistics, such as the mean and median."
Apps are active. They can query data from, retrieve information about , obtain, add to IGB.
- Apps
Don't say:
"Getting information from IGB to a plugin"
This suggest IGB uses push to send data to Apps.
say:
"Ways an IGB App can access program state in IGB"
draft documentation:
https://docs.google.com/document/d/1qYb0MSAV3kiKmv0EZdfS2hqImDMb3FRGG09h-WmkrQI
This issue is very closely related to IGBF-1355, which is still in progress. The part of the documentation that addresses this issue specifically is assembled in section "I want my App to receive as input the set of selected objects from an annotation track. How do I do that?"
The entire document will continue to be refined as we progress with IGBF-1355 and any other related cases.
I'm moving this to Needs first level review.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ivory Blakley [ ieclabau ] |
| Assignee | Anh Moss [ aduong ] |
| Assignee | Anh Moss [ aduong ] | Ivory Blakley [ ieclabau ] |
| Assignee | Ivory Blakley [ ieclabau ] |
| Assignee | Anh Moss [ aduong ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
Overall, this document is good and addresses the questions in this issue.
I have made some comments within the document regarding minor points in terminology and clarification. It is my understanding that this document is still in progress overall (as it is closely related to IGBF-1355, which is still in progress), but it does answer the questions in this issue, so I am moving it to the Ready for Pull Request column.
The link to IGBF-1355: https://jira.transvar.org/browse/IGBF-1355
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Anh Moss [ aduong ] |
| Resolution | Done [ 10000 ] | |
| Status | Ready for Pull Request [ 10304 ] | Closed [ 6 ] |
| Assignee | Ivory Blakley [ ieclabau ] |
| Workflow | Loraine Lab Workflow [ 18043 ] | Fall 2019 Workflow Update [ 19918 ] |
| Workflow | Fall 2019 Workflow Update [ 19918 ] | Revised Fall 2019 Workflow Update [ 22037 ] |
Relevant page in the developers guide:
https://wiki.transvar.org/display/igbdevelopers/Context+Menu+API+QuickStart
Corresponding git repository with example:
https://bitbucket.org/lorainelab/context-menu-api-quickstart
In IGB code base see Menu API module.