Details
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Type:
Improvement
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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
When a user wants to load data without loading a genome first, they can drag and drop a file (such as a .bed) into IGB. What happens behind the scenes is that IGB reads the file and tries to infer the structure of the genome from the file. This tends to work OK, depending on the file, and it is a useful feature.
However, if the user selects File > Open File... they receive a warning <Please select a Genome> and the data files does not get opened. Note: This behavior is the same if the Open File... button is clicked.
The default behavior should be: if a user drags and drops or selects Open File... before selecting a genome version, the data file should be opened within IGB, but a dialog should open with a message informing the user: "A genome sequence has not been selected, some features may be unavailable."
Task:
*Determine how to enable Load File... to open data when no genome is selected.
*Implement a solution.
*When data is loaded without a genome, warn the user "A genome sequence has not been selected, some features may be unavailable."
Attachments
Issue Links
Activity
Removed unused imports and tested the code locally.
Merged to master.
MacOS successful.
Linux testing successful
Issue:- To give a warning message when loading a file without selecting a genome and allow loading of genome sequence data for the FASTA and 2BIT file when file is drag and dropped.
Files changed:-
core/genometry/src/main/resources/genometry.properties
core/genometry/src/main/java/com/affymetrix/genometry/general/DataSet.java
core/igb/src/main/java/com/affymetrix/igb/action/LoadFileAction.java
core/igb/src/main/java/com/affymetrix/igb/view/load/GeneralLoadUtils.java
Testing scenarios:-
1) Drag and drop file in IGB application -
a) If the file is of extension 2bit, bnib, fa, fas, fasta, fna, fsa, mpfa, fa.gz, fas.gz, fasta.gz, fna.gz, fsa.gz or mpfa.gz, it is assumed that the file has
genome sequence data. Once clicked on load sequence button it will load the genome sequence.
b) If the file is of any other extension,
i) If no genome is selected, then once the file is loaded user will get a warning message "A genome sequence has not been selected, some features may be unavailable.". Also on clicking Load Sequence button user will get an error message "A genome sequence has not been selected. Loading sequence data is not possible."
ii) If genome is selected, then no warning message will be displayed and on clicking Load Sequence button, the new file gets loaded on top of the selected genome and there is no error message.
2) Click File -> Open Genome from File... -> select the file from above mentioned extension (as no other file extension will be allowed) --> Click Load Sequence button to load the genome sequence.
Testing results:-
Please check the attached test result for each test scenario.
Code changes:-
https://bitbucket.org/rpatil14/riddhifork-igb/branch/IGBF-1509#diff