nmdp-bioinformatics / phycus

Service used for curation of Haplotype Frequency
GNU Lesser General Public License v3.0
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Final commit Java client #111

Closed kaeaton closed 3 years ago

kaeaton commented 3 years ago

Just a few notes: 1) I did not have time to finish implementing the Advanced option, which is where you can change the url for the database. To do so in the repository before compiling, look or the variable DEFAULT_DB_URL in client/java/freq-tools/src/main/java/org/dash/freq/utilities/Prefs.java. Prefs.java also contains the necessary setters and getters for the database URL, it's just the popup that isn't completed. 2) There is a problem where something about Swagger overwrites the .gitignore file in client/java/freq-client/.gitignore. It literally deletes the second half of the file, creating a scenario where you can upload a lot of files you aren't intending to. There is such a thing as a .swagger-codegen-ignore file, which I have added the .gitignore file to in multiple locations, but nothing seems to stop it. So if you compile the program, be careful of what you commit afterwards, you may get a lot of files in client/java/freq-client/ that you don't want to add. This has been a problem since I received the project. 3) Tabs exist for both labels and DOI, but as those features are incomplete, I commented them out of client/java/freq-tools/src/main/java/org/dash/freq/gui/Gui.java. 4) client/java/README.md has been updated to include the new commands to open the project. The -g flag is for GUI. The original CLI interface commands are listed in client/java/freq-tools/src/main/java/org/dash/main/Main.java, but they didn't really do anything when I got the project, and I did not have time to implement them.

pbashyal-nmdp commented 3 years ago

When I compile, I'm getting the error:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.3:compile (default-compile) on project freq-tools: Compilation failure
[ERROR]  phycus/client/java/freq-tools/src/main/java/org/dash/freq/gui/uploadTab/licensingMenu/LicenseComboBox.java:[25,28] cannot find symbol
[ERROR]   symbol:   method of(int,java.lang.String,int,java.lang.String,int,java.lang.String,int,java.lang.String,int,java.lang.String,int,java.lang.String,int,java.lang.String)
[ERROR]   location: interface java.util.Map
[ERROR]

Map.of is not available until Java 9. The project is currently setup for Java 7.

I'd suggest moving to Java 11. That's the current LTS version.