Add missing optional PC 'get' and 'graph' query parameters

[IgorRodchenkov]

PC service /get and /graph queries have two more parameters:

• pattern (accepts an array of SIF pattern/rule names, when format=SIF or TXT; the default mode is to apply all the pre-defined SIF rules but neighbor-of; e.g., /get?...&format=TXT&pattern=in_complex_with&pattern=controls_state_change_of...)
• subpw (default is 'false'; e.g., /graph?kind=neighborhood&subpw=true&...)

The following values are used, e.g., in the PCViz app (pattern names, on the client-side, are case-insensitive; also, one can use either '-' or '_' in them):

• CONTROLS_STATE_CHANGE_OF
• CONTROLS_EXPRESSION_OF
• CATALYSIS_PRECEDES
• CONTROLS_TRANSPORT_OF
• CONTROLS_PHOSPHORYLATION_OF
• IN_COMPLEX_WITH

@d2fong @logmosier @jvwong

[jvwong]

@IgorRodchenkov thanks for the tip. Regarding 'subpw' option: I don't quite understand what this does, even after reading the description. Is there a simple way to describe what this does?

[IgorRodchenkov]

Sorry @jvwong , the description is not clear (may be let's just forget about 'subpw' parameter for now...)

So, 'subpw=false' is the default.
If you '/get' a pathway, such as http://identifiers.org/reactome/R-HSA-1643685 ("Disease"), which contains sub-pathways (e.g., R-HSA-5357609), or when a PC graph query matches sub-pathways, then, by default, the result model (and output SIF) does not include entities that belong to sub-pathways and do not belong to the given parent pathway (or network - in case of a graph query result).

[jvwong]

OK I see what you mean.