Details
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Type:
Task
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Status: Open (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
Description
Background:
genome.txt is a tab-delimited file IGB reads and uses to populate the Current Genome tab. When a user selects a species and genome version, IGB reads the genome.txt file.
When users select rows in the table, IGB should display the corresponding chromosome/sequence in the main view.
Example genome.txt file: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt
Do the following tests. Report results of each test in a separate comment. Attach files used for testing.
For each test:
- select chromosomes and observe IGB behavior
- view console and report any exceptions
Tests:
- test what happens if a chromosome name contains a space
- test what happens if there is a duplicate line in genome.txt
- test what happens if the same chromosome name is listed twice but with different sizes
- test what happens if there is a trailing space after the length column
- test what happens if a non-ASCII (Unicode) character is used in a chromosome name
Across servers:
- test what happens if the same genome version is available at two different QuickLoad sites but they report different sizes for the same chromosome name
- test what happens if the same genome version is available at two different QuickLoad sites but they report different chromosome names
- test what happens if the same genome version is available at two different QuickLoad sites, the chromsome names and sizes are the same, but the order is different
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Show 5 more links (5 relates to)
Activity
| Description |
____Explanation_____ Tab delimited file with chromosome and length _____Tests_____ Control: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt Create a mod_chromInfo.txt and see if anything is read from there. Naming errors: -Replace tabs with spaces -Reverse name and length -Put an alpha character in the length -use two tabs instead of one -Replace underscore with space -Alternate capitalization -Duplicate a line -Duplicate a line change col1 -Duplicate a line change col2 -Remove a length but keep chrom -Remove a chrom but keep length -Remove a whole line -Sort differently -Add extra column -Add spaces to chrom name -Add unicode char Across servers: -All of above across servers as well. -Create name collision on titles across servers -Create file name collision across servers -Name collision on both columns (Title and file name) but different data |
____Explanation_____ Tab delimited file with chromosome and length _____Tests_____ Control: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt Create a mod_chromInfo.txt and see if anything is read from there. Format errors: -Replace tabs with spaces -Reverse name and length -Put an alpha character in the length -Use two tabs instead of one -Remove a length but keep chrom -Remove a chrom but keep length Data errors: -Duplicate a line (redundant data) -Duplicate a line change col1 (conflicting data) -Duplicate a line change col2 -Add spaces to chrom name -What happens if you have trailing spaces after the length column? -Add unicode char Across servers: -Remove a whole line (Two sites have the same genome version but one genome.txt is missing a line present in the other) -Sort differently (Two sites with differently sorted genome.txt files) -All of above across servers as well. (???) |
| Assignee | Kyle Suttlemyre [ kyle ] |
| Description |
____Explanation_____ Tab delimited file with chromosome and length _____Tests_____ Control: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt Create a mod_chromInfo.txt and see if anything is read from there. Format errors: -Replace tabs with spaces -Reverse name and length -Put an alpha character in the length -Use two tabs instead of one -Remove a length but keep chrom -Remove a chrom but keep length Data errors: -Duplicate a line (redundant data) -Duplicate a line change col1 (conflicting data) -Duplicate a line change col2 -Add spaces to chrom name -What happens if you have trailing spaces after the length column? -Add unicode char Across servers: -Remove a whole line (Two sites have the same genome version but one genome.txt is missing a line present in the other) -Sort differently (Two sites with differently sorted genome.txt files) -All of above across servers as well. (???) |
Background: genome.txt is a tab-delimited file IGB reads and uses to populate the Current Genome tab. When a user selects a species and genome version, IGB reads the genome.txt file. When users select rows in the table, IGB should display the corresponding chromosome/sequence in the main view. Example genome.txt file: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt Do the following tests. Report results of each test in a separate comment. Attach files used for testing. For each test: - select chromosomes and observe IGB behavior - view console and report any exceptions Tests: - test what happens if a chromosome name contains a space - test what happens if there is a duplicate line in contents.txt - test what happens if the same chromosome name is listed twice but with different sizes - test what happens if there is a trailing space after the length column - test what happens if a non-ASCII (Unicode) character is used in a chromosome name Across servers: - test what happens if the same genome version is available at two different QuickLoad sites but they report different sizes for the same chromosome name - test what happens if the same genome version is available at two different QuickLoad sites but they report different chromosome names - test what happens if the same genome version is available at two different QuickLoad sites, the chromsome names and sizes are the same, but the order is different |
| Assignee | Kyle Suttlemyre [ kyle ] |
| Description |
Background: genome.txt is a tab-delimited file IGB reads and uses to populate the Current Genome tab. When a user selects a species and genome version, IGB reads the genome.txt file. When users select rows in the table, IGB should display the corresponding chromosome/sequence in the main view. Example genome.txt file: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt Do the following tests. Report results of each test in a separate comment. Attach files used for testing. For each test: - select chromosomes and observe IGB behavior - view console and report any exceptions Tests: - test what happens if a chromosome name contains a space - test what happens if there is a duplicate line in contents.txt - test what happens if the same chromosome name is listed twice but with different sizes - test what happens if there is a trailing space after the length column - test what happens if a non-ASCII (Unicode) character is used in a chromosome name Across servers: - test what happens if the same genome version is available at two different QuickLoad sites but they report different sizes for the same chromosome name - test what happens if the same genome version is available at two different QuickLoad sites but they report different chromosome names - test what happens if the same genome version is available at two different QuickLoad sites, the chromsome names and sizes are the same, but the order is different |
Background: genome.txt is a tab-delimited file IGB reads and uses to populate the Current Genome tab. When a user selects a species and genome version, IGB reads the genome.txt file. When users select rows in the table, IGB should display the corresponding chromosome/sequence in the main view. Example genome.txt file: http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt Do the following tests. Report results of each test in a separate comment. Attach files used for testing. For each test: - select chromosomes and observe IGB behavior - view console and report any exceptions Tests: - test what happens if a chromosome name contains a space - test what happens if there is a duplicate line in genome.txt - test what happens if the same chromosome name is listed twice but with different sizes - test what happens if there is a trailing space after the length column - test what happens if a non-ASCII (Unicode) character is used in a chromosome name Across servers: - test what happens if the same genome version is available at two different QuickLoad sites but they report different sizes for the same chromosome name - test what happens if the same genome version is available at two different QuickLoad sites but they report different chromosome names - test what happens if the same genome version is available at two different QuickLoad sites, the chromsome names and sizes are the same, but the order is different |
| Attachment | specialChars.txt [ 12362 ] |
| Assignee | Kyle Suttlemyre [ kyle ] | Ann Loraine [ aloraine ] |