GitLab

3dbeda49095faf438840110e9b6e3fccd06a1aef -- Allowed the usage of schemes other than nmd:// in the JSON files. This allows testing with files generated on a local machine.
f689e878a4775b1c4a06a70e5aabbaf2d42be25c -- return code-specific section (named '^x_.*_section.*') as ArchiveSectionJSON
e24727f9a67462d59c5a580888edbc73ac131aeb -- comment on code-specific x_*_section
be56a3083cf035ea0d7d53946581ee1ac4c9e0b4 -- fix repeating-values issue in archive.py (instead of N actual values, N times the first value was returned when looking up indices)
ae7880e302553768a40fa16cef06b848ca33359d -- moved reading mainfile_uri to archiveiterator
75f571c6c99c5377da46b6f56e276689327dfa6e -- Added pid to mongodb. Fixed tests for db changes. Fixed schema and postprocessor for empty pids and repository download uris.

Removed stdout.flush() at backend. Borken Pipe Error seams to exist when stderr is closed in Python3 not relevant with parsing.

json.dump fails for python3 with Broken Pipe Error for IO buffer due to . Trying to fix it with stdout.flush().

Add test/store to MetaInfoStorage, update table_reader in SmartParser and topology extracter of Pymolfile in MDDataAccess

Add missing natoms definition at failback when heroistic reading of trajectory without topology info

-onOpen now executes the callback associated with key None AFTER all
 sections have been opened and section-bound callbacks are executed
-onClose now executes the callback associated with key None BEFORE all
 sections have been closed and section-bound callbacks are executed

-both the onOpen and onClose dictionaries of the constructor can now
 contain the special key None (not as string) which is invoked as
 callback without any section (section/index arguments are None)

-at present, it's the parser's responsibility to ensure that all open
 sections are closed before raising the exception

compact_sha.sha512("blabla").gid("X")

Changed the ParserInterface class to get the main file in the parse()-function instead of the constructor.