Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Minor
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:3
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Sprint:Winter 2018 Sprint 3, Spring 2019 Sprint 1
Description
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. The SNP is present in both files, but IGB only finds it in one of the files.
See Dr. Freese for files.
Computer used - Mac. IGB version 8.5.2
Task:
- Determine if you can reproduce the error using files provided by Dr. Freese
- Investigate & report why this error is occurring
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-497 [ 15559 ] |
| Rank | Ranked higher |
| Epic Link | IGBF-497 [ 15559 ] |
| Rank | Ranked higher |
| Description |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. I have only been able to replicate this with the files we used for the outreach event, which were gzipped and tabix indexed. See Nowlan for files. Computer used - Mac. IGB version 8.5.2 |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring * If a fix is obvious & simple, go ahead and do it. |
| Story Points | 1 | |
| Sprint | Winter 2018 Sprint 3 [ 58 ] | |
| Labels | Beginner |
| Description |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring * If a fix is obvious & simple, go ahead and do it. |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. The SNP is present in both files, but IGB only finds it in one of the files. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring * If a fix is obvious & simple, go ahead and do it. |
| Rank | Ranked higher |
| Attachment | mysteryBabyDad.bed.gz [ 14208 ] | |
| Attachment | mysteryBabyMom.bed.gz [ 14209 ] |
| Attachment | mysteryBabyMom.bed.gz [ 14209 ] |
| Attachment | mysteryBabyDad.bed.gz [ 14208 ] |
| Attachment | diseaseDad.bed.gz [ 14219 ] | |
| Attachment | diseaseDad.bed.gz.tbi [ 14220 ] | |
| Attachment | diseaseMom.bed.gz [ 14221 ] | |
| Attachment | diseaseMom.bed.gz.tbi [ 14222 ] |
| Attachment | Screen Shot 2016-02-18 at 5.20.44 PM.png [ 13275 ] |
| Attachment | missingSearch.png [ 14223 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Rank | Ranked higher |
| Sprint | Winter 2018 Sprint 3 [ 58 ] | Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ] |
| Rank | Ranked higher |
| Story Points | 1 | 3 |
| Description |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. The SNP is present in both files, but IGB only finds it in one of the files. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring * If a fix is obvious & simple, go ahead and do it. |
During the High School outreach event users noticed that searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files.
Files are bed detail format. The search is for the SNP id, which is in both the name (4th) and id (13th) columns in the file. The SNP is present in both files, but IGB only finds it in one of the files. See Dr. Freese for files. Computer used - Mac. IGB version 8.5.2 Task: * Determine if you can reproduce the error using files provided by Dr. Freese * Investigate & report why this error is occurring |
| Attachment | GFF3_example_1_EDITED.gff3 [ 14247 ] |
| Attachment | AfterFix.jpg [ 14252 ] |
Code Changed (Branch) : https://bitbucket.org/svallapu/charan_igb/branch/IGBF-1096-New
Issue: Searching two BED files for a single SNP ID in the advanced search tab would return a hit for only one of the files. Two files contain the similar data.
Before: Search mechanism is using HashSet to store the search results. HashSet collection will eliminate the duplicate objects. Hence it gives single output for the two similar files.
Solution: Advanced Search should return two files when we search for the SNP ID. This SNP ID is present in both the files. Changed the search mechanism to use ArrayList instead of HashSet to get the results. Lot of files are changed because changed classes are extended/ implemented by many other classes.
Tracking the Advanced Search Mechanism: (In all the files, search the methods with ArrayList input variable)
-->SearchModeIDOrProps.java (method: findLocalSyms, call: SearchUtils.findLocalSyms)
-->SearchUtils.java (method: findLocalSyms, call: genomeVersion.SearchProperties) (Set is changed to List)
-->GenomeVersion.java(method: searchProperties, call: seq.searchProperties)
-->Bioseq.java(method: searchProperties, call : getAnnotation
.searchProperties)
-->RootSeqSymmetry.java (method: searchProperties)
-->TypeContainerAnnot.java(method: searchProperties, implemented search using ArrayList)
Testing Steps:
1. Open IGB
2. Download diseaseMom.bed.gz, diseaseDad.bed.gz
3. Unzip them
4. Drag and drop them to IGB
5. Change from manual to genome for both the files.
6. Go to AdvancedSearch and search for "rs1122608" keyword.
7. It should give results from both the files instead of one.
TestResults:
Please find in the attachments.(AfterFix.jpg)
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Tested, the fix has worked.
Dr. [~aloraine], can you please guide if we should modify the existing methods to use ArrayList instead of using HashSets, or add new methods, keeping the original ones as they are, as done by Sai Charan Reddy Vallapureddy on his fork -https://bitbucket.org/svallapu/charan_igb/branch/IGBF-1096-New ?
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
Existing search methods might be used by some other different parts of code. I don't want to disturb other functionalities. That is the reason, I have created new methods for advanced search.
A lot of files have been edited on this branch. This looks like a major re-factoring of the searching functionality in IGB. This new code may be superior and we may be able to safely remove the old code. If it is feasible, I would prefer to remove the old code so that we don't leave two parallel systems in place for future developers to wonder about!
I'm not sure what the next step would be.
I would like to get a code walk-through showing the path of execution.
Before that, everyone needs to know how and when keyword (property-based) searching can happen in the user interface.
Here is documentation from the User's Guide:
https://wiki.transvar.org/display/igbman/Advanced+Search
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Resolution | Done [ 10000 ] | |
| Status | Reviewing [ 10301 ] | Closed [ 6 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Workflow | Loraine Lab Workflow [ 16980 ] | Fall 2019 Workflow Update [ 19764 ] |
| Comment | [ We will review current architecture & discuss re-factoring, using this branch as an extremely useful proof-of-concept and guide. ] |
For next step:
- squash all changes into one commit
- rebase onto the latest master branch, resolving conflicts as needed
- post a link to the new branch here
| Workflow | Fall 2019 Workflow Update [ 19764 ] | Revised Fall 2019 Workflow Update [ 21883 ] |
| Labels | Beginner | Advanced |
The rebased branch code can be found at:
https://bitbucket.org/pkulka10/igb_prutha/src/IGBF-2032/
Test Results.