…-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

…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

…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

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

…loaded files and creating the data source version files, #TASK-5575, #TASK-5564

…#TASK-5576, #TASK-5564

…uilding, #TASK-5576, #TASK-5564

* Support multiple species
* remove sharding code
* remove 'instal' command
* launch genome_info.pl in the genome_info
* update mouse version
* many other...

* Split GenomeDownloader in Conservation and Repeats

…ASK-5564

…5775, #TASK-5564

On branch TASK-5564
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/GenomeDownloadManager.java

On branch TASK-5564
Changes to be committed:
	modified:   cellbase-core/src/test/java/org/opencb/cellbase/core/config/CellBaseConfigurationTest.java
	modified:   cellbase-core/src/test/resources/configuration.yml
	modified:   cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/ConservationBuilderTest.java
	modified:   cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/RepeatsBuilderTest.java
	modified:   cellbase-lib/src/test/resources/configuration.test.yaml
	new file:   cellbase-lib/src/test/resources/conservation/gerpVersion.json
	new file:   cellbase-lib/src/test/resources/conservation/phastConsVersion.json
	new file:   cellbase-lib/src/test/resources/conservation/phyloPVersion.json
	new file:   cellbase-lib/src/test/resources/regulation/motifFeaturesVersion.json
	new file:   cellbase-lib/src/test/resources/regulation/regulatoryBuildVersion.json
	modified:   cellbase-lib/src/test/resources/repeats/repeats.test.json.gz
	renamed:    cellbase-lib/src/test/resources/repeats/windowMasker.txt.gz -> cellbase-lib/src/test/resources/repeats/windowmaskerSdust.txt.gz
	modified:   pom.xml

On branch TASK-5564
Changes to be committed:
	modified:   .github/workflows/task.yml

…K-5564

  - This parser skips possible errors in the .xlsx file
  - No need to use the script fix-gene-symbol.sh (so it is removed)
  - Update configuration files (by removing comments about the fix-gene-symbol.sh references)
  - Add JUnit test for the MiRTarBase parser

On branch TASK-5564
Changes to be committed:
	deleted:    cellbase-app/app/scripts/mirtarbase/fix-gene-symbol.sh
	modified:   cellbase-core/src/main/resources/configuration.yml
	modified:   cellbase-core/src/test/resources/configuration.yml
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/EnsemblGeneBuilder.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/GeneBuilderIndexer.java
	new file:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/MiRTarBaseIndexer.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/RefSeqGeneBuilder.java
	new file:   cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/GeneBuilderIndexerTest.java
	modified:   cellbase-lib/src/test/resources/configuration.test.yaml