[IGBF-4387] Investigate missing IGB link in eFP-Seq Browser - JIRA UNCC

Details

Type: Task
Status: To-Do (View Workflow)
Priority: Major
Resolution: Unresolved
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
2
Epic Link:
Improve IGB for users
Sprint:
Spring 1

Description

Situation: During the eFP-Seq Browser release testing Karthik found that the "Alignments in IGB" link was missing. Looking at the eFP-Seq Browser GitHub page, there is a file cgi-bin/core/custom.js that contains some logic to add the Alignments in IGB link:

if (bam_type === "Amazon AWS") {
 append_str +=
  '<div id="igbLink_' +
  experimentno +
  '">Show: <a href="' +
  igbView_link +
  '" target="_blank" rel="noopener">Alignments in IGB</a></div>';
}

Task: Determine why the Alignments in IGB link is no longer showing up in the eFP-Seq browser.

Attachments

Activity

Ascending order - Click to sort in descending order

Nowlan Freese created issue - 05/Jan/26 3:28 PM

Nowlan Freese made changes - 05/Jan/26 3:28 PM

Field	Original Value	New Value
Epic Link		IGBF-1765 [ 17855 ]

Nowlan Freese made changes - 06/Jan/26 10:39 AM

Description

Situation: During the [eFP-Seq Browser release testing|https://wiki.bioviz.org/confluence/display/ITD/eFP-Seq+Browser] Karthik found that the "Alignments in IGB" link was missing. Looking at the [eFP-Seq Browser GitHub page|https://github.com/BioAnalyticResource/eFP-Seq_Browser], there is a file cgi-bin/core/custom.js that contains some logic to add the Alignments in IGB link:
{quote}if (bam_type === "Amazon AWS") {
append_str +=
  '<div id="igbLink_' +
  experimentno +
  '">Show: <a href="' +
  igbView_link +
  '" target="_blank" rel="noopener">Alignments in IGB</a></div>';
}{quote}

Task: Determine why the Alignments in IGB link is no longer showing up in the eFP-Seq browser.

Situation: During the [eFP-Seq Browser release testing|https://wiki.bioviz.org/confluence/display/ITD/eFP-Seq+Browser] Karthik found that the "Alignments in IGB" link was missing. Looking at the [eFP-Seq Browser GitHub page|https://github.com/BioAnalyticResource/eFP-Seq_Browser], there is a file cgi-bin/core/custom.js that contains some logic to add the Alignments in IGB link:
if (bam_type === "Amazon AWS") {
append_str +=
  '<div id="igbLink_' +
  experimentno +
  '">Show: <a href="' +
  igbView_link +
  '" target="_blank" rel="noopener">Alignments in IGB</a></div>';
}

Task: Determine why the Alignments in IGB link is no longer showing up in the eFP-Seq browser.

Nowlan Freese made changes - 06/Jan/26 10:40 AM

Description

Situation: During the [eFP-Seq Browser release testing|https://wiki.bioviz.org/confluence/display/ITD/eFP-Seq+Browser] Karthik found that the "Alignments in IGB" link was missing. Looking at the [eFP-Seq Browser GitHub page|https://github.com/BioAnalyticResource/eFP-Seq_Browser], there is a file cgi-bin/core/custom.js that contains some logic to add the Alignments in IGB link:
if (bam_type === "Amazon AWS") {
append_str +=
  '<div id="igbLink_' +
  experimentno +
  '">Show: <a href="' +
  igbView_link +
  '" target="_blank" rel="noopener">Alignments in IGB</a></div>';
}

Task: Determine why the Alignments in IGB link is no longer showing up in the eFP-Seq browser.

Situation: During the [eFP-Seq Browser release testing|https://wiki.bioviz.org/confluence/display/ITD/eFP-Seq+Browser] Karthik found that the "Alignments in IGB" link was missing. Looking at the [eFP-Seq Browser GitHub page|https://github.com/BioAnalyticResource/eFP-Seq_Browser], there is a file cgi-bin/core/custom.js that contains some logic to add the Alignments in IGB link:

if (bam_type === "Amazon AWS") {
append_str +=
  '<div id="igbLink_' +
  experimentno +
  '">Show: <a href="' +
  igbView_link +
  '" target="_blank" rel="noopener">Alignments in IGB</a></div>';
}

Task: Determine why the Alignments in IGB link is no longer showing up in the eFP-Seq browser.

Hide

Permalink

Nowlan Freese added a comment - 06/Jan/26 10:43 AM

After discussion with Ann Loraine, Dr. Loraine will reach out to the Provart lab. It is possible the data were moved from Amazon and this is causing an issue.

Show

Nowlan Freese added a comment - 06/Jan/26 10:43 AM After discussion with Ann Loraine , Dr. Loraine will reach out to the Provart lab. It is possible the data were moved from Amazon and this is causing an issue.

Nowlan Freese made changes - 06/Jan/26 10:43 AM

Assignee

Ann Loraine [ aloraine ]

Nowlan Freese made changes - 06/Jan/26 10:44 AM

Description

Situation: During the [eFP-Seq Browser release testing|https://wiki.bioviz.org/confluence/display/ITD/eFP-Seq+Browser] Karthik found that the "Alignments in IGB" link was missing. Looking at the [eFP-Seq Browser GitHub page|https://github.com/BioAnalyticResource/eFP-Seq_Browser], there is a file cgi-bin/core/custom.js that contains some logic to add the Alignments in IGB link:

if (bam_type === "Amazon AWS") {
append_str +=
  '<div id="igbLink_' +
  experimentno +
  '">Show: <a href="' +
  igbView_link +
  '" target="_blank" rel="noopener">Alignments in IGB</a></div>';
}

Task: Determine why the Alignments in IGB link is no longer showing up in the eFP-Seq browser.

Situation: During the [eFP-Seq Browser release testing|https://wiki.bioviz.org/confluence/display/ITD/eFP-Seq+Browser] Karthik found that the "Alignments in IGB" link was missing. Looking at the [eFP-Seq Browser GitHub page|https://github.com/BioAnalyticResource/eFP-Seq_Browser], there is a file [cgi-bin/core/custom.js|https://github.com/BioAnalyticResource/eFP-Seq_Browser/blob/dd51d828cda9e2c93d5c6add87956460576c9353/cgi-bin/core/custom.js#L6] that contains some logic to add the Alignments in IGB link:

if (bam_type === "Amazon AWS") {
append_str +=
  '<div id="igbLink_' +
  experimentno +
  '">Show: <a href="' +
  igbView_link +
  '" target="_blank" rel="noopener">Alignments in IGB</a></div>';
}

Task: Determine why the Alignments in IGB link is no longer showing up in the eFP-Seq browser.

Ann Loraine made changes - 07/Jan/26 12:50 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 07/Jan/26 12:51 PM

Description

Situation: During the [eFP-Seq Browser release testing|https://wiki.bioviz.org/confluence/display/ITD/eFP-Seq+Browser] Karthik found that the "Alignments in IGB" link was missing. Looking at the [eFP-Seq Browser GitHub page|https://github.com/BioAnalyticResource/eFP-Seq_Browser], there is a file [cgi-bin/core/custom.js|https://github.com/BioAnalyticResource/eFP-Seq_Browser/blob/dd51d828cda9e2c93d5c6add87956460576c9353/cgi-bin/core/custom.js#L6] that contains some logic to add the Alignments in IGB link:

if (bam_type === "Amazon AWS") {
append_str +=
  '<div id="igbLink_' +
  experimentno +
  '">Show: <a href="' +
  igbView_link +
  '" target="_blank" rel="noopener">Alignments in IGB</a></div>';
}

Task: Determine why the Alignments in IGB link is no longer showing up in the eFP-Seq browser.

Situation: During the [eFP-Seq Browser release testing|https://wiki.bioviz.org/confluence/display/ITD/eFP-Seq+Browser] Karthik found that the "Alignments in IGB" link was missing. Looking at the [eFP-Seq Browser GitHub page|https://github.com/BioAnalyticResource/eFP-Seq_Browser], there is a file [cgi-bin/core/custom.js|https://github.com/BioAnalyticResource/eFP-Seq_Browser/blob/dd51d828cda9e2c93d5c6add87956460576c9353/cgi-bin/core/custom.js#L6] that contains some logic to add the Alignments in IGB link:

{code}
if (bam_type === "Amazon AWS") {
append_str +=
  '<div id="igbLink_' +
  experimentno +
  '">Show: <a href="' +
  igbView_link +
  '" target="_blank" rel="noopener">Alignments in IGB</a></div>';
}
{code}

Task: Determine why the Alignments in IGB link is no longer showing up in the eFP-Seq browser.

Hide

Permalink

Ann Loraine added a comment - 07/Jan/26 1:03 PM

I just now sent an email to the Provart group to let them know.

Show

Ann Loraine added a comment - 07/Jan/26 1:03 PM I just now sent an email to the Provart group to let them know.

Hide

Permalink

Nowlan Freese added a comment - 09/Jan/26 4:35 PM

Testing different datasets on the eFP-Seq browser for gene AT2G24270:

Araport 11 RNA-seq data: no link to view in IGB
Developmental transcriptome - Klepikova et al: no link to view in IGB
Guard Cell Drought: no link to view in IGB
Pollen: no link to view in IGB

Show

Nowlan Freese added a comment - 09/Jan/26 4:35 PM Testing different datasets on the eFP-Seq browser for gene AT2G24270: Araport 11 RNA-seq data: no link to view in IGB Developmental transcriptome - Klepikova et al: no link to view in IGB Guard Cell Drought: no link to view in IGB Pollen: no link to view in IGB

Ann Loraine made changes - 14/Jan/26 11:21 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 19/Jan/26 11:46 AM

Sprint

Spring 1 [ 233 ]

Spring 1, Spring 2 [ 233, 234 ]

Ann Loraine made changes - 19/Jan/26 11:46 AM

Rank

Ranked higher

Ann Loraine made changes - 22/Jan/26 1:53 PM

Sprint

Spring 1, Spring 2 [ 233, 234 ]

Spring 1 [ 233 ]

People

Assignee:

Ann Loraine

Reporter:

Nowlan Freese

Votes:

0 Vote for this issue

Watchers:

2 Start watching this issue

Dates

Created:

05/Jan/26 3:28 PM

Updated:

22/Jan/26 1:53 PM