MIABIS converter

MIABIS converter is a tool that aims to facilitate the migration of different formats to MIABIS sample exchange compliant XML. It is sample centered and its based on the [miabis-sample-exchange-format] (https://github.com/MIABIS/miabis-sample-exchange-format).

Additionally the tool is able to index TAB files following a given format into Elasticsearch.

At the moment the tool supports the following commands:

usage: miabis-converter
 -c,--cluster <elastic search cluster>      with -i: elastic search
                                            cluster group. It defaults to
                                            localhost:9300
 -d,--delimiter <column delimiter>          with -t, -i: column delimiter.
                                            It defaults to TAB
 -h,--help                                  print this message
 -i,--index <input file(s)>                 indexes a set of files. If
                                            only one file is supplied it
                                            asumes is a MIABIS TAB file,
                                            else five files must be
                                            supplied (sample, biobank,
                                            saple collection, study,
                                            contact information). The list
                                            of files must be separated by
                                            a space.
 -m,--map <map file>                        with -t, -i: miabis mapping
                                            file.
 -n,--name <index name>                     with -i: index name. Biobank
                                            name is recomended.
 -t,--transform <input files>               transforms a set of files to
                                            MIABIS TAB. Five files must be
                                            supplied (sample, biobank,
                                            saple collection, study,
                                            contact information). The list
                                            of files must be separated by
                                            a space.
 -z,--cname <elastic search cluster name>   with -i: elastic search
                                            cluster name. It defaults to
                                            elasticsearch

Examples

Indexing files

How to index a single MIABIS TAB file:

java -jar miabis-converter-1.0.0-SNAPSHOT.jar -i Miabis.tab

How to index a set of files:

java -jar miabis-converter-1.0.0-SNAPSHOT.jar -i sample.txt biobank.txt sampleCollection.txt study.txt contactInfo.txt -m example.mapping.properties

java -jar miabis-converter-1.0.1-SNAPSHOT.jar -i samples.txt biobanks.txt sample_collections.txt studies.txt contacts.txt -m map.properties -n elixir -c localhost:9301 -z C2

Tranform a set of files into MIABIS TAB:

java -jar miabis-converter-1.0.0-SNAPSHOT.jar -t sample.txt biobank.txt sampleCollection.txt study.txt contactInfo.txt -m example.mapping.properties -d ,