Add entity check logging to KB_pattern_writer

[dosumis]

All warnings should be added to log stack in addition to being emitted as STDERR. Currently this only affects entity checks, but log should be generic - allowing for other checks in future.

The point of this is to separate stack traces from more fundamental errors from database loading user facing errors.

[dosumis]

First phase of this is done (see #170). This generates a log on the entity checker - which carries out checks during addition of patterns to the stack. For pattern addition - these pre-addition checks should catch everything (we don't want partial pattern commits), but commit time failures can't be ruled out.

Second phase - add logging to commits. We want this to work uniformly across writer objects.

Overview:

• As usual, every method should return something useful or False
• KB_tools write objects accumulate a stack of cypher statements until .commit() is called.
• KB_tools Writer object commits should return False if any part of the commit stack has failed
• Error messages that indicate failure of a statement in the commit stack are logged (not returned by the commit statement).
• If the error log has any content, then commit returns False, otherwise it returns True. It is the responsibility of the calling script to check for False return and then check the log.
• We need a mechanism to reliably clear the error log between commits. As we are only logging commit-time errors, this can happen at the beginning of a commit. This has the disadvantage that the old error log hangs around until the next commit.
• .get_log => returns log and clears it
• pattern error log is simply a concatenation of edge and node writer error logs.

[dosumis]

CC @matentzn

[dosumis]

#171 Fixes return for pattern writer. More work is needed to standardize across other kb_writer objects, but this has been moved to another ticket
#172