…5387

… #TASK-5407, #TASK-5387

…407, #TASK-5387

…K-5407, #TASK-5387

…ASK-5407, #TASK-5387

…-5564

…ASK-5564

…r issues, #TASK-5775, #TASK-5564

…es and taking into account the version from config file, and fix sonnar issues, #TASK-5775, #TASK-5564

…dding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564

… adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564

… file, adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564

…to take into account the version for miRBase and miRTarBase, #TASK-5775, #TASK-5564

…nd HGMD; and fix some sonnar issues, #TASK-5775, #TASK-5564

…-5564

…K-5564

…#TASK-5775, #TASK-5564

…URLProperties changes, #TASK-5775, #TASK-5564

…URLProperties changes, #TASK-5775, #TASK-5564

… Expression Atlas, Gene Disease Annotation, gnomAD Constraints and GO Annotation downloaders, #TASK-5775, #TASK-5564

…5564

… log messages, #TASK-5564

Resolve Conflicts:
	cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java
	cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/DownloadCommandExecutor.java
	cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/LoadCommandExecutor.java
	cellbase-core/src/main/java/org/opencb/cellbase/core/config/DownloadProperties.java
	cellbase-core/src/main/resources/configuration.yml
	cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java
	cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java

and update to the new changes.

…he genome downloader, #TASK-5564

…from the class EtlCommand and improve log messages, #TASK-5564

…ns, #TASK-5564

…-5564

…K-5564

…nd taking them from the configuration file; update JUnit test and improve log messages, #TASK-5564

…and taking them from the version files (i.e., URLs of the DataSource), improve log/exception messages, and fix sonnar issues, #TASK-5564

…le, #TASK-5564

…checks and log messages, #TASK-5564

…llBaseBuilder to be used by other builders, #TASK-5564

… downloader to the protein builder, #TASK-5564

…K-5564

…,...) fails; and improve log messages, #TASK-5775, #TASK-5564

…wnloader to the regulation builder; and improve regulation builder by adding checks, log messages and fixing sonnar issues, #TASK-5776, #TASK-5564

…ology versions will be taken from the OBO files content, #TASK-5775, #TASK-5564

…rom the OBO files content; and improve log messages, #TASK-5775, #TASK-5564

…sion files before creating the ontology builder, #TASK-5576, #TASK-5564

…ding log messages and refactoring code, #TASK-5576, #TASK-5564

…PharmGKB files from the downloader to the PharmGKB builder and adding log messages, #TASK-5775, #TASK-5564

…and move the function to unzip PharmGKB files from the downloader to the builder, #TASK-5776, #TASK-5564

…sonnar issues, #TASK-5775, #TASK-5564

…rom a given data, #TASK-5775, #TASK-5564

… sonnar issues, #TAK-5776, #TASK-5564

…ASK-5564

…g code and fixing sonnar issues, #TASK-5776, #TASK-5564

…dd log messages, #TASK-5775, #TASK-5564

…cks and log messages, #TASK-5776, #TASK-5564

…-5775, #TASK-5564

…, #TASK-6142, #TASK-5564

…ASK-5776, #TASK-5564

…5, #TASK-5564

…5564

…vements and sonnar fixes), #TASK-5776, #TASK-5564

…ASK-5564

Resolve conflicts:
	cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java
	cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java
	cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/LoadCommandExecutor.java

And add exception to PgsDownloadManager.java

…ilder, #TASK-5407, #TASK-5387

…ile to the build step, adding log messages, fixing sonnar issues,... #TASK-5575, #TASK-5564

…ile to the build step, adding checks and log messages, fixing sonnar issues,... #TASK-5576, #TASK-5564

Resolve conflicts:
	cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java
	cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java
	cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/DownloadCommandExecutor.java

…the splice score downloader to create the splice score version files, #TASK-5575, #TASK-5564