HBPMedical / MIPMap

MIPMap (ex-MIPMapRecuced)

Available functionality

- Translate instance and export to database

[path to jar]/MIPMapReduced.jar [path to mapping task]/mapping_task_simple.xml [path to database config file]/db.properties -db [path to export database config file]/exportdb.properties

- Translate instance and export to csv file

[path to jar]/MIPMapReduced.jar [path to mapping task]/mapping_task_simple.xml [path to database config file]/db.properties -csv [path to export folder]

- Unpivot csv file

-unpivot [path to csv]/inputCsv.csv [path to database config file]/db.properties nameOfNewColumn [path to selected columns file]/selectedColumns.txt {-i(gnore) or -u(npivot} [path to altered columns file]/alteredColumns.txt

Comments

1. If you choose -i the specified columns will be ignored from the unpivot procedure. On the other hand, if you choose -u the columns will be used for the unpivot procedure

2. In the columns.txt the columns must specified line by line

- Change csv delimeter

-csv_delimeter [path to csv]/inputCsv.csv {";" or ":" or tab} {single or double}

Comments

1. You can choose among three options about the input csv current delimeter

   • ";" : If the current csv is separated with semi-colon
   • ":" : If the current csv is separated with colon
   • tab : If the current csv is separated with tabs

2. You can choose among three options about the input csv current quote style

   • single : If the current csv includes single quotes
   • double : If the current csv includes double quotes

- Generate id using columns from source to target table

-generate_id [path to properties file]/file.properties

Properties file commands

1. Specify the source input

   commandSource={csv | db}
   

2. Specify source input path

   sourceInputPath= {[path to csv file]/file.csv | [path to database properties file],[name of the table to extract data]
   

3. Specify the target input

   commandTarget={csv | db}
   

4. Specify target input path

   targetInputPath= {[path to csv file]/file.csv | [path to database properties file],[name of the table to extract data]}
   

5. Names of the target columns

   targetColumns=[col11,col22,col33,generated_id]
   

6. Specify a transformation function to the source columns

   If no transformation function is selected the actual data from the source input are used.

   If any string value lies inside quotes, every tuple in the specific column have this value.

   functionPerColumn=[split(col1,_,0),"constant value",col3]
   

7. Output csv file

   outputFile=[path to csv file]/file.csv
   

Acknowledgements

This project/research received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).