Implementation and tests

[artemik]

First pull request.
@mcupak waiting for your review.

[mcupak]

Awesome work @artemik! I really like how well it works when it comes to details, e.g. you can supply beacon IDs as both "-i beacon1,beacon2" and "-i beacon1 -i beacon2". This is a great tool from usability perspective and I'm sure people will be happy to use it.

I stumbled upon the following problems:

• When I run the tests with mvn test, 5 of them fail with the following error:

Results :

Failed tests:   test(com.dnastack.bob.cli.beacon.BeaconForbiddenTest): No such property: TEST_BEACON_AMPLAB for class: com.dnastack.bob.cli.beacon.BeaconForbiddenTest
  test(com.dnastack.bob.cli.organizations.OrganizationsSuccessTest): No such property: TEST_ORGANIZATIONS for class: com.dnastack.bob.cli.organizations.OrganizationsSuccessTest
  test(com.dnastack.bob.cli.response.ResponseForbiddenTest): No such property: TEST_RESPONSE_AMPLAB for class: com.dnastack.bob.cli.response.ResponseForbiddenTest
  test(com.dnastack.bob.cli.responses.ResponsesAllBeaconsSuccessTest): No such property: TEST_RESPONSES for class: com.dnastack.bob.cli.responses.ResponsesAllBeaconsSuccessTest
  test(com.dnastack.bob.cli.responses.ResponsesForbiddenTest): No such property: TEST_RESPONSES for class: com.dnastack.bob.cli.responses.ResponsesForbiddenTest

Tests run: 13, Failures: 5, Errors: 0, Skipped: 0

I also have the following suggestions:

• It would be good to add the operation name to the commands. For example: organizations get instread of organizations. We will support more operations in the future, e.g. organization/beacon creation, deletion, updates etc. In fact, the server already supports them, but they're disabled until proper security is added. Granted, for now only a single operation would be supported, so I completely understand why you chose to not have it there. It's just for future extension. This should be accounted for in the help messages (list supported operations etc.).
• When launching the program without any arguments, which shows the default help message, a non-zero return value should be specified (similarly to other erroneous operations).
• Some outputs are missing a newline character at the end (help messages as well as regular outputs). This is a Unix convention. Not having that messes up the shell prompt after the run. Examples:

mcupak@... $ java -jar target/cli-1.0-SNAPSHOT-jar-with-dependencies.jar beacon -i amplab
{
  "id" : "amplab",
  "name" : "AMPLab - 1000 Genomes Project",
  "url" : null,
  "organization" : "AMPLab, UC Berkeley",
  "description" : null,
  "homePage" : null,
  "email" : null,
  "aggregator" : false,
  "enabled" : false,
  "visible" : false,
  "createdDate" : 1395273600000,
  "supportedReferences" : [ "HG19", "HG18", "HG38" ],
  "aggregatedBeacons" : null
}mcupak@... $ java -jar target/cli-1.0-SNAPSHOT-jar-with-dependencies.jar beacon
Beacon Network CLI Usage:
 [beacon | beacons | organization |     : Use one of these commands. To get
 organizations | response | responses]    help on each command, type -h with
                                          the corresponding command.
 -u (--url) VAL                         : Beacon Network URL (default =
                                          https://beacon-network.org/api/)
Option "-i (--id)" is requiredmcupak@... $

[artemik]

@mcupak

#1 issue related changes:

• fixed tests compilation fail;
• added inner commands for operations (ex: get, get-all);
• made empty arguments execution return fail code (help message is still returned);
• added missing newline character for outputs.

#3 issue related changes:

• rewrote tests: when "it" profile is used in maven, the tests are run against a real Beacon Network server (the URL is provided by a java property beaconNetwork.test.url, defaults to https://beacon-network.org/api/);
• changed test data (where needed) for it to match real data, therefore can be used for both mocked and integration tests now.

[mcupak]

Awesome, thanks!