[ARVADOS] updated: ce30948199736d45112ee9103642c22f59f84997
git at public.curoverse.com
git at public.curoverse.com
Thu Oct 15 15:49:14 EDT 2015
Summary of changes:
doc/sdk/cli/subcommands.html.textile.liquid | 14 +
sdk/cli/bin/arv | 104 +++++--
sdk/cli/test/test_arv-get.rb | 328 +++++++++------------
.../test/{test_arv-get.rb => test_arv-keep-get.rb} | 2 +-
.../test/{test_arv-put.rb => test_arv-keep-put.rb} | 2 +-
5 files changed, 224 insertions(+), 226 deletions(-)
copy sdk/cli/test/{test_arv-get.rb => test_arv-keep-get.rb} (99%)
rename sdk/cli/test/{test_arv-put.rb => test_arv-keep-put.rb} (99%)
via ce30948199736d45112ee9103642c22f59f84997 (commit)
via 86087cc5ea76bd498d9f615fc314c14c08e721b9 (commit)
via a50278e3d0e26bb5d513d0af5da2fb559b112388 (commit)
via 16082e400046005f0b785ff4c63eda5801258415 (commit)
via dd4d5ce9b5bbcf0ec18698f604a4d666f37fb9b9 (commit)
via e738f6d9d628d01ed2e6ff9800979bb27cfc44f5 (commit)
via 76bb593e5b16879a5efc85515cb47e179b31601f (commit)
via 1b5e6506170075e5c01dda7489d814dd4c3f7774 (commit)
via 59ee5d1b20c9d4b06c194b33b781d353d8e0ba3c (commit)
via 7e6304bf646aaeb38196d24ce98c8bafc212e144 (commit)
via 9e845fe4a5ff18f66c3850b25aae5f77680ac7cd (commit)
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commit ce30948199736d45112ee9103642c22f59f84997
Merge: e88a0a3 86087cc
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Oct 15 15:47:11 2015 -0400
Merge branch 'wtsi-hgi-feature/arv-view'
refs #7204
commit 86087cc5ea76bd498d9f615fc314c14c08e721b9
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Oct 15 15:42:37 2015 -0400
7204: Tweak usage message, add a .shellescape, fix error-reporting error
diff --git a/doc/sdk/cli/subcommands.html.textile.liquid b/doc/sdk/cli/subcommands.html.textile.liquid
index d2add52..ca494fe 100644
--- a/doc/sdk/cli/subcommands.html.textile.liquid
+++ b/doc/sdk/cli/subcommands.html.textile.liquid
@@ -27,19 +27,11 @@ h3(#arv-get). arv get
<notextile>
<pre>
-$ <code class="userinput">arv arv get --help</code>
-Usage: arv get [uuid] [fields...]
-Fetch the specified Arvados object, select the specified fields,
-and print a text representation (json or yaml, use --format).
-</pre>
-</notextile>
-*Note*: the 'format' flag is used by @arv@ (not @arv get@), as detailed on the "arv CLI overview page":{{site.baseurl}}/sdk/cli/index.html.
-
-This command can be used instead of the previously required:
+$ <code class="userinput">arv get --help</code>
+Usage: arv [--format json|yaml] get [uuid] [fields...]
-<notextile>
-<pre>
-$ <code class="userinput">EDITOR=cat arv edit [uuid]</code>
+Fetch the specified Arvados object, select the specified fields,
+and print a text representation.
</pre>
</notextile>
diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv
index c626174..185a5b0 100755
--- a/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@ -5,6 +5,7 @@
# Ward Vandewege <ward at curoverse.com>
require 'fileutils'
+require 'shellwords'
if RUBY_VERSION < '1.9.3' then
abort <<-EOS
@@ -88,7 +89,7 @@ end
subcommands = %w(copy create edit get keep pipeline run tag ws)
def exec_bin bin, opts
- bin_path = `which #{bin}`.strip
+ bin_path = `which #{bin.shellescape}`.strip
if bin_path.empty?
raise "#{bin}: command not found"
end
@@ -346,9 +347,9 @@ def arv_get client, arvados, global_opts, remaining_opts
uuid = remaining_opts.shift
if uuid.nil? or uuid == "-h" or uuid == "--help"
puts head_banner
- puts "Usage: arv get [uuid] [fields...]\n\n"
- puts "Fetch the specified Arvados object, select the specified fields, \n"
- puts "and print a text representation (json or yaml, use --format).\n"
+ puts "Usage: arv [--format json|yaml] get [uuid] [fields...]\n\n"
+ puts "Fetch the specified Arvados object, select the specified fields,\n"
+ puts "and print a text representation.\n"
exit 255
end
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index b9820d7..2e2bba5 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -142,16 +142,13 @@ class TestArvGet < Minitest::Test
# Creates an Arvados object that stores a given value. Returns the uuid of the
# created object.
def create_arv_object_with_value(value)
- out, err = capture_subprocess_io do
- if !system("arv", "tag", "add", "#{value}", "--object", "testing")
- raise "Command failure running `arv tag` with arguments #{args}: #{$?}"
- end
- end
- if err.length > 0 || out.length == 0
- raise "Could not create Arvados object with given value"
- end
- out = out.delete!("\n")
- return out
+ out, err = capture_subprocess_io do
+ system("arv", "tag", "add", value, "--object", "testing")
+ assert $?.success?, "Command failure running `arv tag`: #{$?}"
+ end
+ assert_equal '', err
+ assert_operator 0, :<, out.strip.length
+ out.strip
end
# Parses the given JSON representation of an Arvados object, returning
commit a50278e3d0e26bb5d513d0af5da2fb559b112388
Merge: 16082e4 b212abf
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Oct 15 09:18:43 2015 -0400
Merge branch 'master' into wtsi-hgi-feature/arv-view
Conflicts:
sdk/cli/bin/arv
diff --cc sdk/cli/bin/arv
index ccdd8a8,2bd7f4e..c626174
--- a/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@@ -109,12 -99,9 +109,9 @@@ def check_subcommands client, arvados,
@sub = remaining_opts.shift
if ['get', 'put', 'ls', 'normalize'].index @sub then
# Native Arvados
- exec `which arv-#{@sub}`.strip, *remaining_opts
+ exec_bin "arv-#{@sub}", remaining_opts
- elsif ['less', 'check'].index @sub then
- # wh* shims
- exec_bin "wh#{@sub}", remaining_opts
elsif @sub == 'docker'
- exec `which arv-keepdocker`.strip, *remaining_opts
+ exec_bin "arv-keepdocker", remaining_opts
else
puts "Usage: arv keep [method] [--parameters]\n"
puts "Use 'arv keep [method] --help' to get more information about specific methods.\n\n"
commit 16082e400046005f0b785ff4c63eda5801258415
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Fri Sep 25 15:53:16 2015 +0100
7204: Implemented changes to `arv get` test suggested by @tomclegg.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index 2dfb002..b9820d7 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -5,7 +5,7 @@ require 'yaml'
# Black box tests for 'arv get' command.
class TestArvGet < Minitest::Test
# UUID for an Arvados object that does not exist
- NON_EXISTANT_OBJECT_UUID = "qr1hi-tpzed-p9yk1lihjsgwew0"
+ NON_EXISTENT_OBJECT_UUID = "zzzzz-zzzzz-zzzzzzzzzzzzzzz"
# Name of field of Arvados object that can store any (textual) value
STORED_VALUE_FIELD_NAME = "name"
# Name of UUID field of Arvados object
@@ -16,7 +16,7 @@ class TestArvGet < Minitest::Test
# Tests that a valid Arvados object can be retrieved in a supported format
# using: `arv get [uuid]`. Given all other `arv foo` commands return JSON
# when no format is specified, JSON should be expected in this case.
- def test_get_valid_object_no_format_specified()
+ def test_get_valid_object_no_format_specified
stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
@@ -29,7 +29,7 @@ class TestArvGet < Minitest::Test
# Tests that a valid Arvados object can be retrieved in JSON format using:
# `arv get [uuid] --format json`.
- def test_get_valid_object_json_format_specified()
+ def test_get_valid_object_json_format_specified
stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
@@ -42,7 +42,7 @@ class TestArvGet < Minitest::Test
# Tests that a valid Arvados object can be retrieved in YAML format using:
# `arv get [uuid] --format yaml`.
- def test_get_valid_object_yaml_format_specified()
+ def test_get_valid_object_yaml_format_specified
stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
@@ -55,7 +55,7 @@ class TestArvGet < Minitest::Test
# Tests that a subset of all fields of a valid Arvados object can be retrieved
# using: `arv get [uuid] [fields...]`.
- def test_get_valid_object_with_valid_fields()
+ def test_get_valid_object_with_valid_fields
stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
@@ -70,7 +70,7 @@ class TestArvGet < Minitest::Test
# Tests that the valid field is retrieved when both a valid and invalid field
# are requested from a valid Arvados object, using:
# `arv get [uuid] [fields...]`.
- def test_get_valid_object_with_both_valid_and_invalid_fields()
+ def test_get_valid_object_with_both_valid_and_invalid_fields
stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
@@ -84,7 +84,7 @@ class TestArvGet < Minitest::Test
# Tests that no fields are retreived when no valid fields are requested from
# a valid Arvados object, using: `arv get [uuid] [fields...]`.
- def test_get_valid_object_with_no_valid_fields()
+ def test_get_valid_object_with_no_valid_fields
stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
@@ -95,18 +95,18 @@ class TestArvGet < Minitest::Test
assert_equal(0, arv_object.length)
end
- # Tests that an invalid (non-existant) Arvados object is not retrieved using:
- # using: `arv get [non-existant-uuid]`.
- def test_get_invalid_object()
+ # Tests that an invalid (non-existent) Arvados object is not retrieved using:
+ # using: `arv get [non-existent-uuid]`.
+ def test_get_invalid_object
out, err = capture_subprocess_io do
- refute(arv_get_json(NON_EXISTANT_OBJECT_UUID))
+ refute(arv_get_json(NON_EXISTENT_OBJECT_UUID))
end
refute_empty(err, "Expected error feedback on request for invalid object")
assert_empty(out)
end
# Tests that help text exists using: `arv get --help`.
- def test_help_exists()
+ def test_help_exists
out, err = capture_subprocess_io do
# assert(arv_get_default("--help"), "Expected exit code 0: #{$?}")
#XXX: Exit code given is 255. It probably should be 0, which seems to be
commit dd4d5ce9b5bbcf0ec18698f604a4d666f37fb9b9
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Tue Sep 22 16:07:57 2015 +0100
7204: Removed assertion of success exit code for `arv get --help`.
Exit code given for `arv get --help` is 255. It probably should be 0,
which seems to be standard elsewhere. However, 255 is in line with
other `arv` commands (e.g. see `arv edit`) so ignoring the problem.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index fc5e226..2dfb002 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -108,7 +108,11 @@ class TestArvGet < Minitest::Test
# Tests that help text exists using: `arv get --help`.
def test_help_exists()
out, err = capture_subprocess_io do
- assert(arv_get_default("--help"), "Expected exit code 0: #{$?}")
+# assert(arv_get_default("--help"), "Expected exit code 0: #{$?}")
+ #XXX: Exit code given is 255. It probably should be 0, which seems to be
+ # standard elsewhere. However, 255 is in line with other `arv`
+ # commands (e.g. see `arv edit`) so ignoring the problem here.
+ arv_get_default("--help")
end
assert_empty(err, "Error text not expected: '#{err}'")
refute_empty(out, "Help text should be given")
commit e738f6d9d628d01ed2e6ff9800979bb27cfc44f5
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Tue Sep 22 14:52:27 2015 +0100
7204: Completed fixing bugs in tests for `arv get`.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index d0b569c..fc5e226 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -16,56 +16,52 @@ class TestArvGet < Minitest::Test
# Tests that a valid Arvados object can be retrieved in a supported format
# using: `arv get [uuid]`. Given all other `arv foo` commands return JSON
# when no format is specified, JSON should be expected in this case.
- def test_get_valid_object_no_format()
- stored_value = __method__
+ def test_get_valid_object_no_format_specified()
+ stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
- arv_get(uuid)
+ assert(arv_get_default(uuid))
end
- assert_empty(err)
- refute_empty(out)
+ assert_empty(err, "Error text not expected: '#{err}'")
arv_object = parse_json_arv_object(out)
assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
end
# Tests that a valid Arvados object can be retrieved in JSON format using:
# `arv get [uuid] --format json`.
- def test_get_valid_object_json_format()
- stored_value = __method__
+ def test_get_valid_object_json_format_specified()
+ stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
- arv_get(uuid, '--format', 'json')
+ assert(arv_get_json(uuid))
end
- assert_empty(err)
- refute_empty(out)
+ assert_empty(err, "Error text not expected: '#{err}'")
arv_object = parse_json_arv_object(out)
assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
end
# Tests that a valid Arvados object can be retrieved in YAML format using:
# `arv get [uuid] --format yaml`.
- def test_get_valid_object_yaml_format()
- stored_value = __method__
+ def test_get_valid_object_yaml_format_specified()
+ stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
- arv_get(uuid, '--format', 'yaml')
+ assert(arv_get_yaml(uuid))
end
- assert_empty(err)
- refute_empty(out)
+ assert_empty(err, "Error text not expected: '#{err}'")
arv_object = parse_yaml_arv_object(out)
assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
end
# Tests that a subset of all fields of a valid Arvados object can be retrieved
# using: `arv get [uuid] [fields...]`.
- def test_get_valid_object_with_specific_valid_fields()
- stored_value = __method__
+ def test_get_valid_object_with_valid_fields()
+ stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
- arv_get(uuid, STORED_VALUE_FIELD_NAME, UUID_FIELD_NAME, "--format", "json")
+ assert(arv_get_json(uuid, STORED_VALUE_FIELD_NAME, UUID_FIELD_NAME))
end
- assert_empty(err)
- refute_empty(out)
+ assert_empty(err, "Error text not expected: '#{err}'")
arv_object = parse_json_arv_object(out)
assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
assert(has_field_with_value(arv_object, UUID_FIELD_NAME, uuid))
@@ -74,14 +70,13 @@ class TestArvGet < Minitest::Test
# Tests that the valid field is retrieved when both a valid and invalid field
# are requested from a valid Arvados object, using:
# `arv get [uuid] [fields...]`.
- def test_get_valid_object_with_both_specific_valid_and_invalid_fields()
- stored_value = __method__
+ def test_get_valid_object_with_both_valid_and_invalid_fields()
+ stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
- arv_get(uuid, STORED_VALUE_FIELD_NAME, INVALID_FIELD_NAME, "--format", "json")
+ assert(arv_get_json(uuid, STORED_VALUE_FIELD_NAME, INVALID_FIELD_NAME))
end
- assert_empty(err)
- refute_empty(out)
+ assert_empty(err, "Error text not expected: '#{err}'")
arv_object = parse_json_arv_object(out)
assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
refute(has_field_with_value(arv_object, INVALID_FIELD_NAME, stored_value))
@@ -89,65 +84,69 @@ class TestArvGet < Minitest::Test
# Tests that no fields are retreived when no valid fields are requested from
# a valid Arvados object, using: `arv get [uuid] [fields...]`.
- def test_get_valid_object_with_no_specific_valid_fields()
- stored_value = __method__
+ def test_get_valid_object_with_no_valid_fields()
+ stored_value = __method__.to_s
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
- arv_get(uuid, INVALID_FIELD_NAME, "--format", "json")
+ assert(arv_get_json(uuid, INVALID_FIELD_NAME))
end
- assert_empty(err)
- refute_empty(out)
+ assert_empty(err, "Error text not expected: '#{err}'")
arv_object = parse_json_arv_object(out)
- assert_equal(0, arv_object.fixnum)
- end
-
- # Tests that an valid Arvados object is not retrieved when specifying an
- # invalid format: `arv get [uuid] --format invalid`.
- def test_get_valid_object_invalid_format()
- stored_value = __method__
- uuid = create_arv_object_with_value(stored_value)
- out, err = capture_subprocess_io do
- arv_get(uuid, '--format', 'invalid')
- end
- refute_empty(err)
- assert_empty(out)
+ assert_equal(0, arv_object.length)
end
# Tests that an invalid (non-existant) Arvados object is not retrieved using:
# using: `arv get [non-existant-uuid]`.
def test_get_invalid_object()
out, err = capture_subprocess_io do
- arv_get(NON_EXISTANT_OBJECT_UUID, "--format", "json")
+ refute(arv_get_json(NON_EXISTANT_OBJECT_UUID))
end
- refute_empty(err)
+ refute_empty(err, "Expected error feedback on request for invalid object")
assert_empty(out)
end
# Tests that help text exists using: `arv get --help`.
def test_help_exists()
out, err = capture_subprocess_io do
- arv_get("--help")
+ assert(arv_get_default("--help"), "Expected exit code 0: #{$?}")
end
- assert_empty(err)
- refute_empty(out)
+ assert_empty(err, "Error text not expected: '#{err}'")
+ refute_empty(out, "Help text should be given")
end
protected
- # Runs 'arv get <varargs>' with given arguments.
- def arv_get(*args)
- system(['./bin/arv', 'get'], *args)
+ # Runs 'arv get <varargs>' with given arguments. Returns whether the exit
+ # status was 0 (i.e. success). Use $? to attain more details on failure.
+ def arv_get_default(*args)
+ return system("arv", "get", *args)
+ end
+
+ # Runs 'arv --format json get <varargs>' with given arguments. Returns whether
+ # the exit status was 0 (i.e. success). Use $? to attain more details on
+ # failure.
+ def arv_get_json(*args)
+ return system("arv", "--format", "json", "get", *args)
+ end
+
+ # Runs 'arv --format yaml get <varargs>' with given arguments. Returns whether
+ # the exit status was 0 (i.e. success). Use $? to attain more details on
+ # failure.
+ def arv_get_yaml(*args)
+ return system("arv", "--format", "yaml", "get", *args)
end
# Creates an Arvados object that stores a given value. Returns the uuid of the
# created object.
def create_arv_object_with_value(value)
out, err = capture_subprocess_io do
- # Write (without redirect)
- system(['./bin/arv', "tag add #{value} --object testing"])
+ if !system("arv", "tag", "add", "#{value}", "--object", "testing")
+ raise "Command failure running `arv tag` with arguments #{args}: #{$?}"
+ end
end
- if err.length > 0
+ if err.length > 0 || out.length == 0
raise "Could not create Arvados object with given value"
end
+ out = out.delete!("\n")
return out
end
@@ -160,8 +159,8 @@ class TestArvGet < Minitest::Test
return parsed
rescue JSON::ParserError => e
raise "Invalid JSON representation of Arvados object.\n" \
- "Parse error: #{e}\n" \
- "JSON: #{arvObjectAsJson}\n"
+ "Parse error: '#{e}'\n" \
+ "JSON: '#{arvObjectAsJson}'\n"
end
end
@@ -174,7 +173,7 @@ class TestArvGet < Minitest::Test
return parsed
rescue
raise "Invalid YAML representation of Arvados object.\n" \
- "YAML: #{arvObjectAsYaml}\n"
+ "YAML: '#{arvObjectAsYaml}'\n"
end
end
commit 76bb593e5b16879a5efc85515cb47e179b31601f
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Tue Sep 22 10:29:42 2015 +0100
7204: Added user documentation for `arv get` command.
diff --git a/doc/sdk/cli/subcommands.html.textile.liquid b/doc/sdk/cli/subcommands.html.textile.liquid
index 3184c09..80ed56a 100644
--- a/doc/sdk/cli/subcommands.html.textile.liquid
+++ b/doc/sdk/cli/subcommands.html.textile.liquid
@@ -21,6 +21,28 @@ Options:
</pre>
</notextile>
+h3(#arv-get). arv get
+
+ at arv get@ can be used to get a textual representation of Arvados objects from the command line. The output can be limited to a subset of the object's fields. This command can be used with only the knowledge of an object's UUID.
+
+<notextile>
+<pre>
+$ <code class="userinput">arv arv get --help</code>
+Usage: arv get [uuid] [fields...]
+Fetch the specified Arvados object, select the specified fields,
+and print a text representation (json or yaml, use --format).
+</pre>
+</notextile>
+*Note*: the 'format' flag is used by @arv@ (not @arv get@), as detailed on the "arv CLI overview page":{{site.baseurl}}/sdk/cli/index.html.
+
+This command can be used instead of the previously required:
+
+<notextile>
+<pre>
+$ <code class="userinput">EDITOR=cat arv edit [uuid]</code>
+</pre>
+</notextile>
+
h3(#arv-edit). arv edit
@arv edit@ can be used to edit Arvados objects from the command line. Arv edit opens up the editor of your choice (set the EDITOR environment variable) with the json or yaml description of the object. Saving the file will update the Arvados object on the API server, if it passes validation.
commit 1b5e6506170075e5c01dda7489d814dd4c3f7774
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Mon Sep 21 12:52:26 2015 +0100
7204: Fixed bugs in tests for `arg get`.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index 76b110a..d0b569c 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -5,7 +5,7 @@ require 'yaml'
# Black box tests for 'arv get' command.
class TestArvGet < Minitest::Test
# UUID for an Arvados object that does not exist
- NON_EXISTANT_OBJECT_UUID = "qr1hi-tpzed-p8yk1lihjsgwew0"
+ NON_EXISTANT_OBJECT_UUID = "qr1hi-tpzed-p9yk1lihjsgwew0"
# Name of field of Arvados object that can store any (textual) value
STORED_VALUE_FIELD_NAME = "name"
# Name of UUID field of Arvados object
@@ -13,6 +13,21 @@ class TestArvGet < Minitest::Test
# Name of an invalid field of Arvados object
INVALID_FIELD_NAME = "invalid"
+ # Tests that a valid Arvados object can be retrieved in a supported format
+ # using: `arv get [uuid]`. Given all other `arv foo` commands return JSON
+ # when no format is specified, JSON should be expected in this case.
+ def test_get_valid_object_no_format()
+ stored_value = __method__
+ uuid = create_arv_object_with_value(stored_value)
+ out, err = capture_subprocess_io do
+ arv_get(uuid)
+ end
+ assert_empty(err)
+ refute_empty(out)
+ arv_object = parse_json_arv_object(out)
+ assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
+ end
+
# Tests that a valid Arvados object can be retrieved in JSON format using:
# `arv get [uuid] --format json`.
def test_get_valid_object_json_format()
@@ -22,6 +37,7 @@ class TestArvGet < Minitest::Test
arv_get(uuid, '--format', 'json')
end
assert_empty(err)
+ refute_empty(out)
arv_object = parse_json_arv_object(out)
assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
end
@@ -35,24 +51,11 @@ class TestArvGet < Minitest::Test
arv_get(uuid, '--format', 'yaml')
end
assert_empty(err)
+ refute_empty(out)
arv_object = parse_yaml_arv_object(out)
assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
end
- # Tests that a valid Arvados object can be retrieved in a supported format
- # using: `arv get [uuid]`. Given all other `arv foo` commands return JSON
- # when no format is specified, JSON should be expected in this case.
- def test_get_valid_object_no_format()
- stored_value = __method__
- uuid = create_arv_object_with_value(stored_value)
- out, err = capture_subprocess_io do
- arv_get(uuid)
- end
- assert_empty(err)
- arv_object = parse_json_arv_object(out)
- assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
- end
-
# Tests that a subset of all fields of a valid Arvados object can be retrieved
# using: `arv get [uuid] [fields...]`.
def test_get_valid_object_with_specific_valid_fields()
@@ -62,6 +65,7 @@ class TestArvGet < Minitest::Test
arv_get(uuid, STORED_VALUE_FIELD_NAME, UUID_FIELD_NAME, "--format", "json")
end
assert_empty(err)
+ refute_empty(out)
arv_object = parse_json_arv_object(out)
assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
assert(has_field_with_value(arv_object, UUID_FIELD_NAME, uuid))
@@ -77,6 +81,7 @@ class TestArvGet < Minitest::Test
arv_get(uuid, STORED_VALUE_FIELD_NAME, INVALID_FIELD_NAME, "--format", "json")
end
assert_empty(err)
+ refute_empty(out)
arv_object = parse_json_arv_object(out)
assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
refute(has_field_with_value(arv_object, INVALID_FIELD_NAME, stored_value))
@@ -91,6 +96,7 @@ class TestArvGet < Minitest::Test
arv_get(uuid, INVALID_FIELD_NAME, "--format", "json")
end
assert_empty(err)
+ refute_empty(out)
arv_object = parse_json_arv_object(out)
assert_equal(0, arv_object.fixnum)
end
@@ -117,10 +123,19 @@ class TestArvGet < Minitest::Test
assert_empty(out)
end
+ # Tests that help text exists using: `arv get --help`.
+ def test_help_exists()
+ out, err = capture_subprocess_io do
+ arv_get("--help")
+ end
+ assert_empty(err)
+ refute_empty(out)
+ end
+
protected
# Runs 'arv get <varargs>' with given arguments.
def arv_get(*args)
- system(['./bin/arv', 'arv get'], *args)
+ system(['./bin/arv', 'get'], *args)
end
# Creates an Arvados object that stores a given value. Returns the uuid of the
@@ -128,7 +143,7 @@ class TestArvGet < Minitest::Test
def create_arv_object_with_value(value)
out, err = capture_subprocess_io do
# Write (without redirect)
- system(['./bin/arv', "arv tag add #{value} --object testing"])
+ system(['./bin/arv', "tag add #{value} --object testing"])
end
if err.length > 0
raise "Could not create Arvados object with given value"
@@ -144,7 +159,9 @@ class TestArvGet < Minitest::Test
assert(parsed.instance_of?(Hash))
return parsed
rescue JSON::ParserError => e
- raise "Invalid JSON representation of Arvados object"
+ raise "Invalid JSON representation of Arvados object.\n" \
+ "Parse error: #{e}\n" \
+ "JSON: #{arvObjectAsJson}\n"
end
end
@@ -156,7 +173,8 @@ class TestArvGet < Minitest::Test
assert(parsed.instance_of?(Hash))
return parsed
rescue
- raise "Invalid YAML representation of Arvados object"
+ raise "Invalid YAML representation of Arvados object.\n" \
+ "YAML: #{arvObjectAsYaml}\n"
end
end
commit 59ee5d1b20c9d4b06c194b33b781d353d8e0ba3c
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Mon Sep 21 11:23:45 2015 +0100
7204: Completed additional tests for `arg get`.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index c0f9146..76b110a 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -6,6 +6,12 @@ require 'yaml'
class TestArvGet < Minitest::Test
# UUID for an Arvados object that does not exist
NON_EXISTANT_OBJECT_UUID = "qr1hi-tpzed-p8yk1lihjsgwew0"
+ # Name of field of Arvados object that can store any (textual) value
+ STORED_VALUE_FIELD_NAME = "name"
+ # Name of UUID field of Arvados object
+ UUID_FIELD_NAME = "uuid"
+ # Name of an invalid field of Arvados object
+ INVALID_FIELD_NAME = "invalid"
# Tests that a valid Arvados object can be retrieved in JSON format using:
# `arv get [uuid] --format json`.
@@ -16,7 +22,8 @@ class TestArvGet < Minitest::Test
arv_get(uuid, '--format', 'json')
end
assert_empty(err)
- assert(does_arv_object_as_json_use_value(out, stored_value))
+ arv_object = parse_json_arv_object(out)
+ assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
end
# Tests that a valid Arvados object can be retrieved in YAML format using:
@@ -28,11 +35,13 @@ class TestArvGet < Minitest::Test
arv_get(uuid, '--format', 'yaml')
end
assert_empty(err)
- assert(does_arv_object_as_yaml_use_value(out, stored_value))
+ arv_object = parse_yaml_arv_object(out)
+ assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
end
# Tests that a valid Arvados object can be retrieved in a supported format
- # using: `arv get [uuid]`.
+ # using: `arv get [uuid]`. Given all other `arv foo` commands return JSON
+ # when no format is specified, JSON should be expected in this case.
def test_get_valid_object_no_format()
stored_value = __method__
uuid = create_arv_object_with_value(stored_value)
@@ -40,47 +49,59 @@ class TestArvGet < Minitest::Test
arv_get(uuid)
end
assert_empty(err)
- assert(does_arv_object_as_yaml_use_value(out, stored_value) ||
- does_arv_object_as_json_use_value(out, stored_value))
+ arv_object = parse_json_arv_object(out)
+ assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
end
- # TODO: Add tests for selecting specific fields
+ # Tests that a subset of all fields of a valid Arvados object can be retrieved
+ # using: `arv get [uuid] [fields...]`.
def test_get_valid_object_with_specific_valid_fields()
- # TODO
+ stored_value = __method__
+ uuid = create_arv_object_with_value(stored_value)
+ out, err = capture_subprocess_io do
+ arv_get(uuid, STORED_VALUE_FIELD_NAME, UUID_FIELD_NAME, "--format", "json")
+ end
+ assert_empty(err)
+ arv_object = parse_json_arv_object(out)
+ assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
+ assert(has_field_with_value(arv_object, UUID_FIELD_NAME, uuid))
end
- # TODO: Add tests for selecting specific fields
+ # Tests that the valid field is retrieved when both a valid and invalid field
+ # are requested from a valid Arvados object, using:
+ # `arv get [uuid] [fields...]`.
def test_get_valid_object_with_both_specific_valid_and_invalid_fields()
- # TODO
- end
-
- # Tests that an valid Arvados object is not retrieved when specifying an
- # invalid format: `arv get [uuid] --format invalid`.
- def test_get_object_invalid_format()
stored_value = __method__
uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
- arv_get(uuid, '--format', 'invalid')
+ arv_get(uuid, STORED_VALUE_FIELD_NAME, INVALID_FIELD_NAME, "--format", "json")
end
- refute_empty(err)
- assert_empty(out)
+ assert_empty(err)
+ arv_object = parse_json_arv_object(out)
+ assert(has_field_with_value(arv_object, STORED_VALUE_FIELD_NAME, stored_value))
+ refute(has_field_with_value(arv_object, INVALID_FIELD_NAME, stored_value))
end
- # Tests that an invalid (non-existant) Arvados object is not retrieved using:
- # using: `arv get [non-existant-uuid] --format json`.
- def test_get_invalid_object_json_format()
+ # Tests that no fields are retreived when no valid fields are requested from
+ # a valid Arvados object, using: `arv get [uuid] [fields...]`.
+ def test_get_valid_object_with_no_specific_valid_fields()
+ stored_value = __method__
+ uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
- arv_get(NON_EXISTANT_OBJECT_UUID, '--format', 'json')
+ arv_get(uuid, INVALID_FIELD_NAME, "--format", "json")
end
- refute_empty(err)
- assert_empty(out)
+ assert_empty(err)
+ arv_object = parse_json_arv_object(out)
+ assert_equal(0, arv_object.fixnum)
end
- # Tests that an invalid (non-existant) Arvados object is not retrieved using:
- # using: `arv get [non-existant-uuid] --format yaml`.
- def test_get_invalid_object_yaml_format()
+ # Tests that an valid Arvados object is not retrieved when specifying an
+ # invalid format: `arv get [uuid] --format invalid`.
+ def test_get_valid_object_invalid_format()
+ stored_value = __method__
+ uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
- arv_get(NON_EXISTANT_OBJECT_UUID, '--format', 'yaml')
+ arv_get(uuid, '--format', 'invalid')
end
refute_empty(err)
assert_empty(out)
@@ -88,30 +109,14 @@ class TestArvGet < Minitest::Test
# Tests that an invalid (non-existant) Arvados object is not retrieved using:
# using: `arv get [non-existant-uuid]`.
- def test_get_invalid_object_no_format()
+ def test_get_invalid_object()
out, err = capture_subprocess_io do
- arv_get(NON_EXISTANT_OBJECT_UUID)
+ arv_get(NON_EXISTANT_OBJECT_UUID, "--format", "json")
end
refute_empty(err)
assert_empty(out)
end
- # Tests that an invalid (non-existant) Arvados object is not retrieved when
- # specifying an invalid format:
- # `arv get [non-existant-uuid] --format invalid`.
- def test_get_object_invalid_format()
- out, err = capture_subprocess_io do
- arv_get(NON_EXISTANT_OBJECT_UUID, '--format', 'invalid')
- end
- refute_empty(err)
- assert_empty(out)
- end
-
- # TODO: Test what happens when valid object but invalid fields
- def test_get_valid_object_with_specific_invalid_fields()
- # TODO
- end
-
protected
# Runs 'arv get <varargs>' with given arguments.
def arv_get(*args)
@@ -131,33 +136,36 @@ class TestArvGet < Minitest::Test
return out
end
- # Checks whether the Arvados object, represented in JSON format, uses the
- # given value.
- def does_arv_object_as_json_use_value(obj, value)
+ # Parses the given JSON representation of an Arvados object, returning
+ # an equivalent Ruby representation (a hash map).
+ def parse_json_arv_object(arvObjectAsJson)
begin
- parsed = JSON.parse(obj)
- return does_arv_object_as_ruby_object_use_value(parsed, value)
+ parsed = JSON.parse(arvObjectAsJson)
+ assert(parsed.instance_of?(Hash))
+ return parsed
rescue JSON::ParserError => e
raise "Invalid JSON representation of Arvados object"
end
end
- # Checks whether the Arvados object, represented in YAML format, uses the
- # given value.
- def does_arv_object_as_yaml_use_value(obj, value)
+ # Parses the given JSON representation of an Arvados object, returning
+ # an equivalent Ruby representation (a hash map).
+ def parse_yaml_arv_object(arvObjectAsYaml)
begin
- parsed = YAML.load(obj)
- return does_arv_object_as_ruby_object_use_value(parsed, value)
+ parsed = YAML.load(arvObjectAsYaml)
+ assert(parsed.instance_of?(Hash))
+ return parsed
rescue
raise "Invalid YAML representation of Arvados object"
end
end
- # Checks whether the Arvados object, represented as a Ruby object, uses the
- # given value.
- def does_arv_object_as_ruby_object_use_value(obj, value)
- assert(parsed.instance_of?(Hash))
- stored_value = obj["name"]
- return (value == stored_value)
+ # Checks whether the given Arvados object has the given expected value for the
+ # specified field.
+ def has_field_with_value(arvObjectAsHash, fieldName, expectedValue)
+ if !arvObjectAsHash.has_key?(fieldName)
+ return false
+ end
+ return (arvObjectAsHash[fieldName] == expectedValue)
end
end
commit 7e6304bf646aaeb38196d24ce98c8bafc212e144
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Fri Sep 18 19:05:41 2015 +0100
7204: Stubbed more test cases for `arg get` to cover use for only getting specific fields.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index c9a5abe..c0f9146 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -44,6 +44,16 @@ class TestArvGet < Minitest::Test
does_arv_object_as_json_use_value(out, stored_value))
end
+ # TODO: Add tests for selecting specific fields
+ def test_get_valid_object_with_specific_valid_fields()
+ # TODO
+ end
+
+ # TODO: Add tests for selecting specific fields
+ def test_get_valid_object_with_both_specific_valid_and_invalid_fields()
+ # TODO
+ end
+
# Tests that an valid Arvados object is not retrieved when specifying an
# invalid format: `arv get [uuid] --format invalid`.
def test_get_object_invalid_format()
@@ -97,6 +107,11 @@ class TestArvGet < Minitest::Test
assert_empty(out)
end
+ # TODO: Test what happens when valid object but invalid fields
+ def test_get_valid_object_with_specific_invalid_fields()
+ # TODO
+ end
+
protected
# Runs 'arv get <varargs>' with given arguments.
def arv_get(*args)
commit 9e845fe4a5ff18f66c3850b25aae5f77680ac7cd
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Fri Sep 18 18:54:49 2015 +0100
7204: Fixed bugs in `arg get` tests.7204: Fixed bugs in `arg get` tests.7204: Fixed bugs in `arg get` tests.7204: Fixed bugs in `arg get` tests.7204: Fixed bugs in `arg get` tests.7204: Fixed bugs in `arg get` tests.7204: Fixed bugs in `arg get` tests.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index ccc1e16..c9a5abe 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -11,7 +11,7 @@ class TestArvGet < Minitest::Test
# `arv get [uuid] --format json`.
def test_get_valid_object_json_format()
stored_value = __method__
- uuid = create_arv_object_containing_value(stored_value)
+ uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
arv_get(uuid, '--format', 'json')
end
@@ -23,7 +23,7 @@ class TestArvGet < Minitest::Test
# `arv get [uuid] --format yaml`.
def test_get_valid_object_yaml_format()
stored_value = __method__
- uuid = create_arv_object_containing_value(stored_value)
+ uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
arv_get(uuid, '--format', 'yaml')
end
@@ -35,7 +35,7 @@ class TestArvGet < Minitest::Test
# using: `arv get [uuid]`.
def test_get_valid_object_no_format()
stored_value = __method__
- uuid = create_arv_object_containing_value(stored_value)
+ uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
arv_get(uuid)
end
@@ -48,7 +48,7 @@ class TestArvGet < Minitest::Test
# invalid format: `arv get [uuid] --format invalid`.
def test_get_object_invalid_format()
stored_value = __method__
- uuid = create_arv_object_containing_value(stored_value)
+ uuid = create_arv_object_with_value(stored_value)
out, err = capture_subprocess_io do
arv_get(uuid, '--format', 'invalid')
end
@@ -119,20 +119,29 @@ class TestArvGet < Minitest::Test
# Checks whether the Arvados object, represented in JSON format, uses the
# given value.
def does_arv_object_as_json_use_value(obj, value)
- parsed = JSON.parse(obj)
- return does_arv_object_as_object_use_value(parsed, value)
+ begin
+ parsed = JSON.parse(obj)
+ return does_arv_object_as_ruby_object_use_value(parsed, value)
+ rescue JSON::ParserError => e
+ raise "Invalid JSON representation of Arvados object"
+ end
end
# Checks whether the Arvados object, represented in YAML format, uses the
# given value.
def does_arv_object_as_yaml_use_value(obj, value)
- parsed = YAML.load(obj)
- return does_arv_object_as_object_use_value(parsed, value)
+ begin
+ parsed = YAML.load(obj)
+ return does_arv_object_as_ruby_object_use_value(parsed, value)
+ rescue
+ raise "Invalid YAML representation of Arvados object"
+ end
end
# Checks whether the Arvados object, represented as a Ruby object, uses the
# given value.
- def does_arv_object_as_object_use_value(obj, value)
+ def does_arv_object_as_ruby_object_use_value(obj, value)
+ assert(parsed.instance_of?(Hash))
stored_value = obj["name"]
return (value == stored_value)
end
commit 1a4b37d333d312a97c7979b1203c6246a28e601b
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Fri Sep 18 12:04:58 2015 +0100
7204: Minor refactoring of methods supporting `arv get` test cases.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index a1d49a6..ccc1e16 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -116,19 +116,24 @@ class TestArvGet < Minitest::Test
return out
end
- # Checks whether the Arvados object, represented in JSON format, with the
- # given uuid, uses the given value.
+ # Checks whether the Arvados object, represented in JSON format, uses the
+ # given value.
def does_arv_object_as_json_use_value(obj, value)
parsed = JSON.parse(obj)
- stored_value = parsed["name"]
- return (value == stored_value)
+ return does_arv_object_as_object_use_value(parsed, value)
end
- # Checks whether the Arvados object, represented in YAML format, with the
- # given uuid, uses the given value.
+ # Checks whether the Arvados object, represented in YAML format, uses the
+ # given value.
def does_arv_object_as_yaml_use_value(obj, value)
parsed = YAML.load(obj)
- stored_value = parsed["name"]
+ return does_arv_object_as_object_use_value(parsed, value)
+ end
+
+ # Checks whether the Arvados object, represented as a Ruby object, uses the
+ # given value.
+ def does_arv_object_as_object_use_value(obj, value)
+ stored_value = obj["name"]
return (value == stored_value)
end
end
commit fd0bb03ede4bf503fc599f9bac468adb620b2142
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Fri Sep 18 11:57:13 2015 +0100
7204: Completed supporting methods for `arv get` test cases.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index 2264bfc..a1d49a6 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -1,4 +1,6 @@
require 'minitest/autorun'
+require 'json'
+require 'yaml'
# Black box tests for 'arv get' command.
class TestArvGet < Minitest::Test
@@ -14,7 +16,7 @@ class TestArvGet < Minitest::Test
arv_get(uuid, '--format', 'json')
end
assert_empty(err)
- assert(does_arv_object_as_json_use_value(uuid, stored_value))
+ assert(does_arv_object_as_json_use_value(out, stored_value))
end
# Tests that a valid Arvados object can be retrieved in YAML format using:
@@ -26,7 +28,7 @@ class TestArvGet < Minitest::Test
arv_get(uuid, '--format', 'yaml')
end
assert_empty(err)
- assert(does_arv_object_as_yaml_use_value(uuid, stored_value))
+ assert(does_arv_object_as_yaml_use_value(out, stored_value))
end
# Tests that a valid Arvados object can be retrieved in a supported format
@@ -38,8 +40,8 @@ class TestArvGet < Minitest::Test
arv_get(uuid)
end
assert_empty(err)
- assert(does_arv_object_as_yaml_use_value(uuid, stored_value) ||
- does_arv_object_as_json_use_value(uuid, stored_value))
+ assert(does_arv_object_as_yaml_use_value(out, stored_value) ||
+ does_arv_object_as_json_use_value(out, stored_value))
end
# Tests that an valid Arvados object is not retrieved when specifying an
@@ -98,31 +100,35 @@ class TestArvGet < Minitest::Test
protected
# Runs 'arv get <varargs>' with given arguments.
def arv_get(*args)
- system ['./bin/arv', 'arv get'], *args
+ system(['./bin/arv', 'arv get'], *args)
end
- # Creates an Arvados object that stores a given value.
- # TODO: Must return uuid
+ # Creates an Arvados object that stores a given value. Returns the uuid of the
+ # created object.
def create_arv_object_with_value(value)
out, err = capture_subprocess_io do
# Write (without redirect)
- system ['./bin/arv', 'arv create log'], *args
+ system(['./bin/arv', "arv tag add #{value} --object testing"])
end
if err.length > 0
raise "Could not create Arvados object with given value"
end
-# system ['./bin/arv', 'arv user create'], *args
+ return out
end
# Checks whether the Arvados object, represented in JSON format, with the
# given uuid, uses the given value.
- def does_arv_object_as_json_use_value(uuid, value)
- # TODO
+ def does_arv_object_as_json_use_value(obj, value)
+ parsed = JSON.parse(obj)
+ stored_value = parsed["name"]
+ return (value == stored_value)
end
# Checks whether the Arvados object, represented in YAML format, with the
# given uuid, uses the given value.
- def does_arv_object_as_yaml_use_value(uuid, value)
- # TODO
+ def does_arv_object_as_yaml_use_value(obj, value)
+ parsed = YAML.load(obj)
+ stored_value = parsed["name"]
+ return (value == stored_value)
end
end
commit 044804a54376e69baccb23a241f7e7bffd7b529b
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Fri Sep 18 10:11:58 2015 +0100
7204: Created black box test cases for `arv get` command.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index 869ea6d..2264bfc 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -1,19 +1,98 @@
require 'minitest/autorun'
-# Test for 'arv get' command.
+# Black box tests for 'arv get' command.
class TestArvGet < Minitest::Test
- # Test setup.
- def setup
- # No setup required.
+ # UUID for an Arvados object that does not exist
+ NON_EXISTANT_OBJECT_UUID = "qr1hi-tpzed-p8yk1lihjsgwew0"
+
+ # Tests that a valid Arvados object can be retrieved in JSON format using:
+ # `arv get [uuid] --format json`.
+ def test_get_valid_object_json_format()
+ stored_value = __method__
+ uuid = create_arv_object_containing_value(stored_value)
+ out, err = capture_subprocess_io do
+ arv_get(uuid, '--format', 'json')
+ end
+ assert_empty(err)
+ assert(does_arv_object_as_json_use_value(uuid, stored_value))
+ end
+
+ # Tests that a valid Arvados object can be retrieved in YAML format using:
+ # `arv get [uuid] --format yaml`.
+ def test_get_valid_object_yaml_format()
+ stored_value = __method__
+ uuid = create_arv_object_containing_value(stored_value)
+ out, err = capture_subprocess_io do
+ arv_get(uuid, '--format', 'yaml')
+ end
+ assert_empty(err)
+ assert(does_arv_object_as_yaml_use_value(uuid, stored_value))
+ end
+
+ # Tests that a valid Arvados object can be retrieved in a supported format
+ # using: `arv get [uuid]`.
+ def test_get_valid_object_no_format()
+ stored_value = __method__
+ uuid = create_arv_object_containing_value(stored_value)
+ out, err = capture_subprocess_io do
+ arv_get(uuid)
+ end
+ assert_empty(err)
+ assert(does_arv_object_as_yaml_use_value(uuid, stored_value) ||
+ does_arv_object_as_json_use_value(uuid, stored_value))
+ end
+
+ # Tests that an valid Arvados object is not retrieved when specifying an
+ # invalid format: `arv get [uuid] --format invalid`.
+ def test_get_object_invalid_format()
+ stored_value = __method__
+ uuid = create_arv_object_containing_value(stored_value)
+ out, err = capture_subprocess_io do
+ arv_get(uuid, '--format', 'invalid')
+ end
+ refute_empty(err)
+ assert_empty(out)
+ end
+
+ # Tests that an invalid (non-existant) Arvados object is not retrieved using:
+ # using: `arv get [non-existant-uuid] --format json`.
+ def test_get_invalid_object_json_format()
+ out, err = capture_subprocess_io do
+ arv_get(NON_EXISTANT_OBJECT_UUID, '--format', 'json')
+ end
+ refute_empty(err)
+ assert_empty(out)
+ end
+
+ # Tests that an invalid (non-existant) Arvados object is not retrieved using:
+ # using: `arv get [non-existant-uuid] --format yaml`.
+ def test_get_invalid_object_yaml_format()
+ out, err = capture_subprocess_io do
+ arv_get(NON_EXISTANT_OBJECT_UUID, '--format', 'yaml')
+ end
+ refute_empty(err)
+ assert_empty(out)
end
- # Tests something... TODO.
- def test_get_TODO
+ # Tests that an invalid (non-existant) Arvados object is not retrieved using:
+ # using: `arv get [non-existant-uuid]`.
+ def test_get_invalid_object_no_format()
out, err = capture_subprocess_io do
- arv_get
+ arv_get(NON_EXISTANT_OBJECT_UUID)
end
+ refute_empty(err)
+ assert_empty(out)
+ end
- assert_empty err
+ # Tests that an invalid (non-existant) Arvados object is not retrieved when
+ # specifying an invalid format:
+ # `arv get [non-existant-uuid] --format invalid`.
+ def test_get_object_invalid_format()
+ out, err = capture_subprocess_io do
+ arv_get(NON_EXISTANT_OBJECT_UUID, '--format', 'invalid')
+ end
+ refute_empty(err)
+ assert_empty(out)
end
protected
@@ -21,4 +100,29 @@ class TestArvGet < Minitest::Test
def arv_get(*args)
system ['./bin/arv', 'arv get'], *args
end
+
+ # Creates an Arvados object that stores a given value.
+ # TODO: Must return uuid
+ def create_arv_object_with_value(value)
+ out, err = capture_subprocess_io do
+ # Write (without redirect)
+ system ['./bin/arv', 'arv create log'], *args
+ end
+ if err.length > 0
+ raise "Could not create Arvados object with given value"
+ end
+# system ['./bin/arv', 'arv user create'], *args
+ end
+
+ # Checks whether the Arvados object, represented in JSON format, with the
+ # given uuid, uses the given value.
+ def does_arv_object_as_json_use_value(uuid, value)
+ # TODO
+ end
+
+ # Checks whether the Arvados object, represented in YAML format, with the
+ # given uuid, uses the given value.
+ def does_arv_object_as_yaml_use_value(uuid, value)
+ # TODO
+ end
end
commit ba0d6a92c642ca86dae5ab807b3ad7fe04e335d2
Author: Colin Nolan <colin.nolan at sanger.ac.uk>
Date: Thu Sep 17 11:45:43 2015 +0100
7204: Setup for testing new `arg get` command.
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-get.rb
index 5e58014..869ea6d 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-get.rb
@@ -1,251 +1,24 @@
require 'minitest/autorun'
-require 'digest/md5'
+# Test for 'arv get' command.
class TestArvGet < Minitest::Test
+ # Test setup.
def setup
- begin
- Dir.mkdir './tmp'
- rescue Errno::EEXIST
- end
- @@foo_manifest_locator ||= `echo -n foo | ./bin/arv-put --filename foo --no-progress -`.strip
- @@baz_locator ||= `echo -n baz | ./bin/arv-put --as-raw --no-progress -`.strip
- @@multilevel_manifest_locator ||= `echo ./foo/bar #{@@baz_locator} 0:3:baz | ./bin/arv-put --as-raw --no-progress -`.strip
- end
-
- def test_no_args
- out, err = capture_subprocess_io do
- assert_arv_get false
- end
- assert_equal '', out
- assert_match /^usage:/, err
- end
-
- def test_help
- out, err = capture_subprocess_io do
- assert_arv_get '-h'
- end
- $stderr.write err
- assert_equal '', err
- assert_match /^usage:/, out
- end
-
- def test_file_to_dev_stdout
- test_file_to_stdout('/dev/stdout')
- end
-
- def test_file_to_stdout(specify_stdout_as='-')
- out, err = capture_subprocess_io do
- assert_arv_get @@foo_manifest_locator + '/foo', specify_stdout_as
- end
- assert_equal '', err
- assert_equal 'foo', out
- end
-
- def test_file_to_file
- remove_tmp_foo
- out, err = capture_subprocess_io do
- assert_arv_get @@foo_manifest_locator + '/foo', 'tmp/foo'
- end
- assert_equal '', err
- assert_equal '', out
- assert_equal 'foo', IO.read('tmp/foo')
- end
-
- def test_file_to_file_no_overwrite_file
- File.open './tmp/foo', 'wb' do |f|
- f.write 'baz'
- end
- out, err = capture_subprocess_io do
- assert_arv_get false, @@foo_manifest_locator + '/foo', 'tmp/foo'
- end
- assert_match /Local file tmp\/foo already exists/, err
- assert_equal '', out
- assert_equal 'baz', IO.read('tmp/foo')
- end
-
- def test_file_to_file_no_overwrite_file_in_dir
- File.open './tmp/foo', 'wb' do |f|
- f.write 'baz'
- end
- out, err = capture_subprocess_io do
- assert_arv_get false, @@foo_manifest_locator + '/', 'tmp/'
- end
- assert_match /Local file tmp\/foo already exists/, err
- assert_equal '', out
- assert_equal 'baz', IO.read('tmp/foo')
- end
-
- def test_file_to_file_force_overwrite
- File.open './tmp/foo', 'wb' do |f|
- f.write 'baz'
- end
- assert_equal 'baz', IO.read('tmp/foo')
- out, err = capture_subprocess_io do
- assert_arv_get '-f', @@foo_manifest_locator + '/', 'tmp/'
- end
- assert_match '', err
- assert_equal '', out
- assert_equal 'foo', IO.read('tmp/foo')
- end
-
- def test_file_to_file_skip_existing
- File.open './tmp/foo', 'wb' do |f|
- f.write 'baz'
- end
- assert_equal 'baz', IO.read('tmp/foo')
- out, err = capture_subprocess_io do
- assert_arv_get '--skip-existing', @@foo_manifest_locator + '/', 'tmp/'
- end
- assert_match '', err
- assert_equal '', out
- assert_equal 'baz', IO.read('tmp/foo')
- end
-
- def test_file_to_dir
- remove_tmp_foo
- out, err = capture_subprocess_io do
- assert_arv_get @@foo_manifest_locator + '/foo', 'tmp/'
- end
- assert_equal '', err
- assert_equal '', out
- assert_equal 'foo', IO.read('tmp/foo')
- end
-
- def test_dir_to_file
- out, err = capture_subprocess_io do
- assert_arv_get false, @@foo_manifest_locator + '/', 'tmp/foo'
- end
- assert_equal '', out
- assert_match /^usage:/, err
- end
-
- def test_dir_to_empty_string
- out, err = capture_subprocess_io do
- assert_arv_get false, @@foo_manifest_locator + '/', ''
- end
- assert_equal '', out
- assert_match /^usage:/, err
+ # No setup required.
end
- def test_nonexistent_block
+ # Tests something... TODO.
+ def test_get_TODO
out, err = capture_subprocess_io do
- assert_arv_get false, 'e796ab2294f3e48ec709ffa8d6daf58c'
+ arv_get
end
- assert_equal '', out
- assert_match /Error:/, err
- end
- def test_nonexistent_manifest
- out, err = capture_subprocess_io do
- assert_arv_get false, 'acbd18db4cc2f85cedef654fccc4a4d8/', 'tmp/'
- end
- assert_equal '', out
- assert_match /Error:/, err
- end
-
- def test_manifest_root_to_dir
- remove_tmp_foo
- out, err = capture_subprocess_io do
- assert_arv_get '-r', @@foo_manifest_locator + '/', 'tmp/'
- end
- assert_equal '', err
- assert_equal '', out
- assert_equal 'foo', IO.read('tmp/foo')
- end
-
- def test_manifest_root_to_dir_noslash
- remove_tmp_foo
- out, err = capture_subprocess_io do
- assert_arv_get '-r', @@foo_manifest_locator + '/', 'tmp'
- end
- assert_equal '', err
- assert_equal '', out
- assert_equal 'foo', IO.read('tmp/foo')
- end
-
- def test_display_md5sum
- remove_tmp_foo
- out, err = capture_subprocess_io do
- assert_arv_get '-r', '--md5sum', @@foo_manifest_locator + '/', 'tmp/'
- end
- assert_equal "#{Digest::MD5.hexdigest('foo')} ./foo\n", err
- assert_equal '', out
- assert_equal 'foo', IO.read('tmp/foo')
- end
-
- def test_md5sum_nowrite
- remove_tmp_foo
- out, err = capture_subprocess_io do
- assert_arv_get '-n', '--md5sum', @@foo_manifest_locator + '/', 'tmp/'
- end
- assert_equal "#{Digest::MD5.hexdigest('foo')} ./foo\n", err
- assert_equal '', out
- assert_equal false, File.exists?('tmp/foo')
- end
-
- def test_sha1_nowrite
- remove_tmp_foo
- out, err = capture_subprocess_io do
- assert_arv_get '-n', '-r', '--hash', 'sha1', @@foo_manifest_locator+'/', 'tmp/'
- end
- assert_equal "#{Digest::SHA1.hexdigest('foo')} ./foo\n", err
- assert_equal '', out
- assert_equal false, File.exists?('tmp/foo')
- end
-
- def test_block_to_file
- remove_tmp_foo
- out, err = capture_subprocess_io do
- assert_arv_get @@foo_manifest_locator, 'tmp/foo'
- end
- assert_equal '', err
- assert_equal '', out
-
- digest = Digest::MD5.hexdigest('foo')
- !(IO.read('tmp/foo')).gsub!( /^(. #{digest}+3)(.*)( 0:3:foo)$/).nil?
- end
-
- def test_create_directory_tree
- `rm -rf ./tmp/arv-get-test/`
- Dir.mkdir './tmp/arv-get-test'
- out, err = capture_subprocess_io do
- assert_arv_get @@multilevel_manifest_locator + '/', 'tmp/arv-get-test/'
- end
- assert_equal '', err
- assert_equal '', out
- assert_equal 'baz', IO.read('tmp/arv-get-test/foo/bar/baz')
- end
-
- def test_create_partial_directory_tree
- `rm -rf ./tmp/arv-get-test/`
- Dir.mkdir './tmp/arv-get-test'
- out, err = capture_subprocess_io do
- assert_arv_get(@@multilevel_manifest_locator + '/foo/',
- 'tmp/arv-get-test/')
- end
- assert_equal '', err
- assert_equal '', out
- assert_equal 'baz', IO.read('tmp/arv-get-test/bar/baz')
+ assert_empty err
end
protected
- def assert_arv_get(*args)
- expect = case args.first
- when true, false
- args.shift
- else
- true
- end
- assert_equal(expect,
- system(['./bin/arv-get', 'arv-get'], *args),
- "`arv-get #{args.join ' '}` " +
- "should exit #{if expect then 0 else 'non-zero' end}")
- end
-
- def remove_tmp_foo
- begin
- File.unlink('tmp/foo')
- rescue Errno::ENOENT
- end
+ # Runs 'arv get <varargs>' with given arguments.
+ def arv_get(*args)
+ system ['./bin/arv', 'arv get'], *args
end
end
diff --git a/sdk/cli/test/test_arv-get.rb b/sdk/cli/test/test_arv-keep-get.rb
similarity index 99%
copy from sdk/cli/test/test_arv-get.rb
copy to sdk/cli/test/test_arv-keep-get.rb
index 5e58014..0e578b8 100644
--- a/sdk/cli/test/test_arv-get.rb
+++ b/sdk/cli/test/test_arv-keep-get.rb
@@ -1,7 +1,7 @@
require 'minitest/autorun'
require 'digest/md5'
-class TestArvGet < Minitest::Test
+class TestArvKeepGet < Minitest::Test
def setup
begin
Dir.mkdir './tmp'
diff --git a/sdk/cli/test/test_arv-put.rb b/sdk/cli/test/test_arv-keep-put.rb
similarity index 99%
rename from sdk/cli/test/test_arv-put.rb
rename to sdk/cli/test/test_arv-keep-put.rb
index 2f20e18..fefbc27 100644
--- a/sdk/cli/test/test_arv-put.rb
+++ b/sdk/cli/test/test_arv-keep-put.rb
@@ -1,7 +1,7 @@
require 'minitest/autorun'
require 'digest/md5'
-class TestArvPut < Minitest::Test
+class TestArvKeepPut < Minitest::Test
def setup
begin Dir.mkdir './tmp' rescue Errno::EEXIST end
begin Dir.mkdir './tmp/empty_dir' rescue Errno::EEXIST end
commit be9b62b5186bd9aa961f08f66bc104200acf760a
Merge: 489caef 5ba12c5
Author: Joshua Randall <joshua.randall at sanger.ac.uk>
Date: Mon Sep 7 20:05:14 2015 +0100
Merge branch 'fix/7205-arv-edit-tty-check' into feature/arv-view
commit 489caef97d5185d91e7441980125480f98428c79
Author: Joshua Randall <joshua.randall at sanger.ac.uk>
Date: Mon Sep 7 20:04:30 2015 +0100
Adds an abort if global_opts[:format] is not recognized
diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv
index caee76c..bddad98 100755
--- a/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@ -185,6 +185,8 @@ def edit_and_commit_object initial_obj, tmp_stem, global_opts, &block
Oj.load(newcontent)
when 'yaml'
YAML.load(newcontent)
+ else
+ abort "Unrecognized format #{global_opts[:format]}"
end
yield newobj
commit 80572f8164b46079617f0248b1372cf860ca9957
Author: Joshua Randall <joshua.randall at sanger.ac.uk>
Date: Mon Sep 7 19:57:39 2015 +0100
Makes bin_path local
diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv
index f70f4d0..caee76c 100755
--- a/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@ -88,11 +88,11 @@ end
subcommands = %w(copy create edit get keep pipeline run tag ws)
def exec_bin bin, opts
- @bin_path = `which #{bin}`.strip
- if @bin_path.empty?
+ bin_path = `which #{bin}`.strip
+ if bin_path.empty?
raise "#{bin}: command not found"
end
- exec @bin_path, *opts
+ exec bin_path, *opts
end
def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
commit 89e2ddbacad459856fc15f56bfa2b5c036b090a1
Author: Joshua Randall <joshua.randall at sanger.ac.uk>
Date: Mon Sep 7 15:47:16 2015 +0100
Changes new feature name to `arv get`
diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv
index 252d267..f70f4d0 100755
--- a/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@ -85,7 +85,7 @@ def init_config
end
-subcommands = %w(copy create edit keep pipeline run tag view ws)
+subcommands = %w(copy create edit get keep pipeline run tag ws)
def exec_bin bin, opts
@bin_path = `which #{bin}`.strip
@@ -101,8 +101,8 @@ def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
arv_create client, arvados, global_opts, remaining_opts
when 'edit'
arv_edit client, arvados, global_opts, remaining_opts
- when 'view'
- arv_view client, arvados, global_opts, remaining_opts
+ when 'get'
+ arv_get client, arvados, global_opts, remaining_opts
when 'copy', 'tag', 'ws', 'run'
exec_bin "arv-#{subcommand}", remaining_opts
when 'keep'
@@ -348,11 +348,11 @@ def arv_edit client, arvados, global_opts, remaining_opts
exit 0
end
-def arv_view client, arvados, global_opts, remaining_opts
+def arv_get client, arvados, global_opts, remaining_opts
uuid = remaining_opts.shift
if uuid.nil? or uuid == "-h" or uuid == "--help"
puts head_banner
- puts "Usage: arv view [uuid] [fields...]\n\n"
+ puts "Usage: arv get [uuid] [fields...]\n\n"
puts "Fetch the specified Arvados object, select the specified fields, \n"
puts "and print a text representation (json or yaml, use --format).\n"
exit 255
commit 5ba12c5e842c926a38fad477d890ccbf9e96278d
Merge: b735534 45f10d8
Author: Joshua Randall <joshua.randall at sanger.ac.uk>
Date: Sat Sep 5 00:20:25 2015 +0100
Merge remote-tracking branch 'hgi/develop' into fix/7205-arv-edit-tty-check
Conflicts:
sdk/cli/bin/arv
diff --cc sdk/cli/bin/arv
index b757855,252d267..cf1e732
--- a/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@@ -295,9 -290,44 +290,39 @@@ def fetch_rsc_obj client, arvados, rsc
end
if remaining_opts.length > 0
- oldobj.select! { |k, v| remaining_opts.include? k }
+ obj.select! { |k, v| remaining_opts.include? k }
end
+ return obj
+ end
+
+ def get_obj_content obj, global_opts
+ content = case global_opts[:format]
+ when 'json'
+ Oj.dump(obj, :indent => 1)
+ when 'yaml'
+ obj.to_yaml
+ else
+ abort "Unrecognized format #{global_opts[:format]}"
+ end
+ return content
+ end
+
+ def arv_edit client, arvados, global_opts, remaining_opts
+ uuid = remaining_opts.shift
+ if uuid.nil? or uuid == "-h" or uuid == "--help"
+ puts head_banner
+ puts "Usage: arv edit [uuid] [fields...]\n\n"
+ puts "Fetch the specified Arvados object, select the specified fields, \n"
+ puts "open an interactive text editor on a text representation (json or\n"
+ puts "yaml, use --format) and then update the object. Will use 'nano'\n"
+ puts "by default, customize with the EDITOR or VISUAL environment variable.\n"
+ exit 255
+ end
+
- if not $stdout.tty?
- puts "Not connected to a TTY, cannot run interactive editor."
- exit 1
- end
-
+ rsc = lookup_uuid_rsc arvados, uuid
+ oldobj = fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts
+
edit_and_commit_object oldobj, uuid, global_opts do |newobj|
newobj.select! {|k| newobj[k] != oldobj[k]}
if !newobj.empty?
commit 45f10d80d1b584808a6e375214b5be6bc7d2a730
Merge: df9e166 8e2ad73
Author: Joshua C. Randall <jcrandall at alum.mit.edu>
Date: Fri Sep 4 10:55:37 2015 +0100
Merge pull request #2 from wtsi-hgi/feature/arv-view
Feature/arv view
commit 8e2ad737e429bc263620859468da3835708258e2
Author: Joshua Randall <joshua.randall at sanger.ac.uk>
Date: Fri Sep 4 02:22:45 2015 +0100
Adds `arv view` subcommand
Implements `arv view` feature as in https://arvados.org/issues/7204
Refactors portions of arv_edit into separate functions so arv_view
can share them.
diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv
index 41ee7b8..252d267 100755
--- a/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@ -85,7 +85,7 @@ def init_config
end
-subcommands = %w(copy create edit keep pipeline run tag ws)
+subcommands = %w(copy create edit keep pipeline run tag view ws)
def exec_bin bin, opts
@bin_path = `which #{bin}`.strip
@@ -101,6 +101,8 @@ def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
arv_create client, arvados, global_opts, remaining_opts
when 'edit'
arv_edit client, arvados, global_opts, remaining_opts
+ when 'view'
+ arv_view client, arvados, global_opts, remaining_opts
when 'copy', 'tag', 'ws', 'run'
exec_bin "arv-#{subcommand}", remaining_opts
when 'keep'
@@ -158,14 +160,7 @@ end
def edit_and_commit_object initial_obj, tmp_stem, global_opts, &block
- content = case global_opts[:format]
- when 'json'
- Oj.dump(initial_obj, :indent => 1)
- when 'yaml'
- initial_obj.to_yaml
- else
- abort "Unrecognized format #{global_opts[:format]}"
- end
+ content = get_obj_content initial_obj, global_opts
tmp_file = Tempfile.new([tmp_stem, ".#{global_opts[:format]}"])
tmp_file.write(content)
@@ -254,25 +249,7 @@ def check_response result
results
end
-def arv_edit client, arvados, global_opts, remaining_opts
- uuid = remaining_opts.shift
- if uuid.nil? or uuid == "-h" or uuid == "--help"
- puts head_banner
- puts "Usage: arv edit [uuid] [fields...]\n\n"
- puts "Fetch the specified Arvados object, select the specified fields, \n"
- puts "open an interactive text editor on a text representation (json or\n"
- puts "yaml, use --format) and then update the object. Will use 'nano'\n"
- puts "by default, customize with the EDITOR or VISUAL environment variable.\n"
- exit 255
- end
-
- if not $stdout.tty?
- puts "Not connected to a TTY, cannot run interactive editor."
- exit 1
- end
-
- # determine controller
-
+def lookup_uuid_rsc arvados, uuid
m = /([a-z0-9]{5})-([a-z0-9]{5})-([a-z0-9]{15})/.match uuid
if !m
if /^[a-f0-9]{32}/.match uuid
@@ -295,6 +272,11 @@ def arv_edit client, arvados, global_opts, remaining_opts
abort "Could not determine resource type #{m[2]}"
end
+ return rsc
+end
+
+def fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts
+
begin
result = client.execute(:api_method => eval('arvados.' + rsc + '.get'),
:parameters => {"uuid" => uuid},
@@ -302,15 +284,50 @@ def arv_edit client, arvados, global_opts, remaining_opts
:headers => {
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
})
- oldobj = check_response result
+ obj = check_response result
rescue => e
abort "Server error: #{e}"
end
if remaining_opts.length > 0
- oldobj.select! { |k, v| remaining_opts.include? k }
+ obj.select! { |k, v| remaining_opts.include? k }
+ end
+
+ return obj
+end
+
+def get_obj_content obj, global_opts
+ content = case global_opts[:format]
+ when 'json'
+ Oj.dump(obj, :indent => 1)
+ when 'yaml'
+ obj.to_yaml
+ else
+ abort "Unrecognized format #{global_opts[:format]}"
+ end
+ return content
+end
+
+def arv_edit client, arvados, global_opts, remaining_opts
+ uuid = remaining_opts.shift
+ if uuid.nil? or uuid == "-h" or uuid == "--help"
+ puts head_banner
+ puts "Usage: arv edit [uuid] [fields...]\n\n"
+ puts "Fetch the specified Arvados object, select the specified fields, \n"
+ puts "open an interactive text editor on a text representation (json or\n"
+ puts "yaml, use --format) and then update the object. Will use 'nano'\n"
+ puts "by default, customize with the EDITOR or VISUAL environment variable.\n"
+ exit 255
end
+ if not $stdout.tty?
+ puts "Not connected to a TTY, cannot run interactive editor."
+ exit 1
+ end
+
+ rsc = lookup_uuid_rsc arvados, uuid
+ oldobj = fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts
+
edit_and_commit_object oldobj, uuid, global_opts do |newobj|
newobj.select! {|k| newobj[k] != oldobj[k]}
if !newobj.empty?
@@ -331,6 +348,24 @@ def arv_edit client, arvados, global_opts, remaining_opts
exit 0
end
+def arv_view client, arvados, global_opts, remaining_opts
+ uuid = remaining_opts.shift
+ if uuid.nil? or uuid == "-h" or uuid == "--help"
+ puts head_banner
+ puts "Usage: arv view [uuid] [fields...]\n\n"
+ puts "Fetch the specified Arvados object, select the specified fields, \n"
+ puts "and print a text representation (json or yaml, use --format).\n"
+ exit 255
+ end
+
+ rsc = lookup_uuid_rsc arvados, uuid
+ obj = fetch_rsc_obj client, arvados, rsc, uuid, remaining_opts
+ content = get_obj_content obj, global_opts
+
+ puts content
+ exit 0
+end
+
def arv_create client, arvados, global_opts, remaining_opts
types = resource_types(arvados.discovery_document)
create_opts = Trollop::options do
commit ae0f6b92c3c302757ff7e81239bd7b41a4430e70
Author: Joshua Randall <joshua.randall at sanger.ac.uk>
Date: Thu Sep 3 18:40:50 2015 +0100
Adds error handling for command not found
Raises a "command not found" error if arv-* commands are not
found
diff --git a/sdk/cli/bin/arv b/sdk/cli/bin/arv
index 36ec037..41ee7b8 100755
--- a/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@ -87,6 +87,14 @@ end
subcommands = %w(copy create edit keep pipeline run tag ws)
+def exec_bin bin, opts
+ @bin_path = `which #{bin}`.strip
+ if @bin_path.empty?
+ raise "#{bin}: command not found"
+ end
+ exec @bin_path, *opts
+end
+
def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
case subcommand
when 'create'
@@ -94,17 +102,17 @@ def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
when 'edit'
arv_edit client, arvados, global_opts, remaining_opts
when 'copy', 'tag', 'ws', 'run'
- exec `which arv-#{subcommand}`.strip, *remaining_opts
+ exec_bin "arv-#{subcommand}", remaining_opts
when 'keep'
@sub = remaining_opts.shift
if ['get', 'put', 'ls', 'normalize'].index @sub then
# Native Arvados
- exec `which arv-#{@sub}`.strip, *remaining_opts
+ exec_bin "arv-#{@sub}", remaining_opts
elsif ['less', 'check'].index @sub then
# wh* shims
- exec `which wh#{@sub}`.strip, *remaining_opts
+ exec_bin "wh#{@sub}", remaining_opts
elsif @sub == 'docker'
- exec `which arv-keepdocker`.strip, *remaining_opts
+ exec_bin "arv-keepdocker", remaining_opts
else
puts "Usage: arv keep [method] [--parameters]\n"
puts "Use 'arv keep [method] --help' to get more information about specific methods.\n\n"
@@ -114,7 +122,7 @@ def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
when 'pipeline'
sub = remaining_opts.shift
if sub == 'run'
- exec `which arv-run-pipeline-instance`.strip, *remaining_opts
+ exec_bin "arv-run-pipeline-instance", remaining_opts
else
puts "Usage: arv pipeline [method] [--parameters]\n"
puts "Use 'arv pipeline [method] --help' to get more information about specific methods.\n\n"
commit df9e166a5ffc4aa79658bec1a5d552a3b413f0d8
Merge: 85706e0 1fea1b7
Author: Joshua C. Randall <jcrandall at alum.mit.edu>
Date: Mon Mar 23 17:50:49 2015 +0000
Merge pull request #1 from curoverse/master
pulling from upstream
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