CLI¶
MainExtractor¶
- entry point:
de.unirostock.sems.masymos.main.MainExtractor
| Argument | Type | Required | Default | Description |
|---|---|---|---|---|
-dbPath |
String | true | / | pointsthepath of your database, if no DB exists one will be created |
-directory |
String | annoOnly==false | / | points to the directory containing SBML, CellML, Sed-ML files, also OWL files can be processed |
-type |
String | annoOnly==false | SBML | specifies the expected type of input P2M is working in the intended usage if one wants to index Path2Models files |
-ontology |
String | type==OWL | / | is expected when -type is OWL, used to define the ontology namespace |
-quiet |
boolean | false | false | rewires the stdOut to dev0, faster but no debugging |
-noAnno |
boolean | false | false | creates only the model structures but does not resolve and index model annotations |
-annoOnly |
boolean | false | false | creates only the annotation index |
-fileMode |
boolean | false | false | lst-file, if parameter not given |
- The arguments
-noAnnoand-annoOnlycan not be used together, obviously. - If
-annoOnlyis provided all other parameters except for-dbPathare ignored.
Creating the annotation index is time consuming, it spawns several Threads, uses MiriamWebService to resolve all annotations into URLs and subsequently downloads several hundred webpages for text extraction and index creation.
MainIndex¶
- entry point: de.unirostock.sems.masymos.main.MainIndex
| Argument | Type | Required | Default | Description |
|---|---|---|---|---|
-dbPath |
String | true | / | pointsthepath of your database, if no DB exists one will be created |
-deleteIndex |
bool | false | false | if true, delete all created index structures |
MainAnalyzer¶
- entry point: de.unirostock.sems.masymos.main.MainAnalyzer
The MainAnalyzer allows to play around with some customized analysers, for more information go. This is handy if you want to check how text and queries are processed.