Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.2.0
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Fall 7, Fall 5, Fall 6, Fall 7, Fall 8
Description
Situation: I've noticed an occasional error in the logs when loading GFF files in IGB. It's not currently well-understood how GFF files are being parsed in IGB which is making the debugging process for this issue difficult.
Task: Reproduce the error by following the instructions below, then investigate the IGB codebase to determine what's supposed to happen when a GFF file is parsed and loaded in IGB. For example, is the "##FASTA" section in a GFF file supposed to be parsed as the reference sequence when no genome is loaded in IGB? Please report your findings on this ticket.
- Open IGB
- Download prodigal_Lambda_phage_sequences.gff from Google Drive (may need permission - https://drive.google.com/drive/folders/14noPsmKYMxX9jgHYQhkjqaTGzT8z8bSK?usp=drive_link)
- Without selecting a genome, drag and drop prodigal_Lambda_phage_sequences.gff into IGB.
Note: Files for testing are also available via the Loraine Lab Google Drive: https://drive.google.com/drive/folders/1MLsVItXNcskfiCAg62GFmxWc1-NR40Tx?usp=drive_link
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Link | This issue relates to IGBF-4008 [ IGBF-4008 ] |
| Assignee | Udaya Chinta [ uchinta ] |
| Sprint | Fall 7 [ 208 ] | Fall 7, Fall 8 [ 208, 209 ] |
| Rank | Ranked higher |
| Sprint | Fall 7, Winter 1 [ 208, 209 ] | Fall 7, Spring 1 [ 208, 210 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 7, Spring 1 [ 208, 210 ] | Fall 7, Spring 3 [ 208, 212 ] |
| Sprint | Fall 7, Spring 3 [ 208, 212 ] | Fall 7, Spring 5 [ 208, 214 ] |
| Sprint | Fall 7, Spring 5 [ 208, 214 ] | Fall 7 [ 208 ] |
| Rank | Ranked higher |
| Assignee | Udaya Chinta [ uchinta ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
| Sprint | Fall 7 [ 208 ] | Fall 7, Fall 5 [ 208, 228 ] |
| Sprint | Fall 7, Fall 5 [ 208, 228 ] | Fall 7, Fall 5, Fall 6 [ 208, 228, 229 ] |
| Rank | Ranked higher |
| Sprint | Fall 7, Fall 5, Fall 6 [ 208, 228, 229 ] | Fall 7, Fall 5, Fall 6, Fall 7 [ 208, 228, 229, 230 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | prodigal_Lambda_phage_sequences_FIXED.gff [ 18962 ] | |
| Attachment | prodigal_Lambda_phage_sequences.fasta [ 18963 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Sprint | Fall 7, Fall 5, Fall 6, Fall 7 [ 208, 228, 229, 230 ] | Fall 7, Fall 5, Fall 6, Fall 7, Fall 8 [ 208, 228, 229, 230, 231 ] |
| Rank | Ranked higher |
| Summary | Investigate: GFF parsing logic | Fix GFF null pointer exception when FASTA included |
| Assignee | Nowlan Freese [ nfreese ] | saideepthi jagarapu [ sjagarap ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Security | Hidden [ 10001 ] |
| Security | Hidden [ 10001 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Attachment | prodigal_Lambda_phage_sequences_FIXED.gff [ 18962 ] |
| Attachment | prodigal_Lambda_phage_sequences.fasta [ 18963 ] |
| Description |
*Situation:* I've noticed an occasional error in the logs when loading GFF files in IGB. It's not currently well-understood how GFF files are being parsed in IGB which is making the debugging process for this issue difficult.
*Task:* Reproduce the error by following the instructions below, then investigate the IGB codebase to determine what's supposed to happen when a GFF file is parsed and loaded in IGB. For example, is the "##FASTA" section in a GFF file supposed to be parsed as the reference sequence when no genome is loaded in IGB? Please report your findings on this ticket. # Open IGB # Download *prodigal_Lambda_phage_sequences.gff* from Google Drive (https://drive.google.com/drive/folders/14noPsmKYMxX9jgHYQhkjqaTGzT8z8bSK?usp=drive_link) # *Without selecting a genome*, drag and drop *prodigal_Lambda_phage_sequences.gff* into IGB. |
*Situation:* I've noticed an occasional error in the logs when loading GFF files in IGB. It's not currently well-understood how GFF files are being parsed in IGB which is making the debugging process for this issue difficult.
*Task:* Reproduce the error by following the instructions below, then investigate the IGB codebase to determine what's supposed to happen when a GFF file is parsed and loaded in IGB. For example, is the "##FASTA" section in a GFF file supposed to be parsed as the reference sequence when no genome is loaded in IGB? Please report your findings on this ticket. # Open IGB # Download *prodigal_Lambda_phage_sequences.gff* from Google Drive (https://drive.google.com/drive/folders/14noPsmKYMxX9jgHYQhkjqaTGzT8z8bSK?usp=drive_link) # *Without selecting a genome*, drag and drop *prodigal_Lambda_phage_sequences.gff* into IGB. Note: Files for testing are also available via the Loraine Lab Google Drive: https://drive.google.com/drive/folders/1MLsVItXNcskfiCAg62GFmxWc1-NR40Tx?usp=drive_link |
| Description |
*Situation:* I've noticed an occasional error in the logs when loading GFF files in IGB. It's not currently well-understood how GFF files are being parsed in IGB which is making the debugging process for this issue difficult.
*Task:* Reproduce the error by following the instructions below, then investigate the IGB codebase to determine what's supposed to happen when a GFF file is parsed and loaded in IGB. For example, is the "##FASTA" section in a GFF file supposed to be parsed as the reference sequence when no genome is loaded in IGB? Please report your findings on this ticket. # Open IGB # Download *prodigal_Lambda_phage_sequences.gff* from Google Drive (https://drive.google.com/drive/folders/14noPsmKYMxX9jgHYQhkjqaTGzT8z8bSK?usp=drive_link) # *Without selecting a genome*, drag and drop *prodigal_Lambda_phage_sequences.gff* into IGB. Note: Files for testing are also available via the Loraine Lab Google Drive: https://drive.google.com/drive/folders/1MLsVItXNcskfiCAg62GFmxWc1-NR40Tx?usp=drive_link |
*Situation:* I've noticed an occasional error in the logs when loading GFF files in IGB. It's not currently well-understood how GFF files are being parsed in IGB which is making the debugging process for this issue difficult.
*Task:* Reproduce the error by following the instructions below, then investigate the IGB codebase to determine what's supposed to happen when a GFF file is parsed and loaded in IGB. For example, is the "##FASTA" section in a GFF file supposed to be parsed as the reference sequence when no genome is loaded in IGB? Please report your findings on this ticket. # Open IGB # Download *prodigal_Lambda_phage_sequences.gff* from Google Drive (may need permission - https://drive.google.com/drive/folders/14noPsmKYMxX9jgHYQhkjqaTGzT8z8bSK?usp=drive_link) # *Without selecting a genome*, drag and drop *prodigal_Lambda_phage_sequences.gff* into IGB. Note: Files for testing are also available via the Loraine Lab Google Drive: https://drive.google.com/drive/folders/1MLsVItXNcskfiCAg62GFmxWc1-NR40Tx?usp=drive_link |
| Fix Version/s | 10.2.0 [ 11100 ] |