qbicsoftware / geo-uploader-cli Goto Github PK

Please compile properly so that the MainEntryPoint class does not need to be specified. Why -cp and not -jar? Please fix this

There are a bunch of files that should be deleted from the repo:

-remove immediately all qbic project related tables and infos such as outputQGVIN.xlsx, QJWAB_identifiers,geo-uploader-cliQGVIN.xlsx,geo-uploader-cliQJWAB.xlsx,geo_template.xlsx...

-also remove the files .attach_pid17092, etc from the repo

please remove all excel files with project info from the release zip/tar containers.
Examples in release 0.2.2:
geo-uploader-cliQGVIN.xlsx
geo-uploader-cliQJWAB.xlsx
outputQGVIN

Please also check the other releases.

the colours of the template file are lost. Any idea, why?
see link to the template here:
https://www.ncbi.nlm.nih.gov/geo/info/examples/seq_template_v2.1.xls

the tool also duplicates the samples

Hi Timo.
could you please take a look at this:

heumos@wave ~/Downloads> java -cp geo-uploader-cli.jar life.qbic.cli.main.MainEntryPoint -u afaaj01 -p QMSUI -o geo_output/ -c config.yaml Parse commands openBis connection established Password: Logged in successfully to openBis Normal constructor Found project QMSUI for user afaaj01 null Check the application log in logs/app.log for more details. WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

heumos@wave ~/Downloads> java -cp geo-uploader-cli.jar life.qbic.cli.main.MainEntryPoint -u afaaj01 -p QMHBS -o geo_output/ -c config.yaml Parse commands openBis connection established Password: Logged in successfully to openBis Normal constructor Found project QMHBS for user afaaj01 null Check the application log in logs/app.log for more details. WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Best, Simon

Please revise the readme to make clear that you cannot download the config.yaml, but have to create it based on the info given in the readme.txt file.

We use Maven for dependency management, so there is no need to maintain the classes directory.

This repository is 208 MB.

Maybe there is a good reason why this folder exists, but I cannot think of one.

Pro:Geo-uploader StefanC$ java -jar geo-uploader-cli-1.2-jar-with-dependencies.jar -p QXXXX -o test -c config.yaml
11:34:45.557 [main] DEBUG life.qbic.cli.main.MainEntryPoint - Starting Main tool
11:34:45.715 [main] WARN life.qbic.cli.ToolExecutor - Missing tool descriptor file. Make sure the file tool.properties is located in the classpath
11:34:45.719 [main] WARN life.qbic.cli.ToolExecutor - Missing value in tool.properties file for property 'tool.version', using default value '1.0.0-SNAPSHOT'
11:34:45.720 [main] WARN life.qbic.cli.ToolExecutor - Missing value in tool.properties file for property 'tool.repo.url', using default value 'http://github.com/qbicsoftware'
11:34:45.720 [main] WARN life.qbic.cli.ToolExecutor - Missing value in tool.properties file for property 'tool.name', using default value 'QBiC toolset'
11:34:45.723 [main] DEBUG life.qbic.cli.ToolExecutor - Starting execution
11:34:45.724 [main] INFO life.qbic.cli.main.MainTool - Parse commands
Password:
11:34:53.765 [main] DEBUG life.qbic.core.authentication.PostmanSessionManager - ch.systemsx.cisd.common.exceptions.UserFailureException: No 'password' specified.
11:34:53.765 [main] ERROR life.qbic.core.authentication.PostmanSessionManager - Connection to openBIS failed.
Could not connect to openBis. Check your config file
11:34:53.766 [Thread-1] DEBUG life.qbic.cli.ToolExecutor - Shutting down

As stated in our SOPs and the development guide, repositories should contain encrypted maven credentials to be able to deploy to our Nexus repository.

The tool has still issues with paired end versus single end. For project QUSXG is states it is paired-end but it is actually single-end

Using the latest stable release to retrieve projects with no samples or non-sequencing sample results in a non sensical excel. It would be good to first of all report this in the log and secondly to get an empty but valid excel.

please add -c command to example usage in readme and make clear that when someone is not giving a config file, the example file will be used.
Also make sure to add in the readme that the config file needs to be created.

We propose that in the next release there should be a download of the jar file and a small zip containing the config.yaml plus the template.xlsx file

excel table looks fine, add warning if some of the entries (basically go through the config) could not be filled.

checksum calculation, please indicate how the file should look like (-f option)

Tool does not work for all projects: QMSUI, QMHBS do not work.
Please fix and test for these projects again. If it still fails the tool should give feedback why (see also Issue Excel output).

please make a new release for this tool including and example config.yaml and the geo template into the zip container.