Tweak help message
Fixup for 30994a91: move format_exception to exceptions module
PTFM-13652: improved prefix bash variable

Summary: Added tests, and code, that implements the improved bash prefix variable. It takes patterns into account, and also the '.gz' suffix.

Test Plan: An additional test app, prefix_patterns, was added to the file_load subdirectory.

Reviewers: klai

Reviewed By: klai

Differential Revision: https://phabricator.dnanexus.com/D148
PTFM-13152 Remove app-specific validations when building applets.

Summary:
Additionally check for existence of applet with same name in
destination before uploading resources when "dx build" not
supplied with "-f" or "-a" flag and add tests for building applets.

Remove do_build_step and do_upload_step from build_and_upload_locally() declaration.

Add lint fixes and minor changes.

Test Plan: ./test_dxclient.py TestDXBuildApp

Reviewers: psung

Reviewed By: psung

Subscribers: psung

Differential Revision: https://phabricator.dnanexus.com/D149
Bash vars bugfix and style improvements
Changelog and version updates for v0.124.0, UA 1.5.5
PTFM-13730: expanding the bash path variable

Summary: Expanding the bash path variable, and uplifting the tests accordingly.

Test Plan: Improved the file_load/vars test.

Reviewers: klai

Reviewed By: klai

Differential Revision: https://phabricator.dnanexus.com/D155
Bump concurrent.futures dependency from v2.1.2 to v2.2.0

Also rewrite the monkey-patch for threadpool executor that
incorporates the fix for http://bugs.python.org/issue16284.
Bump requests dependency from v2.3.0 to v2.4.3
Changelog and version updates for v0.125.0
Fix instability in dx-toolkit file/deepdirs test

Summary:
Adding a wait-for-close flag, when uploading a file. This is part of the dx-upload-all-outputs
script.

Test Plan: Existing tests, especially file/deepdirs.

Reviewers: klai

Reviewed By: klai

Subscribers: bagee

Differential Revision: https://phabricator.dnanexus.com/D160
Mock API debug tools
Java bindings: various environment-handling fixes

* DXHTTPRequest: better error message when no security context set
* DXJob.describe() now makes API call with custom environment if set
* New factory method DXProject.newProjectWithEnvironment to support
  setting custom environment
PTFM-12951 Move EE dependency installation code into dxpy
Java: compound ($and/$or) type queries when finding data objs

Summary:
* Introduce method FindDataObjectsRequestBuilder.withTypes
* Extract function serializeCompoundQuery

Test Plan: Unit tests. All existing and new tests passed.

Reviewers: pnguyen

Reviewed By: pnguyen

Differential Revision: https://phabricator.dnanexus.com/D158
[PTFM-13637] Don't append -lgcc_eh when CC=clang

Summary: * When building jq with clang, omit the -lgcc_eh flag to avoid an error from the compiler.

Test Plan: Performed test builds on an OS X 10.7 builder with gcc and clang, and on Ubuntu 14.04 with gcc.

Reviewers: psung

Reviewed By: psung

Subscribers: akislyuk

Differential Revision: https://phabricator.dnanexus.com/D164
Prevent weird output when code is wrapped in multiple "err_exit"s

Basically, the first err_exit will raise a SystemExit. The second and
subsequent ones should just pass that through unmolested.
Improve keyboard interrupt handling

Summary: Print "^C\n" instead of KeyboardInterrupt

Test Plan: existing tests

Reviewers: psung

Reviewed By: psung

Differential Revision: https://phabricator.dnanexus.com/D168
Preserve original stacktrace; obviates need for print-and-rethrow
PTFM-13536: confusing error by 'dx cp'

Summary: Refactoring of the 'dx cp' command, adding another test case to the test suite.

Test Plan: Additional test case added to the TestDXCp test suite.

Reviewers: klai

Reviewed By: klai

Differential Revision: https://phabricator.dnanexus.com/D169