From faaefa1b4866e6e33182ebe4272ad260ab6299f6 Mon Sep 17 00:00:00 2001 From: brettin Date: Thu, 9 Jul 2015 13:56:42 -0500 Subject: [PATCH 1/6] fixed compile error --- scripts/ws-cp.pl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/ws-cp.pl b/scripts/ws-cp.pl index f428b6e..8c63ce1 100644 --- a/scripts/ws-cp.pl +++ b/scripts/ws-cp.pl @@ -30,10 +30,10 @@ =head1 COMMAND-LINE OPTIONS ]); my $paths = Bio::P3::Workspace::ScriptHelpers::process_paths([$ARGV[0],$ARGV[1]]); my $res = Bio::P3::Workspace::ScriptHelpers::wscall("copy",{ - objects => [$paths] + objects => [$paths], overwrite => $opt->overwrite, recursive => $opt->recursive, - move => $ops->move + move => $opt->move }); print "Files copied to new destinations:\n"; -Bio::P3::Workspace::ScriptHelpers::print_wsmeta_table($res); \ No newline at end of file +Bio::P3::Workspace::ScriptHelpers::print_wsmeta_table($res); From 45a66134917e4fb411352480ecedc9c27232af61 Mon Sep 17 00:00:00 2001 From: non Date: Mon, 27 Jul 2015 23:37:47 -0500 Subject: [PATCH 2/6] Committing new testing framework, which permits the coding of tests for server and client infrastructure in a single place. Other tests are removed. IF still needed, they can be restored, or ideally, reimplemented within the new testing framework. --- lib/Bio/P3/Workspace/ScriptHelpers.pm | 22 +- lib/Bio/P3/Workspace/WorkspaceImpl.pm | 14 + lib/Bio/P3/Workspace/WorkspaceTests.pm | 504 +++++++++++++++++++++ t/client-tests/auth.t | 51 --- t/client-tests/create.t | 122 ----- t/client-tests/create_subdir.t | 101 ----- t/client-tests/create_upload_node.t | 95 ---- t/client-tests/fba | 1 + t/client-tests/gf | 1 + t/client-tests/min.t | 51 --- t/client-tests/small-contigs.fasta.gz | Bin 100092 -> 0 bytes t/client-tests/test.cfg | 8 + t/client-tests/testmodel | 1 + t/client-tests/tests.t | 5 + t/client-tests/upload_to_node.t | 130 ------ t/client-tests/workspace-full-api-test.t | 411 ----------------- t/client-tests/ws.t | 166 ------- t/server-tests/fba | 1 + t/server-tests/gf | 1 + t/server-tests/test.cfg | 8 + t/server-tests/testmodel | 1 + t/server-tests/tests.t | 5 + t/server-tests/testserver.cfg | 27 ++ t/server-tests/workspace-test.t | 547 ----------------------- 24 files changed, 590 insertions(+), 1683 deletions(-) create mode 100644 lib/Bio/P3/Workspace/WorkspaceTests.pm delete mode 100644 t/client-tests/auth.t delete mode 100644 t/client-tests/create.t delete mode 100644 t/client-tests/create_subdir.t delete mode 100644 t/client-tests/create_upload_node.t create mode 100644 t/client-tests/fba create mode 100644 t/client-tests/gf delete mode 100644 t/client-tests/min.t delete mode 100644 t/client-tests/small-contigs.fasta.gz create mode 100644 t/client-tests/test.cfg create mode 100644 t/client-tests/testmodel create mode 100644 t/client-tests/tests.t delete mode 100644 t/client-tests/upload_to_node.t delete mode 100644 t/client-tests/workspace-full-api-test.t delete mode 100644 t/client-tests/ws.t create mode 100644 t/server-tests/fba create mode 100644 t/server-tests/gf create mode 100644 t/server-tests/test.cfg create mode 100644 t/server-tests/testmodel create mode 100644 t/server-tests/tests.t create mode 100644 t/server-tests/testserver.cfg delete mode 100644 t/server-tests/workspace-test.t diff --git a/lib/Bio/P3/Workspace/ScriptHelpers.pm b/lib/Bio/P3/Workspace/ScriptHelpers.pm index 1317a5e..b5be6e4 100644 --- a/lib/Bio/P3/Workspace/ScriptHelpers.pm +++ b/lib/Bio/P3/Workspace/ScriptHelpers.pm @@ -282,10 +282,12 @@ sub login { my $ua = LWP::UserAgent->new(); my $res = $ua->post($url,$content); if (!$res->is_success) { - Bio::P3::Workspace::ScriptHelpers::SetConfig({ - token => undef, - user_id => undef - }); + if (!defined($params->{tokenonly}) || $params->{tokenonly} == 0) { + Bio::P3::Workspace::ScriptHelpers::SetConfig({ + token => undef, + user_id => undef + }); + } return undef; } my $token; @@ -295,11 +297,13 @@ sub login { my $data = decode_json $res->content; $token = $data->{token}; } - Bio::P3::Workspace::ScriptHelpers::SetConfig({ - token => $token, - user_id => $params->{user_id}, - password => undef - }); + if (!defined($params->{tokenonly}) || $params->{tokenonly} == 0) { + Bio::P3::Workspace::ScriptHelpers::SetConfig({ + token => $token, + user_id => $params->{user_id}, + password => undef + }); + } return $token; } diff --git a/lib/Bio/P3/Workspace/WorkspaceImpl.pm b/lib/Bio/P3/Workspace/WorkspaceImpl.pm index 5496a17..beaa88f 100644 --- a/lib/Bio/P3/Workspace/WorkspaceImpl.pm +++ b/lib/Bio/P3/Workspace/WorkspaceImpl.pm @@ -710,6 +710,8 @@ sub _delete_validated_object_set { #Delete the specified workspace and all the objects it contains** sub _delete_workspace { my ($self,$wsobj) = @_; + if (!defined($wsobj->{owner}) || length($wsobj->{owner}) == 0) {$self->_error("Owner not specified in deletion!");} + if (!defined($wsobj->{name}) || length($wsobj->{name}) == 0) {$self->_error("Top directory not specified in deletion!");} rmtree($self->_db_path()."/".$wsobj->{owner}."/".$wsobj->{name}); $self->_mongodb()->get_collection('workspaces')->remove({uuid => $wsobj->{uuid}}); $self->_mongodb()->get_collection('objects')->remove({workspace_uuid => $wsobj->{uuid}}); @@ -717,6 +719,11 @@ sub _delete_workspace { #Delete the specified object** sub _delete_object { my ($self,$obj,$nodeletefiles) = @_; + #Ensuring all parts of object path have nonzero length + if (!defined($obj->{wsobj}->{owner}) || length($obj->{wsobj}->{owner}) == 0) {$self->_error("Owner not specified in deletion!");} + if (!defined($obj->{wsobj}->{name}) || length($obj->{wsobj}->{name}) == 0) {$self->_error("Top directory not specified in deletion!");} + if (!defined($obj->{path}) || length($obj->{path}) == 0) {$self->_error("Path not specified in deletion!");} + if (!defined($obj->{name}) || length($obj->{name}) == 0) {$self->_error("Name not specified in deletion!");} if ($obj->{folder} == 1) { my $objs = $self->_get_directory_contents($obj,0); for (my $i=0; $i < @{$objs}; $i++) { @@ -799,6 +806,8 @@ sub _create { #This function creates workspaces** sub _create_workspace { my ($self,$specs) = @_; + if (!defined($specs->{user}) || length($specs->{user}) == 0) {$self->_error("Owner not specified in creation!");} + if (!defined($specs->{workspace}) || length($specs->{workspace}) == 0) {$self->_error("Top directory not specified in creation!");} #Creating workspace directory on disk File::Path::mkpath ($self->_db_path()."/".$specs->{user}."/".$specs->{workspace}); #Creating workspace object in mongodb @@ -828,6 +837,7 @@ sub _create_object { my ($self,$specs) = @_; $specs->{path} =~ s/^\/+//; $specs->{path} =~ s/\/+$//; + my $uuid = Data::UUID->new()->create_str(); if (defined($specs->{move}) && $specs->{move} == 1) { $uuid = $specs->{data}->{uuid}; @@ -854,6 +864,10 @@ sub _create_object { if (!-e $self->{_params}->{"script-path"}."/ws-autometa-".$specs->{type}.".pl") { $object->{autometadata} = {}; } + if (!defined($object->{wsobj}->{owner}) || length($object->{wsobj}->{owner}) == 0) {$self->_error("Owner not specified in creation!");} + if (!defined($object->{wsobj}->{name}) || length($object->{wsobj}->{name}) == 0) {$self->_error("Top directory not specified in creation!");} + if (!defined($object->{path}) || length($object->{path}) == 0) {$self->_error("Path not specified in creation!");} + if (!defined($object->{name}) || length($object->{name}) == 0) {$self->_error("Name not specified in creation!");} if ($specs->{type} eq "folder") { #Creating folder on file system $object->{autometadata} = {}; diff --git a/lib/Bio/P3/Workspace/WorkspaceTests.pm b/lib/Bio/P3/Workspace/WorkspaceTests.pm new file mode 100644 index 0000000..89e497b --- /dev/null +++ b/lib/Bio/P3/Workspace/WorkspaceTests.pm @@ -0,0 +1,504 @@ +{ + package Bio::P3::Workspace::WorkspaceTests; + + use strict; + use Bio::P3::Workspace::ScriptHelpers; + use Test::More; + use Data::Dumper; + use Config::Simple; + + sub new { + my($class,$bin) = @_; + my $c = Config::Simple->new(); + $c->read($bin."/test.cfg"); + my $self = { + testcount => 0, + dumpoutput => 0, + user => $c->param("WorkspaceTest.user"), + password => $c->param("WorkspaceTest.password"), + usertwo => $c->param("WorkspaceTest.adminuser"), + passwordtwo => $c->param("WorkspaceTest.adminpassword"), + token => undef, + tokentwo => undef, + url => $c->param("WorkspaceTest.url"), + testoutput => {} + }; + $self->{token} = Bio::P3::Workspace::ScriptHelpers::login({ + user_id => $self->{user}, password => $self->{password},tokenonly => 1 + }); + $self->{tokentwo} = Bio::P3::Workspace::ScriptHelpers::login({ + user_id => $self->{adminuser}, password => $self->{adminpassword},tokenonly => 1 + }); + $ENV{KB_INTERACTIVE} = 1; + if (defined($c->param("WorkspaceTest.serverconfig"))) { + $ENV{KB_DEPLOYMENT_CONFIG} = $c->param("WorkspaceTest.serverconfig"); + } + if (defined($c->param("WorkspaceTest.dumpoutput"))) { + $self->{dumpoutput} = $c->param("WorkspaceTest.dumpoutput"); + } + if (!defined($self->{url}) || $self->{url} eq "impl") { + print "Loading server with this config: ".$ENV{KB_DEPLOYMENT_CONFIG}."\n"; + require "Bio/P3/Workspace/WorkspaceImpl.pm"; + $self->{obj} = Bio::P3::Workspace::WorkspaceImpl->new(); + } else { + require "Bio/P3/Workspace/WorkspaceClient.pm"; + $self->{clientobj} = Bio::P3::Workspace::WorkspaceClient->new($self->{url},token => $self->{token}); + $self->{clientobjtwo} = Bio::P3::Workspace::WorkspaceClient->new($self->{url},token => $self->{tokentwo}); + } + return bless $self, $class; + } + + sub set_user { + my($self,$user) = @_; + if (!defined($self->{url}) || $self->{url} eq "impl") { + if ($user == 2) { + $Bio::P3::Workspace::WorkspaceImpl::CallContext = Bio::P3::Workspace::WorkspaceImpl::CallContext->new($self->{tokentwo},"test",$self->{usertwo}); + } else { + $Bio::P3::Workspace::WorkspaceImpl::CallContext = Bio::P3::Workspace::WorkspaceImpl::CallContext->new($self->{token},"test",$self->{user}); + } + } else { + if ($user == 2) { + $self->{obj} = $self->{clientobjtwo}; + } else { + $self->{obj} = $self->{clientobj}; + } + } + } + + sub test_harness { + my($self,$function,$parameters,$name,$tests,$fail_to_pass,$dependency,$user) = @_; + $self->set_user($user); + $self->{testoutput}->{$name} = { + output => undef, + "index" => $self->{testcount}, + tests => $tests, + command => $function, + parameters => $parameters, + dependency => $dependency, + fail_to_pass => $fail_to_pass, + pass => 1, + function => 1, + status => "Failed initial function test!" + }; + $self->{testcount}++; + if (defined($dependency) && $self->{testoutput}->{$dependency}->{function} != 1) { + $self->{testoutput}->{$name}->{pass} = -1; + $self->{testoutput}->{$name}->{function} = -1; + $self->{testoutput}->{$name}->{status} = "Test skipped due to failed dependency!"; + return; + } + my $output; + eval { + if (defined($parameters)) { + $output = $self->{obj}->$function($parameters); + } else { + $output = $self->{obj}->$function(); + } + }; + $self->{completetestcount}++; + if (defined($output)) { + $self->{testoutput}->{$name}->{output} = $output; + $self->{testoutput}->{$name}->{function} = 1; + if (defined($fail_to_pass) && $fail_to_pass == 1) { + $self->{testoutput}->{$name}->{pass} = 0; + $self->{testoutput}->{$name}->{status} = $name." worked, but should have failed!"; + ok $self->{testoutput}->{$name}->{pass} == 1, $self->{testoutput}->{$name}->{status}; + } else { + ok 1, $name." worked as expected!"; + for (my $i=0; $i < @{$tests}; $i++) { + $self->{completetestcount}++; + $tests->[$i]->[2] = eval $tests->[$i]->[0]; + if ($tests->[$i]->[2] == 0) { + $self->{testoutput}->{$name}->{pass} = 0; + $self->{testoutput}->{$name}->{status} = $name." worked, but sub-tests failed!"; + } + ok $tests->[$i]->[2] == 1, $tests->[$i]->[1]; + } + } + } else { + $self->{testoutput}->{$name}->{function} = 0; + if (defined($fail_to_pass) && $fail_to_pass == 1) { + $self->{testoutput}->{$name}->{pass} = 1; + $self->{testoutput}->{$name}->{status} = "Command failed as expected!"; + } else { + $self->{testoutput}->{$name}->{pass} = 0; + $self->{testoutput}->{$name}->{status} = "Command failed to function at all!"; + } + ok $self->{testoutput}->{$name}->{pass} == 1, $self->{testoutput}->{$name}->{status}; + } + if ($self->{dumpoutput}) { + print "$function output:\n".Data::Dumper->Dump([$output])."\n\n"; + } + return $output; + } + + sub run_tests { + my($self) = @_; + ok(system("curl -h > /dev/null 2>&1") == 0, "curl is installed"); + ok(system("curl $url > /dev/null 2>&1") == 0, "$url is reachable"); + $self->{completetestcount} += 2; + + #Clearing out previous test results + my $output = $self->test_harness("ls",{ + paths => ["/".$self->{usertwo}], + },"Initial listing of all workspaces owned by ".$self->{usertwo},[],0,undef,2); + if (defined($output->{"/".$self->{usertwo}})) { + my $hash = {}; + for (my $i=0; $i < @{$output->{"/".$self->{usertwo}}}; $i++) { + my $item = $output->{"/".$self->{usertwo}}->[$i]; + if ($item->[2].$item->[0] eq "/".$self->{usertwo}."/TestWorkspace") { + my $output = $self->test_harness("delete",{ + objects => ["/".$self->{usertwo}."/TestWorkspace"], + force => 1, + deleteDirectories => 1, + adminmode => 1 + },"Deleting TestWorkspace ".$self->{usertwo},[],0,undef,2); + } + } + } + + $output = $self->test_harness("ls",{ + paths => ["/".$self->{user}], + },"Initial listing of all workspaces owned by ".$self->{user},[],0,undef,1); + if (defined($output->{"/".$self->{user}})) { + my $hash = {}; + for (my $i=0; $i < @{$output->{"/".$self->{user}}}; $i++) { + my $item = $output->{"/".$self->{user}}->[$i]; + if ($item->[2].$item->[0] eq "/".$self->{user}."/TestWorkspace") { + my $output = $self->test_harness("delete",{ + objects => ["/".$self->{user}."/TestWorkspace"], + force => 1, + deleteDirectories => 1, + adminmode => 1 + },"Deleting TestWorkspace of ".$self->{user},[],0,undef,1); + } elsif ($item->[2].$item->[0] eq "/".$self->{user}."/TestAdminWorkspace") { + my $output = $self->test_harness("delete",{ + objects => ["/".$self->{user}."/TestAdminWorkspace"], + force => 1, + deleteDirectories => 1, + adminmode => 1 + },"Deleting TestAdminWorkspace of ".$self->{user},[],0,undef,2); + } + } + } + + #Creating a private workspace as "$testuserone" + $output = $self->test_harness("create",{ + objects => [["/".$self->{user}."/TestWorkspace","folder",{description => "My first workspace!"},undef]], + permission => "n" + },"Creating top level TestWorkspace directory for ".$self->{user},[],0,undef,1); + #user = reviewer + #usertwo = chenry + + #Creating a public workspace as "$testusertwo" + $output = $self->test_harness("create",{ + objects => [["/".$self->{usertwo}."/TestWorkspace","folder",{description => "My first workspace!"},undef]], + permission => "r" + },"Creating top level TestWorkspace directory for ".$self->{usertwo},[],0,undef,2); + + #Testing testusertwo acting as an adminitrator + $output = $self->test_harness("create",{ + objects => [["/".$self->{user}."/TestAdminWorkspace","folder",{description => "My first admin workspace!"},undef,0]], + permission => "r", + adminmode => 1, + setowner => $self->{user} + },"Creating top level TestAdminWorkspace for ".$self->{user}." as ".$self->{usertwo}." as admin",[],0,undef,2); + + #Attempting to make a workspace for another user + $output = $self->test_harness("create",{ + objects => [["/".$self->{user}."/TestWorkspaceTwo","folder",{description => "My second workspace!"},undef]], + permission => "r" + },"Creating top level directory TestWorkspaceTwo for ".$self->{user}." as ".$self->{usertwo}." should fail",[],1,undef,2); + + #Listing workspaces as user one + $output = $self->test_harness("ls",{ + paths => ["/".$self->{user}] + },"Using ls function as user one",["\$output->{\"/".$self->{user}."\"}->[0]->[5] eq ".$self->{user}],0,undef,1); + + #Listing workspaces as user two + $output = $self->test_harness("ls",{ + paths => ["/".$self->{usertwo}] + },"Using ls function as user two",["\$output->{\"/".$self->{usertwo}."\"}->[0]->[5] eq \"".$self->{usertwo}."\""],0,undef,2); + + #Getting workspace metadata + $output = $self->test_harness("get",{ + metadata_only => 1, + objects => ["/".$self->{usertwo}."/TestWorkspace"] + },"Using get function to retrieve TestWorkspace metadata only",[["defined(\$output->[0]->[0])","Metadata for object contained in output"]],0,undef,2); + + #Saving an object + $output = $self->test_harness("create",{ + objects => [["/".$self->{user}."/TestWorkspace/testdir/testdir2/testdir3/testobj","genome",{"Description" => "My first object!"},{ + id => "83333.1", + scientific_name => "Escherichia coli", + domain => "Bacteria", + dna_size => 4000000, + num_contigs => 1, + gc_content => 0.5, + taxonomy => "Bacteria", + features => [{}] + }]] + },"Creating a genome object",[ + ["defined(\$output->[0])","Getting metadata for created object back"], + ["\$output->[0]->[1] eq \"genome\"","Object has type genome"] + ],0,undef,1); + + #Recreating an existing folder + $output = $self->test_harness("create",{ + objects => [["/".$self->{user}."/TestWorkspace/testdir","folder",{"Description" => "My recreated folder!"},undef]] + },"Recreating new object folder",[["!defined(\$output->[0])","Recreation of existing folder returns empty array"]],0,undef,1); + + #Saving contigs + $output = $self->test_harness("create",{ + objects => [["/".$self->{user}."/TestWorkspace/testdir/testdir2/testdir3/contigs","contigs",{"Description" => "My first contigs!"},">gi|284931009|gb|CP001873.1| Mycoplasma gallisepticum str. F, complete genome + TTTTTATTATTAACCATGAGAATTGTTGATAAATCTGTGGATAACTCTAAAAAAATTCCGGATTTATAAA + AGTACATTAAAATATTTATATTTTAATGTAAATATTATATCACTTTTTCACAAAAACGTGTATTATATAT + AAGGAGTTTTGTAAATTATTTAACTATATTACTATGTAATATAGTTATTATATCAAAACAAACTAAAACA + GTAGAGCAACCTTTAAAAATTAACTAAAAACTAAATACAAATTTGTTTATAGACGAAAGTTTTTCTATTA + ATATCCCCACATTAACTCTATCAAAACCCCTATACTAAAAAAAACACACTCTGAATACATAACTTGTATG + TAAAGTTTGAGTGAAGTTAAATCGCTTTAATATTGTAACAATATTGTTTGTAAAAATATTTATTTAATAT + GAAAAAAATATTGTGATTTTTATCGGAAATATTGTGATTTTCTAATTCAGGCCAATTAAAAATATCAAAA + CTAATTACTTAAATAAAAATATCAATAAATAAATTAAAAAACTTATTAACATTTCTACTAAGAGAGTTCG + TATTTGGAAATAATATTAAAGTAATACACAATATTAAAAAAATATTATTAGTATTTAAACGATTAAGTAC + TTTTTCATTCTTTTGTCTATCTGTAAAAGACACTAGGTAAGGATTACTTTATTAACAAGATAAAGAGAAA + AGAATTTATTTTTAATAATACGATTTTAATATTTTTAAAATATTATTCAATTTACGTTGTTTTATTACCA + AAAATAGAATATTAAAACAATATTTATAAGTTAATTAAAATTAATACTTTTTAAAACAAAACAACAATAT + TATTTCAATATGGTCACAGTAGTCACAATAAAGTTGATAATATTTAAATAATATTAATTAAATATTTATT + CAAGAATTTATTATTCTTGAATAACAGCAAAAAACTTTTATAGAACTGAAGAGCATTCTTAAAAAAGAAA + AAACCTAATGCTAACGGCATCAGAACTAACTAATACGAAAATAATATTTGATTACAAGAGAAGCAAATAA + TATTGTTAAGGGATCAATATTGTAATAATATTAAAATCATATCATAGAAGGTTAATGCTTACCAGTAATA + CTACTAACAGATAGTTTAATGTAGATGTATTAATATTGTAATAATATTAAAGTCATATTGTAAAAAGTTT + ATCTTTAGCAAAAAATACTACTAAACGGAGAATTTAATATAGATATATCATTAATATTTAAATAATATTA + CTTCATAAGGAAGCAATAATAACAAATATTCTTAACTTATAAATAAGCAATATATTAATAATATGGTAAC + AATATTGTTTTAATACTACATTCGTAATAAAGCTAGTTTAAGAGAATATTAAAATAATATTGGTTTGAAA + CTGTTAAAAATTATCTTTCTTAACAATATTGCCAAATCCGATTTTGCTTTACTTCAACGGGAATAAGTTT + TTAACTAAACTTTGCACTCTAATTACTAAAATATAAAAACAAACTTAGGACTAAAAAGATTTGAAATGAT + TAGCGTAAGGCTGAGGTTTTAGTTTAAATATACAAAGTAAAGTATTTTTTATTTAAAACAAGTTTTAAAA + ATACCAAAATGATATTTTATTAATATTGTTATCTATATCAAGATTTATAATATGTTTTCTTGAGCACTTT + TTTTCAAGATTGCCTAATAATAATATATTTTTAATATTTAATTACTAGGAAAATAATATTGCGAAAATTA" + ]] + },"Saving genome contigs",[ + ["defined(\$output->[0])","Getting metadata for created object back"], + ["\$output->[0]->[1] eq \"contigs\"","Object has type contigs"] + ],0,undef,1); + + #Creating shock nodes + $output = $self->test_harness("create",{ + objects => [["/".$self->{user}."/TestWorkspace/testdir/testdir2/testdir3/shockobj","genome",{"Description" => "My first shock object!"}]], + createUploadNodes => 1 + },"Creating an upload node",[ + ["defined(\$output->[0])","Getting metadata for created object back"], + ["\$output->[0]->[1] eq \"genome\"","Object has type genome"], + ["defined(\$output->[0]->[11])","Shock URL is returned"] + + ],0,undef,1); + + #Uploading file to newly created shock node + print "Filename:".$self->{bin}."/testdata.txt\n"; + my $req = HTTP::Request::Common::POST($output->[0]->[11],Authorization => "OAuth ".$self->{token},Content_Type => 'multipart/form-data',Content => [upload => [$self->{bin}."/testdata.txt"]]); + $req->method('PUT'); + my $ua = LWP::UserAgent->new(); + my $res = $ua->request($req); + if ($self->{dumpoutput} == 1) { + print "File uploaded:\n".Data::Dumper->Dump([$res])."\n\n"; + } + + #Updating metadata + $output = $self->test_harness("update_metadata",{ + objects => [["/".$self->{user}."/TestWorkspace/testdir/testdir2/testdir3/shockobj",undef,undef,0]], + autometadata => 0, + adminmode => 1 + },"Running update metadata function",[ + ["defined(\$output->[0])","Metadata update should return metadata for updated object"] + ],0,undef,2); + + #Retrieving shock object through workspace API + $output = $self->test_harness("get",{ + objects => ["/".$self->{user}."/TestWorkspace/testdir/testdir2/testdir3/shockobj"] + },"Running get function to retreive shock object",[ + ["defined(\$output->[0])","Get function should return the object retrieved"] + ],0,undef,1); + + #Listing objects + $output = $self->test_harness("ls",{ + paths => ["/".$self->{user}."/TestWorkspace/testdir/testdir2"], + excludeDirectories => 0, + excludeObjects => 0, + recursive => 1 + },"Running ls function recursively on directory",[ + ["defined(\$output->{\"/".$self->{user}."/TestWorkspace/testdir/testdir2\"})","Returns contents of subdirectory"] + ],0,undef,1); + + $output = $self->test_harness("ls",{ + paths => ["/".$self->{user}."/TestWorkspace"], + excludeDirectories => 0, + excludeObjects => 0, + recursive => 0 + },"Running basic ls on workspace",[ + ["defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[0]) && !defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[1])","Returns contents with only one item"] + ],0,undef,1); + + $output = $self->test_harness("ls",{ + paths => ["/".$self->{user}."/TestWorkspace"], + excludeDirectories => 1, + excludeObjects => 0, + recursive => 1 + },"Running ls on workspace recursively with directories excluded",[ + ["defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[0]) && !defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[2])","Returns contents with only two items"] + ],0,undef,1); + + $output = $self->test_harness("ls",{ + paths => ["/".$self->{user}."/TestWorkspace"], + excludeDirectories => 0, + excludeObjects => 1, + recursive => 1 + },"Running ls on workspace recursively with objects excluded",[ + ["defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[2]) && !defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[3])","Returns contents with only three items"] + ],0,undef,1); + + #Listing objects hierarchically + $output = $self->test_harness("ls",{ + paths => ["/".$self->{user}."/TestWorkspace"], + excludeDirectories => 0, + excludeObjects => 0, + recursive => 1, + fullHierachicalOutput => 1 + },"Running ls on workspace with hierarchical output",[ + ["defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}) && defined(\$output->{\"/".$self->{user}."/TestWorkspace/testdir\"})","Output folders exist as keys in output structure"] + ],0,undef,1); + + #Copying workspace object + $output = $self->test_harness("copy",{ + objects => [["/".$self->{user}."/TestWorkspace/testdir","/".$self->{usertwo}."/TestWorkspace/copydir"]], + recursive => 1 + },"Copying to read only workspace fails",[],1,undef,1); + + #Changing workspace permissions + $output = $self->test_harness("copy",{ + path => "/".$self->{usertwo}."/TestWorkspace", + permissions => [[$self->{user},"w"]] + },"Resetting permissions on workspace",[],0,undef,2); + + #Listing workspace permission + $output = $self->test_harness("list_permissions",{ + objects => ["/".$self->{usertwo}."/TestWorkspace"] + },"Listing workspace permissions",[ + ["defined(\$output->{\"/".$self->{usertwo}."/TestWorkspace\"}->[0])","Workspace permissions returned"] + ],0,undef,2); + + #Copying workspace object + $output = $self->test_harness("copy",{ + objects => [["/".$self->{user}."/TestWorkspace/testdir","/".$self->{usertwo}."/TestWorkspace/copydir"]], + recursive => 1 + },"Copying object from one user workspace to another",[],0,undef,1); + + #Listing contents of workspace with copied objects + $output = $self->test_harness("ls",{ + paths => ["/".$self->{usertwo}."/TestWorkspace"], + excludeDirectories => 0, + excludeObjects => 0, + recursive => 1 + },"Listing contents of copied workspace",[ + ["defined(\$output->{\"/".$self->{usertwo}."/TestWorkspace\"}->[0])","ls on copied workspace succeeded to return output"] + ],0,undef,1); + + #Changing global workspace permissions + $output = $self->test_harness("set_permissions",{ + path => "/".$self->{user}."/TestWorkspace", + new_global_permission => "w" + },"Successfully changed global permissions!",[],0,undef,1); + + #Moving objects + $output = $self->test_harness("copy",{ + objects => [["/".$self->{usertwo}."/TestWorkspace/copydir","/".$self->{user}."/TestWorkspace/movedir"]], + recursive => 1, + move => 1 + },"Successfully ran copy to move objects!",[],0,undef,2); + + #Deleting an object + $output = $self->test_harness("delete",{ + objects => ["/".$self->{user}."/TestWorkspace/movedir/testdir2/testdir3/testobj","/".$self->{user}."/TestWorkspace/movedir/testdir2/testdir3/shockobj"] + },"Successfully deleted object!",[],0,undef,1); + + $output = $self->test_harness("delete",{ + objects => ["/".$self->{user}."/TestWorkspace/movedir/testdir2/testdir3"], + force => 1, + deleteDirectories => 1 + },"Successfully deleted folder!",[],0,undef,1); + + #Deleting a directory + $output = $self->test_harness("delete",{ + objects => ["/".$self->{user}."/TestWorkspace/movedir"], + force => 1, + deleteDirectories => 1 + },"Successfully deleted top-level directory!",[],0,undef,1); + + #Creating a directory + $output = $self->test_harness("create",{ + objects => [["/".$self->{user}."/TestWorkspace/emptydir","folder",{},undef]] + },"Successfully created a workspace directory!",[],0,undef,1); + + #Getting an object + $output = $self->test_harness("get",{ + objects => ["/".$self->{user}."/TestWorkspace/testdir/testdir2/testdir3/testobj"] + },"Successfully retrieved an object!",[ + ["defined(\$output->[0]->[1])","Object retrieved with all data"] + ],0,undef,1); + + #Getting an object by reference + $output = $self->test_harness("get",{ + objects => [$output->[0]->[0]->[4]] + },"Successfully retrieved an object by UUID!",[ + ["defined(\$output->[0]->[1])","Object retrieved with all data"] + ],0,undef,1); + + #Deleting workspaces + $output = $self->test_harness("delete",{ + objects => ["/".$self->{user}."/TestWorkspace"], + force => 1, + deleteDirectories => 1 + },"Deleting entire top level directory for ".$self->{user}."!",[],0,undef,1); + + $output = $self->test_harness("delete",{ + objects => ["/".$self->{usertwo}."/TestWorkspace"], + force => 1, + deleteDirectories => 1 + },"Deleting entire top level directory for ".$self->{usertwo}."!",[],0,undef,2); + + done_testing($self->{completetestcount}); + } +} + +{ + package Bio::P3::Workspace::WorkspaceImpl::CallContext; + + use strict; + + sub new { + my($class,$token,$method,$user) = @_; + my $self = { + token => $token, + method => $method, + user_id => $user + }; + return bless $self, $class; + } + sub user_id { + my($self) = @_; + return $self->{user_id}; + } + sub token { + my($self) = @_; + return $self->{token}; + } + sub method { + my($self) = @_; + return $self->{method}; + } + sub log_debug { + my($self,$msg) = @_; + print STDERR $msg."\n"; + } +} + +1; \ No newline at end of file diff --git a/t/client-tests/auth.t b/t/client-tests/auth.t deleted file mode 100644 index eb05aa8..0000000 --- a/t/client-tests/auth.t +++ /dev/null @@ -1,51 +0,0 @@ -use strict; -use UUID; - -use Bio::P3::Workspace::WorkspaceClient; -use Bio::P3::Workspace::WorkspaceImpl; - -# logout -!system('kbase-logout') or die $!; - -# check to see if token exists in home dir -print "check for token: ", `grep token $ENV{HOME}/.kbase_config`, "\n"; - -# create a random workspace name -my($uuid, $workspace); -UUID::generate($uuid); -UUID::unparse($uuid, $workspace); - -# create the create_workspace_params -my $create_workspace_params = { - workspace => $workspace, - permission => "a", - metadata => {'owner' => 'brettin'}, -}; - -eval { - # create an unauthenticated client - my $obj1 = Bio::P3::Workspace::WorkspaceClient->new(); - - # create a worksapace with unauthenticated client - my $output1 = $obj1->create_workspace($create_workspace_params); -}; -if ($@) { - print "unsuccessful unauthencitaed attempt to creat workspace\n"; -} - -# authenticate -!system('kbase-login', 'kbasetest', '-p', '@Suite525') or die $!; - -# check to see if token exists in home dir -print "check for token", `grep token $ENV{HOME}/.kbase_config`, "\n"; - -eval { - # create an authenticated client - my $obj2 = Bio::P3::Workspace::WorkspaceClient->new(); - - # create a workspace with authenticated client - my $output2 = $obj2->create_workspace($create_workspace_params); -}; -if ($@) { - print "unsuccessful authenticated attempt to create workspace\n"; -} diff --git a/t/client-tests/create.t b/t/client-tests/create.t deleted file mode 100644 index c18d204..0000000 --- a/t/client-tests/create.t +++ /dev/null @@ -1,122 +0,0 @@ - -use strict vars; -use Test::More; -use Test::Exception; -use Config::Simple; -use JSON; -use Data::Dumper; -use UUID; - -my($cfg, $url, ); - -if (defined $ENV{KB_DEPLOYMENT_CONFIG} && -e $ENV{KB_DEPLOYMENT_CONFIG}) { - $cfg = new Config::Simple($ENV{KB_DEPLOYMENT_CONFIG}) or - die "can not create Config object"; - pass "using $ENV{KB_DEPLOYMENT_CONFIG} for configs"; -} -else { - $cfg = new Config::Simple(syntax=>'ini'); - $cfg->param('workspace.service-host', '127.0.0.1'); - $cfg->param('workspace.service-port', '7125'); - pass "using hardcoded Config values"; -} - -$url = "http://" . $cfg->param('workspace.service-host') . - ":" . $cfg->param('workspace.service-port'); - -ok(system("curl -h > /dev/null 2>&1") == 0, "curl is installed"); -ok(system("curl $url > /dev/null 2>&1") == 0, "$url is reachable"); - -BEGIN { - use_ok( Bio::P3::Workspace::WorkspaceClient ); - use_ok( Bio::P3::Workspace::WorkspaceImpl ); -} - -# create a client -my $obj; -isa_ok ($obj = Bio::P3::Workspace::WorkspaceClient->new(), Bio::P3::Workspace::WorkspaceClient); - -# create a workspace for each permission value and then delete it -my $full_obj_path = '/' . 'brettin' . '/' . new_uuid("brettin"); -my $obj_type = 'folder'; # folder, -my $user_meta = undef; -my $obj_data = undef; - -my $object = [$full_obj_path, $obj_type, $user_meta, $obj_data]; -my $objects = [$object]; -my $perm = 'w'; -my $cun = undef; -my $dl = undef; -my $ow = undef; -my $create_params = { - objects => $objects, - permission => $perm, - createUploadNodes => $cun, - downloadLinks => $dl, - overwrite => $ow -}; -# metadata => {'owner' => 'brettin'}, -#}; - -# create a ws -ok($obj->create($create_params), "can call create"); - -# create a duplicate ws -# ok($obj->create($create_params), "can call create"); - -{ - # create a ws and check return is defined, contains arrays, and has values - my $full_obj_path = '/' . 'brettin' . '/' . new_uuid("brettin"); - my $obj_type = 'folder'; # folder, - my $user_meta = undef; - my $obj_data = undef; - - my $object = [$full_obj_path, $obj_type, $user_meta, $obj_data]; - my $objects = [$object]; - my $perm = 'w'; - my $cun = undef; - my $dl = undef; - my $ow = undef; - my $create_params = { - objects => $objects, - permission => $perm, - createUploadNodes => $cun, - downloadLinks => $dl, - overwrite => $ow - }; - - my $output; - - ok($output = $obj->create($create_params), "create workspace returns output"); - ok(ref $output->[0] eq 'ARRAY', "output is contains arrays"); - ok($output->[0]->[0], "Object meta has name " . $output->[0]->[0]); - ok($output->[0]->[1], "Object meta has type " . $output->[0]->[1]); - ok($output->[0]->[2], "Object meta has path " . $output->[0]->[2]); - ok($output->[0]->[3], "Object meta has timestamp " . $output->[0]->[3]); - ok($output->[0]->[4], "Object meta has id " . $output->[0]->[4]); - ok($output->[0]->[5], "Object meta has owner " . $output->[0]->[5]); - ok($output->[0]->[6] == 0, "Object meta has size " . $output->[0]->[6]); - ok($output->[0]->[7], "Object meta has user meta " . $output->[0]->[7]); - ok($output->[0]->[8], "Object meta has auto meta " . $output->[0]->[8]); - ok($output->[0]->[9], "Object meta has user perm " . $output->[0]->[9]); - ok($output->[0]->[10], "Object meta has global perm " . $output->[0]->[10]); - ok($output->[0]->[11] eq '', "Object meta has shock url " . $output->[0]->[11]); - - - -} -done_testing(); - - -sub new_uuid { - my $prefix = shift if @_; - - my($uuid, $string); - UUID::generate($uuid); - UUID::unparse($uuid, $string); - - my $return = $string; - $return = $prefix . '-' . $string if defined $prefix; - - return $return; -} diff --git a/t/client-tests/create_subdir.t b/t/client-tests/create_subdir.t deleted file mode 100644 index 241cfe5..0000000 --- a/t/client-tests/create_subdir.t +++ /dev/null @@ -1,101 +0,0 @@ -use strict vars; -use Test::More; -use Test::Exception; -use Config::Simple; -use JSON; -use Data::Dumper; -use UUID; - -my($cfg, $url, ); -my $username = 'brettin'; - -if (defined $ENV{KB_DEPLOYMENT_CONFIG} && -e $ENV{KB_DEPLOYMENT_CONFIG}) { - $cfg = new Config::Simple($ENV{KB_DEPLOYMENT_CONFIG}) or - die "can not create Config object"; - pass "using $ENV{KB_DEPLOYMENT_CONFIG} for configs"; -} -else { - $cfg = new Config::Simple(syntax=>'ini'); - $cfg->param('workspace.service-host', '127.0.0.1'); - $cfg->param('workspace.service-port', '7125'); - pass "using hardcoded Config values"; -} - -$url = "http://" . $cfg->param('workspace.service-host') . - ":" . $cfg->param('workspace.service-port'); - -ok(system("curl -h > /dev/null 2>&1") == 0, "curl is installed"); -ok(system("curl $url > /dev/null 2>&1") == 0, "$url is reachable"); - -BEGIN { - use_ok( Bio::P3::Workspace::WorkspaceClient ); - use_ok( Bio::P3::Workspace::WorkspaceImpl ); -} - - - -# create a client -my $obj; -isa_ok ($obj = Bio::P3::Workspace::WorkspaceClient->new(), Bio::P3::Workspace::WorkspaceClient); - - -my $perms = {'w' => 'write', 'r' => 'read', 'a' => 'admin', 'n' => 'none' }; -foreach my $perm (sort keys %$perms) { - - # create a workspace for each permission value and then delete it - my $create_workspace_params = { - workspace => new_uuid("brettin"), - permission => $perm, - metadata => {'owner' => 'brettin'}, - }; - - my $output; - ok($output = $obj->create_workspace($create_workspace_params), "can create workspace with perm=$perm"); - - # create_workspace_directory - my $path = "local_" . $perm; - - my $cwsd_params = { directory => '/' . - $username . '/' . - $create_workspace_params->{workspace} . '/' . - $path, - metadata => {'owner' => 'brettin'}, - }; - - - ok(my $dir = $obj->create_workspace_directory($cwsd_params), "can create worksapce directory using " . $cwsd_params->{WorkspacePath}); - - -} - - - - - - - - - - - - - - - - - -done_testing(); - - -sub new_uuid { - my $prefix = shift if @_; - - my($uuid, $string); - UUID::generate($uuid); - UUID::unparse($uuid, $string); - - my $return = $string; - $return = $prefix . '-' . $string if defined $prefix; - - return $return; -} diff --git a/t/client-tests/create_upload_node.t b/t/client-tests/create_upload_node.t deleted file mode 100644 index 3f44522..0000000 --- a/t/client-tests/create_upload_node.t +++ /dev/null @@ -1,95 +0,0 @@ -use strict vars; -use Test::More; -use Test::Exception; -use Config::Simple; -use UUID; - -my($cfg, $url, ); -my $username = 'brettin'; - -if (defined $ENV{KB_DEPLOYMENT_CONFIG} && -e $ENV{KB_DEPLOYMENT_CONFIG}) { - $cfg = new Config::Simple($ENV{KB_DEPLOYMENT_CONFIG}) or - die "can not create Config object"; - pass "using $ENV{KB_DEPLOYMENT_CONFIG} for configs"; -} -else { - $cfg = new Config::Simple(syntax=>'ini'); - $cfg->param('Workspace.service-host', '127.0.0.1'); - $cfg->param('Workspace.service-port', '7125'); - pass "using hardcoded Config values"; -} - -$url = "http://" . $cfg->param('Workspace.service-host') . - ":" . $cfg->param('Workspace.service-port'); - -ok(system("curl -h > /dev/null 2>&1") == 0, "curl is installed"); -ok(system("curl $url > /dev/null 2>&1") == 0, "$url is reachable"); - -BEGIN { - use_ok( Bio::P3::Workspace::WorkspaceClient ); - use_ok( Bio::P3::Workspace::WorkspaceImpl ); -} - - - -# create a client -my $obj; -isa_ok ($obj = Bio::P3::Workspace::WorkspaceClient->new(), Bio::P3::Workspace::WorkspaceClient); - - - -# create a workspace -my $perm = 'w'; -my $create_workspace_params = { - workspace => new_uuid("brettin"), - permission => $perm, - metadata => {'owner' => 'brettin'}, -}; - -ok($obj->create_workspace($create_workspace_params), "can create workspace with perm=$perm"); - - - - -# can create -my $create_upload_node_params = { objects => [["", "", "", ""]], overwrite => 1 }; - -my @v = ("/" . $username . "/" . $create_workspace_params->{workspace} . "/"); # this should be a valid ws path -my @w = ("", undef, 'my-name'); # this is the object name -my @x = ("String", 'Genome', 'Unspecified' ); # this is the object type -my @y = (undef, {}, { 'comment' => 'for testing only' }); - -for (my $n=0; $n<@v; $n++) { - for (my $o=0; $o<@w; $o++) { - for (my $p=0; $p<@x; $p++) { - for (my $q=0; $q<@y; $q++) { - $create_upload_node_params->{objects}->[0]->[0] = $v[$n], - $create_upload_node_params->{objects}->[0]->[1] = $w[$o], - $create_upload_node_params->{objects}->[0]->[2] = $x[$p], - $create_upload_node_params->{objects}->[0]->[3] = $y[$q], - ok(my $ret = $obj->create_upload_node($create_upload_node_params), - "can create_upload_node with path: $v[$n], object name: $w[$o], object type: $x[$p], metadata: $y[$q]"); - } - } - } -} - - - - -done_testing(); - - - -sub new_uuid { - my $prefix = shift if @_; - - my($uuid, $string); - UUID::generate($uuid); - UUID::unparse($uuid, $string); - - my $return = $string; - $return = $prefix . '-' . $string if defined $prefix; - - return $return; -} diff --git a/t/client-tests/fba b/t/client-tests/fba new file mode 100644 index 0000000..ad2e234 --- /dev/null +++ b/t/client-tests/fba @@ -0,0 +1 @@ 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diff --git a/t/client-tests/min.t b/t/client-tests/min.t deleted file mode 100644 index 682fcfe..0000000 --- a/t/client-tests/min.t +++ /dev/null @@ -1,51 +0,0 @@ -use strict vars; -use Test::More; -use Test::Exception; -use Config::Simple; - -my($cfg, $url, ); -my $username = 'brettin'; - -if (defined $ENV{KB_DEPLOYMENT_CONFIG} && -e $ENV{KB_DEPLOYMENT_CONFIG}) { - $cfg = new Config::Simple($ENV{KB_DEPLOYMENT_CONFIG}) or - die "can not create Config object"; - pass "using $ENV{KB_DEPLOYMENT_CONFIG} for configs"; -} -else { - $cfg = new Config::Simple(syntax=>'ini'); - $cfg->param('Workspace.service-host', '127.0.0.1'); - $cfg->param('Workspace.service-port', '7125'); - pass "using hardcoded Config values"; -} - -$url = "http://" . $cfg->param('Workspace.service-host') . - ":" . $cfg->param('Workspace.service-port'); - -ok(system("curl -h > /dev/null 2>&1") == 0, "curl is installed"); -ok(system("curl $url > /dev/null 2>&1") == 0, "$url is reachable"); - -BEGIN { - use_ok( 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+++ b/t/client-tests/test.cfg @@ -0,0 +1,8 @@ +[WorkspaceTest] +user=reviewer +password= +adminuser=chenry +adminpassword= +url=http://p3.theseed.org/services/Workspace +dumpoutput=0 +serverconfig=testserver.cfg \ No newline at end of file diff --git a/t/client-tests/testmodel b/t/client-tests/testmodel new file mode 100644 index 0000000..5bc16c2 --- /dev/null +++ b/t/client-tests/testmodel @@ -0,0 +1 @@ +{"template_ref":"/chenry/public/modelsupport/templates/GramNegative.modeltemplate||","genome_ref":"/chenry/genomes/test/.Buchnera_aphidicola/Buchnera_aphidicola.genome||","source":"PATRIC","biomasses":[{"dna":0.026,"rna":0.0655,"cofactor":0.1,"energy":41.257,"name":"GramPositiveBiomass auto 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genome."},"start_time":1432783583,"hostname":"https://p3.theseed.org/services/ProbModelSEED","elapsed_time":7,"parameters":{"template_model":null,"fulldb":"0","output_file":"TestModel","media":"/chenry/public/modelsupport/media/Complete","output_path":"/chenry/models","genome":"/chenry/genomes/test/.Buchnera_aphidicola/Buchnera_aphidicola.genome"},"job_output":"","end_time":1432783590,"id":0,"output_files":[["/chenry/models/TestModel"]]},"gapgens":[],"id":"TestModel","type":"GenomeScale","gapfillings":[]} diff --git a/t/client-tests/tests.t b/t/client-tests/tests.t new file mode 100644 index 0000000..2f6bb7d --- /dev/null +++ b/t/client-tests/tests.t @@ -0,0 +1,5 @@ +use FindBin qw($Bin); +use Bio::ModelSEED::ProbModelSEED::ProbModelSEEDTests; + +my $tester = Bio::P3::Workspace::WorkspaceTests->new($bin); +$tester->run_tests(); \ No newline at end of file diff --git a/t/client-tests/upload_to_node.t b/t/client-tests/upload_to_node.t deleted file mode 100644 index 6e86198..0000000 --- a/t/client-tests/upload_to_node.t +++ /dev/null @@ -1,130 +0,0 @@ -use strict vars; -use Test::More; -use Test::Exception; -use Config::Simple; -use UUID; -use Bio::KBase::AuthToken; -use Data::Dumper; - -my($cfg, $url, ); -my $username = 'brettin'; -my $infile = "./t/client-tests/small-contigs.fasta.gz"; - -if (defined $ENV{KB_DEPLOYMENT_CONFIG} && -e $ENV{KB_DEPLOYMENT_CONFIG}) { - $cfg = new Config::Simple($ENV{KB_DEPLOYMENT_CONFIG}) or - die "can not create Config object"; - pass "using $ENV{KB_DEPLOYMENT_CONFIG} for configs"; -} -else { - $cfg = new Config::Simple(syntax=>'ini'); - $cfg->param('Workspace.service-host', '127.0.0.1'); - $cfg->param('Workspace.service-port', '7125'); - pass "using hardcoded Config values"; -} - -# the service is reachable -$url = "http://" . $cfg->param('Workspace.service-host') . - ":" . $cfg->param('Workspace.service-port'); -ok(system("curl -h > /dev/null 2>&1") == 0, "curl is installed"); -ok(system("curl $url > /dev/null 2>&1") == 0, "$url is reachable"); - -BEGIN { - use_ok( Bio::P3::Workspace::WorkspaceClient ); - use_ok( Bio::P3::Workspace::WorkspaceImpl ); -} - - -# create a client -my $obj; -isa_ok ($obj = Bio::P3::Workspace::WorkspaceClient->new(), Bio::P3::Workspace::WorkspaceClient); - - -# create a workspace -my $perm = 'w'; -my $create_workspace_params = { - workspace => new_uuid("brettin"), - permission => $perm, - metadata => {'owner' => 'brettin'}, -}; -ok($obj->create_workspace($create_workspace_params), - "can create workspace with parameters\n" . - Dumper $create_workspace_params ); - - -# can create -my $create_upload_node_params = { objects => [[]], overwrite => 1 }; -my $path = '/brettin/' . $create_workspace_params->{workspace} . '/'; -my $obj_name = $infile; -my $obj_type = 'Contigs'; -my %metadata = {owner => 'brettin', testonly => 1}; -my $rnodes; -$create_upload_node_params->{objects}->[0]->[0] = $path, -$create_upload_node_params->{objects}->[0]->[1] = $obj_name, -$create_upload_node_params->{objects}->[0]->[2] = $obj_type, -$create_upload_node_params->{objects}->[0]->[3] = \%metadata, - - -ok($rnodes = $obj->create_upload_node($create_upload_node_params), - "can create_upload_node with params\n" . - Dumper $create_upload_node_params . "\n" . - "and return is\n" . - Dumper $rnodes ); - - -# can put data to created node -my $auth_header; -ok(my $tok = Bio::KBase::AuthToken->new(), "can create token object"); -$auth_header = "-H 'Authorization: OAuth $tok->{token}'" if $tok->{token}; -my $cmd = "curl -s $auth_header -X PUT -F upload=\@$infile $rnodes->[0] > /dev/null"; -ok(system($cmd) == 0, "can put data to shock node at\n $rnodes->[0]"); -# print $cmd; - - -# can see the data in the workspace -my $list_workspace_params = { - directory => '/brettin/' . $create_workspace_params->{workspace} . '/', - includeSubDirectories => 1, - excludeObjects => 0, - Recursive => 1 -}; - -my $output; -ok($output = $obj->list_workspace_contents($list_workspace_params), "can call list_workspace_contents"); -print Dumper $output; -undef $output; - -# can get data -my $ret; -my $get_objects_params = { - objects => [[$path, $obj_name]], - metadata_only => 1 -}; -ok($ret = $obj->get_objects($get_objects_params), "can call get_objects for metadata"); -ok (ref $ret->[0]->{info} eq "ARRAY", "get_objects return info is array ref"); -print Dumper $ret; - - -$get_objects_params->{metadata_only} = 0; -ok($ret = $obj->get_objects($get_objects_params), "can call get_objects for data"); -ok (exists $ret->[0]->{data} , "data exists in get_objects return"); -ok (defined $ret->[0]->{data} , "data defined in get_objects return"); -# print Dumper $ret; - - -# done testing -done_testing(); - - -# helper routines -sub new_uuid { - my $prefix = shift if @_; - - my($uuid, $string); - UUID::generate($uuid); - UUID::unparse($uuid, $string); - - my $return = $string; - $return = $prefix . '-' . $string if defined $prefix; - - return $return; -} diff --git a/t/client-tests/workspace-full-api-test.t b/t/client-tests/workspace-full-api-test.t deleted file mode 100644 index 1598c07..0000000 --- a/t/client-tests/workspace-full-api-test.t +++ /dev/null @@ -1,411 +0,0 @@ -use FindBin qw($Bin); -use Test::More; -use Config::Simple; -use JSON; -use Data::Dumper; -use Bio::P3::Workspace::WorkspaceClient; -use Bio::KBase::AuthToken; -use File::Path; -use REST::Client; -use LWP::UserAgent; -use JSON::XS; -use HTTP::Request::Common; -my $test_count = 39; - -BEGIN { - use_ok( Bio::P3::Workspace::WorkspaceClient ); -} - -if (!defined($ENV{P3WORKSPACEURL})) { - $ENV{P3WORKSPACEURL} = "http://p3.theseed.org/services/Workspace"; -} -my $url = $ENV{P3WORKSPACEURL}; - -ok(system("curl -h > /dev/null 2>&1") == 0, "curl is installed"); -ok(system("curl $url > /dev/null 2>&1") == 0, "$url is reachable"); - -my $testuserone = "reviewer"; -my $testusertwo = "chenry"; -my $tokenObj = Bio::KBase::AuthToken->new( - user_id => $testuserone, password => 'reviewer',ignore_authrc => 1 -); - -my $wsone; -isa_ok ($wsone = Bio::P3::Workspace::WorkspaceClient->new($url,user_id => 'reviewer', password => 'reviewer'), Bio::P3::Workspace::WorkspaceClient); - -my $wstwo; -isa_ok ($wstwo = Bio::P3::Workspace::WorkspaceClient->new($url,token => "un=chenry|tokenid=03B0C858-7A70-11E4-9DE6-FDA042A49C03|expiry=1449094224|client_id=chenry|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|sig=085255b952c8db3ddd7e051ac4a729f719f22e531ddbc0a3edd86a895da851faa93249a7347c75324dc025b977e9ac7c4e02fb4c966ec6003ecf90d3148e35160265dbcdd235658deeed0ec4e0c030efee923fda1a55e8cc6f116bcd632fa6a576d7bf4a794554d2d914b54856e1e7ac2b071f81a8841d142123095f6af957cc"), Bio::P3::Workspace::WorkspaceClient); - -#Setting context to authenticated user one - -can_ok("Bio::P3::Workspace::WorkspaceClient", qw( - create - get - ls - copy - delete - set_permissions - list_permissions - version - ) -); - -#Clearing out previous test results -my $output = $wstwo->ls({ - paths => [""], - adminmode => 1 -}); -if (defined($output->{""})) { - my $hash = {}; - for (my $i=0; $i < @{$output->{""}}; $i++) { - my $item = $output->{""}->[$i]; - print $item->[2].$item->[0]."\n"; - $hash->{$item->[2].$item->[0]} = 1; - } - if (defined($hash->{"/chenry/TestWorkspace"})) { - $output = $wstwo->delete({ - objects => ["/chenry/TestWorkspace"], - force => 1, - deleteDirectories => 1, - adminmode => 1 - }); - } - if (defined($hash->{"/reviewer/TestWorkspace"})) { - $output = $wstwo->delete({ - objects => ["/reviewer/TestWorkspace"], - force => 1, - deleteDirectories => 1, - adminmode => 1 - }); - } - if (defined($hash->{"/reviewer/TestAdminWorkspace"})) { - $output = $wstwo->delete({ - objects => ["/reviewer/TestAdminWorkspace"], - force => 1, - deleteDirectories => 1, - adminmode => 1 - }); - } -} - -#Creating a private workspace as "$testuserone" -$output = $wsone->create({ - objects => [["/reviewer/TestWorkspace","folder",{description => "My first workspace!"},undef]], - permission => "n" -}); -ok defined($output), "Successfully created a top level directory!"; -print "create output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Creating a public workspace as "$testusertwo" -$output = $wstwo->create({ - objects => [["/chenry/TestWorkspace","folder",{description => "My first workspace!"},undef]], - permission => "r" -}); -ok defined($output), "Successfully created a top level directory!"; -print "create output:\n".Data::Dumper->Dump($output)."\n\n"; -#Testing testusertwo acting as an adminitrator -$output = $wstwo->create({ - objects => [["/reviewer/TestAdminWorkspace","folder",{description => "My first admin workspace!"},undef,0]], - permission => "r", - adminmode => 1, - setowner => "reviewer" -}); -ok defined($output), "Successfully created a top level directory!"; -print "create output:\n".Data::Dumper->Dump($output)."\n\n"; -#Attempting to make a workspace for another user -$output = undef; -eval { - $output = $wstwo->create({ - objects => [["/reviewer/TestWorkspace","folder",{description => "My second workspace!"},undef]], - permission => "r" - }); -}; -ok !defined($output), "Creating a top level directory for another user should fail!"; -#Getting workspace metadata -$output = $wstwo->get({ - metadata_only => 1, - objects => ["/chenry/TestWorkspace"] -}); -ok defined($output), "Successfully ran get function to retrieve workspace metadata!"; -print "get output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Listing workspaces as "$testusertwo" -$output = $wstwo->ls({ - paths => [""] -}); -ok defined($output->{""}->[0]), "Successfully ran ls function on got one workspace back!"; -print "list_workspaces output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Listing workspaces as "$testuserone" -$output = $wsone->ls({ - paths => [""] -}); -ok defined($output->{""}->[2]), "Successfully ran ls function on got three workspaces back!"; -print "ls output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Listing workspaces as "$testuserone" but restricting to owned only -$output = $wsone->ls({ - paths => ["/$testuserone/"] -}); -ok defined($output->{"/$testuserone/"}->[1]) && !defined($output->{"/$testuserone/"}->[2]), "Successfully ran ls function and got two workspaces back!"; -print "list_workspaces output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Saving an object -$output = $wsone->create({ - objects => [["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/testobj","genome",{"Description" => "My first object!"},{ - id => "83333.1", - scientific_name => "Escherichia coli", - domain => "Bacteria", - dna_size => 4000000, - num_contigs => 1, - gc_content => 0.5, - taxonomy => "Bacteria", - features => [{}] - }]] -}); -ok defined($output->[0]), "Successfully ran save_objects action!"; -print "save_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Recreating an existing folder -$output = $wsone->create({ - objects => [["/$testuserone/TestWorkspace/testdir","folder",{"Description" => "My recreated folder!"},undef]] -}); -ok !defined($output->[0]), "Successfully recreated workspace folder with no errors!"; - -#Saving contigs -$output = $wsone->create({ - objects => [["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/contigs","contigs",{"Description" => "My first contigs!"},">gi|284931009|gb|CP001873.1| Mycoplasma gallisepticum str. F, complete genome -TTTTTATTATTAACCATGAGAATTGTTGATAAATCTGTGGATAACTCTAAAAAAATTCCGGATTTATAAA -AGTACATTAAAATATTTATATTTTAATGTAAATATTATATCACTTTTTCACAAAAACGTGTATTATATAT -AAGGAGTTTTGTAAATTATTTAACTATATTACTATGTAATATAGTTATTATATCAAAACAAACTAAAACA -GTAGAGCAACCTTTAAAAATTAACTAAAAACTAAATACAAATTTGTTTATAGACGAAAGTTTTTCTATTA -ATATCCCCACATTAACTCTATCAAAACCCCTATACTAAAAAAAACACACTCTGAATACATAACTTGTATG -TAAAGTTTGAGTGAAGTTAAATCGCTTTAATATTGTAACAATATTGTTTGTAAAAATATTTATTTAATAT -GAAAAAAATATTGTGATTTTTATCGGAAATATTGTGATTTTCTAATTCAGGCCAATTAAAAATATCAAAA -CTAATTACTTAAATAAAAATATCAATAAATAAATTAAAAAACTTATTAACATTTCTACTAAGAGAGTTCG -TATTTGGAAATAATATTAAAGTAATACACAATATTAAAAAAATATTATTAGTATTTAAACGATTAAGTAC -TTTTTCATTCTTTTGTCTATCTGTAAAAGACACTAGGTAAGGATTACTTTATTAACAAGATAAAGAGAAA -AGAATTTATTTTTAATAATACGATTTTAATATTTTTAAAATATTATTCAATTTACGTTGTTTTATTACCA -AAAATAGAATATTAAAACAATATTTATAAGTTAATTAAAATTAATACTTTTTAAAACAAAACAACAATAT -TATTTCAATATGGTCACAGTAGTCACAATAAAGTTGATAATATTTAAATAATATTAATTAAATATTTATT -CAAGAATTTATTATTCTTGAATAACAGCAAAAAACTTTTATAGAACTGAAGAGCATTCTTAAAAAAGAAA -AAACCTAATGCTAACGGCATCAGAACTAACTAATACGAAAATAATATTTGATTACAAGAGAAGCAAATAA -TATTGTTAAGGGATCAATATTGTAATAATATTAAAATCATATCATAGAAGGTTAATGCTTACCAGTAATA -CTACTAACAGATAGTTTAATGTAGATGTATTAATATTGTAATAATATTAAAGTCATATTGTAAAAAGTTT -ATCTTTAGCAAAAAATACTACTAAACGGAGAATTTAATATAGATATATCATTAATATTTAAATAATATTA -CTTCATAAGGAAGCAATAATAACAAATATTCTTAACTTATAAATAAGCAATATATTAATAATATGGTAAC -AATATTGTTTTAATACTACATTCGTAATAAAGCTAGTTTAAGAGAATATTAAAATAATATTGGTTTGAAA -CTGTTAAAAATTATCTTTCTTAACAATATTGCCAAATCCGATTTTGCTTTACTTCAACGGGAATAAGTTT -TTAACTAAACTTTGCACTCTAATTACTAAAATATAAAAACAAACTTAGGACTAAAAAGATTTGAAATGAT -TAGCGTAAGGCTGAGGTTTTAGTTTAAATATACAAAGTAAAGTATTTTTTATTTAAAACAAGTTTTAAAA -ATACCAAAATGATATTTTATTAATATTGTTATCTATATCAAGATTTATAATATGTTTTCTTGAGCACTTT -TTTTCAAGATTGCCTAATAATAATATATTTTTAATATTTAATTACTAGGAAAATAATATTGCGAAAATTA"]] -}); -ok defined($output->[0]), "Successfully ran save_objects action!"; -print "save_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Creating shock nodes -$output = $wsone->create({ - objects => [["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/shockobj","genome",{"Description" => "My first shock object!"}]], - createUploadNodes => 1 -}); -ok defined($output->[0]), "Successfully ran create_upload_node action!"; -print "create_upload_node output:\n".Data::Dumper->Dump($output)."\n\n"; -#Uploading file to newly created shock node -print "Filename:".$Bin."/testdata.txt\n"; -my $req = HTTP::Request::Common::POST($output->[0]->[11],Authorization => "OAuth ".$ctxone->{token},Content_Type => 'multipart/form-data',Content => [upload => [$Bin."/testdata.txt"]]); -$req->method('PUT'); -my $ua = LWP::UserAgent->new(); -my $res = $ua->request($req); -print "File uploaded:\n".Data::Dumper->Dump([$res])."\n\n"; - -#Updating metadata -$output = $wstwo->update_metadata({ - objects => [["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/shockobj",undef,undef,0]], - autometadata => 0, - adminmode => 1 -}); -ok defined($output->[0]), "Successfully ran update_metadata action!"; -print "update_metadata output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Retrieving shock object through workspace API -$output = $wsone->get({ - objects => ["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/shockobj"] -}); -ok defined($output->[0]), "Successfully ran get function!"; -print "get_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Listing objects -$output = $wsone->ls({ - paths => ["/$testuserone/TestWorkspace/testdir/testdir2"], - excludeDirectories => 0, - excludeObjects => 0, - recursive => 1 -}); -ok defined($output->{"/$testuserone/TestWorkspace/testdir/testdir2"}), "Successfully listed all workspace contents!"; -print "ls output:\n".Data::Dumper->Dump([$output])."\n\n"; -$output = $wsone->ls({ - paths => ["/$testuserone/TestWorkspace"], - excludeDirectories => 0, - excludeObjects => 0, - recursive => 0 -}); -ok defined($output->{"/$testuserone/TestWorkspace"}->[0]) && !defined($output->{"/$testuserone/TestWorkspace"}->[1]), "Successfuly listed workspace contents nonrecursively!"; -print "list_workspace_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; -$output = $wsone->ls({ - paths => ["/$testuserone/TestWorkspace"], - excludeDirectories => 1, - excludeObjects => 0, - recursive => 1 -}); -ok defined($output->{"/$testuserone/TestWorkspace"}->[0]) && !defined($output->{"/$testuserone/TestWorkspace"}->[2]), "Successfully listed workspace contents without directories!"; -print "list_workspace_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; -$output = $wsone->ls({ - paths => ["/$testuserone/TestWorkspace"], - excludeDirectories => 0, - excludeObjects => 1, - recursive => 1 -}); -ok defined($output->{"/$testuserone/TestWorkspace"}->[2]) && !defined($output->{"/$testuserone/TestWorkspace"}->[3]), "Successfully listed workspace contents without objects!"; -print "list_workspace_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Listing objects hierarchically -$output = $wsone->ls({ - paths => ["/$testuserone/TestWorkspace"], - excludeDirectories => 0, - excludeObjects => 0, - recursive => 1, - fullHierachicalOutput => 1 -}); -ok defined($output->{"/$testuserone/TestWorkspace"}) && defined($output->{"/$testuserone/TestWorkspace/testdir"}), "Successfully listed workspace contents hierarchically!"; -print "list_workspace_hierarchical_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Copying workspace object -$output = undef; -eval { -$output = $wsone->copy({ - objects => [["/$testuserone/TestWorkspace/testdir","/$testusertwo/TestWorkspace/copydir"]], - recursive => 1 -}); -}; -ok !defined($output), "Copying to a read only workspace fails!"; - -#Setting context to authenticated user one -$Bio::P3::Workspace::Service::CallContext = $ctxtwo; - -#Changing workspace permissions -$output = $wstwo->set_permissions({ - path => "/$testusertwo/TestWorkspace", - permissions => [[$testuserone,"w"]] -}); -ok defined($output), "Successfully ran set_workspace_permissions function!"; -print "set_workspace_permissions output:\n".Data::Dumper->Dump($output)."\n\n"; -#Listing workspace permission -$output = $wstwo->list_permissions({ - objects => ["/$testusertwo/TestWorkspace"] -}); -ok defined($output->{"/$testusertwo/TestWorkspace"}->[0]), "Successfully ran list_workspace_permissions function!"; -print "list_workspace_permissions output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Copying workspace object -$output = $wsone->copy({ - objects => [["/$testuserone/TestWorkspace/testdir","/$testusertwo/TestWorkspace/copydir"]], - recursive => 1 -}); -ok defined($output), "Successfully ran copy_objects function!"; -print "copy_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Listing contents of workspace with copied objects -$output = $wsone->ls({ - paths => ["/$testusertwo/TestWorkspace"], - excludeDirectories => 0, - excludeObjects => 0, - recursive => 1 -}); -ok defined($output->{"/$testusertwo/TestWorkspace"}->[0]), "Successfully listed workspace contents!"; -print "list_workspace_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Changing global workspace permissions -$output = $wsone->set_permissions({ - path => "/$testuserone/TestWorkspace", - new_global_permission => "w" -}); -ok defined($output), "Successfully changed global permissions!"; -print "reset_global_permission output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Setting context to authenticated user two -$Bio::P3::Workspace::Service::CallContext = $ctxtwo; - -#Moving objects -$output = $wstwo->copy({ - objects => [["/$testusertwo/TestWorkspace/copydir","/$testuserone/TestWorkspace/movedir"]], - recursive => 1, - move => 1 -}); -ok defined($output), "Successfully ran copy to move objects!"; -print "move_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Setting context to authenticated user one -$Bio::P3::Workspace::Service::CallContext = $ctxone; - -#Deleting an object -$output = $wsone->delete({ - objects => ["/$testuserone/TestWorkspace/movedir/testdir2/testdir3/testobj","/$testuserone/TestWorkspace/movedir/testdir2/testdir3/shockobj"] -}); -ok defined($output), "Successfully ran delete_objects function on object!"; -print "delete_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -$output = $wsone->delete({ - objects => ["/$testuserone/TestWorkspace/movedir/testdir2/testdir3"], - force => 1, - deleteDirectories => 1 -}); -ok defined($output), "Successfully ran delete_objects function on directory!"; -print "delete_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Deleting a directory -$output = $wsone->delete({ - objects => ["/$testuserone/TestWorkspace/movedir"], - force => 1, - deleteDirectories => 1 -}); -ok defined($output), "Successfully ran delete_workspace_directory function!"; -print "delete_workspace_directory output:\n".Data::Dumper->Dump($output)."\n\n"; -#Creating a directory -$output = $wsone->create({ - objects => [["/$testuserone/TestWorkspace/emptydir","folder",{},undef]] -}); -ok defined($output), "Successfully ran create_workspace_directory function!"; -print "create_workspace_directory output:\n".Data::Dumper->Dump($output)."\n\n"; -#Getting an object -$output = $wsone->get({ - objects => ["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/testobj"] -}); -ok defined($output->[0]->[1]), "Successfully ran get_objects function!"; -print "get_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Getting an object by reference -$output = $wsone->get({ - objects => [$output->[0]->[0]->[4]] -}); -ok defined($output->[0]->[1]), "Successfully ran get_objects_by_reference function!"; -print "get_objects_by_reference output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Deleting workspaces -$output = $wsone->delete({ - objects => ["/$testuserone/TestWorkspace"], - force => 1, - deleteDirectories => 1 -}); -ok defined($output), "Successfully ran delete_workspace function!"; -print "delete_workspace output:\n".Data::Dumper->Dump($output)."\n\n"; - -$output = $wstwo->delete({ - objects => ["/$testusertwo/TestWorkspace"], - force => 1, - deleteDirectories => 1 -}); -ok defined($output), "Successfully ran delete_workspace function!"; -print "delete_workspace output:\n".Data::Dumper->Dump($output)."\n\n"; - -done_testing($test_count); \ No newline at end of file diff --git a/t/client-tests/ws.t b/t/client-tests/ws.t deleted file mode 100644 index 363b171..0000000 --- a/t/client-tests/ws.t +++ /dev/null @@ -1,166 +0,0 @@ -use strict vars; -use Test::More; -use Test::Exception; -use Config::Simple; -use JSON; -use Data::Dumper; -use UUID; - -my($cfg, $url, ); -my $username = "brettin"; - - -if (defined $ENV{KB_DEPLOYMENT_CONFIG} && -e $ENV{KB_DEPLOYMENT_CONFIG}) { - $cfg = new Config::Simple($ENV{KB_DEPLOYMENT_CONFIG}) or - die "can not create Config object"; - pass "using $ENV{KB_DEPLOYMENT_CONFIG} for configs"; -} -else { - $cfg = new Config::Simple(syntax=>'ini'); - $cfg->param('workspace.service-host', '127.0.0.1'); - $cfg->param('workspace.service-port', '7125'); - pass "using hardcoded Config values"; -} - -$url = "http://" . $cfg->param('workspace.service-host') . - ":" . $cfg->param('workspace.service-port'); - -ok(system("curl -h > /dev/null 2>&1") == 0, "curl is installed"); -ok(system("curl $url > /dev/null 2>&1") == 0, "$url is reachable"); - -BEGIN { - use_ok( Bio::P3::Workspace::WorkspaceClient ); - use_ok( Bio::P3::Workspace::WorkspaceImpl ); -} - -can_ok("Bio::P3::Workspace::WorkspaceClient", qw( - create_workspace - save_objects - create_upload_node - get_objects - get_objects_by_reference - list_workspace_contents - list_workspace_hierarchical_contents - list_workspaces - search_for_workspaces - search_for_workspace_objects - create_workspace_directory - copy_objects - move_objects - delete_workspace - delete_objects - delete_workspace_directory - reset_global_permission - set_workspace_permissions - list_workspace_permissions - - ) -); - -# create a client -my $obj; -isa_ok ($obj = Bio::P3::Workspace::WorkspaceClient->new(), Bio::P3::Workspace::WorkspaceClient); - -# create a workspace for each permission value and then delete it -my $perms = {'w' => 'write', 'r' => 'read', 'a' => 'admin', 'n' => 'none' }; -foreach my $perm (sort keys %$perms) { - - my $create_workspace_params = { - workspace => new_uuid("$username"), - permission => $perm, - metadata => {'owner' => '$username'}, - }; - - my $output; - ok($output = $obj->create_workspace($create_workspace_params), "can create workspace with perm=$perm"); - - my $list_workspaces_params = {owned_only => 1, no_public => 1}; - ok($output = $obj->list_workspaces($list_workspaces_params), "can list owned_only, no_public workspaces perm=$perm"); - # print_wsmeta($output); - - $list_workspaces_params = {owned_only => 1, no_public => 0}; - ok($output = $obj->list_workspaces($list_workspaces_params), "can list owned_only workspaces perm=$perm"); - # print_wsmeta($output); - - $list_workspaces_params = {owned_only => 0, no_public => 1}; - ok($output = $obj->list_workspaces($list_workspaces_params), "can list no_public workspaces perm=$perm"); - # print_wsmeta($output); - - $list_workspaces_params = {owned_only => 0, no_public => 0}; - ok($output = $obj->list_workspaces($list_workspaces_params), "can list workspace perm=$perm"); - # print_wsmeta($output); - - # delete workspace - my $delete; - my $delete_workspace_params = {'workspace' => $create_workspace_params->{'workspace'}}; - ok($delete = $obj->delete_workspace($delete_workspace_params), "can delete workspace"); -} - - -# create_workspace_directory -# create a workspace for each permission value and then delete it -my $perms = {'w' => 'write', 'r' => 'read', 'a' => 'admin', 'n' => 'none' }; -foreach my $perm (sort keys %$perms) { - my $cws_params = { - workspace => new_uuid("$username"), - permission => $perm, - metadata => {'owner' => '$username'}, - }; - my $cwsd_params = { - directory => "/$username" . "/" . $cws_params->{workspace} . "/" . new_uuid("dir"), - metadata => {'owner' => '$username'}, - }; - my $delete_workspace_params = { - 'workspace' => $cws_params->{'workspace'} - }; - - ok(my $ws = $obj->create_workspace($cws_params), "can create workspace"); - ok(my $dir = $obj->create_workspace_directory($cwsd_params), "can create worksapce directory");; - ok(my $delete = $obj->delete_workspace($delete_workspace_params), "can delete workspace"); -} - - -# add an object to a workspace - - -# delete an object from a workspace - - -# delete a workspace - - - - -done_testing(); - -sub new_uuid { - my $prefix = shift if @_; - - my($uuid, $string); - UUID::generate($uuid); - UUID::unparse($uuid, $string); - - my $return = $string; - $return = $prefix . '-' . $string if defined $prefix; - - return $return; -} - - -sub print_wsmeta { - my $output = shift; - print ref($output), "\n"; - foreach my $mt (@{$output}) { - print "WorkspaceID: $mt->[0]\n"; - print "WorkspaceName: $mt->[1]\n"; - print "Username: $mt->[2]\n"; - print "timestamp: $mt->[3]\n"; - print "num_objects: $mt->[4]\n"; - print "user_permission: ", $mt->[5], "\n"; - print "global_permission: ", $mt->[6], "\n"; - print "num_directories: $mt->[7]\n"; - print "UserMetadata: $mt->[8]\n"; - } - print "\n"; -} - diff --git a/t/server-tests/fba b/t/server-tests/fba new file mode 100644 index 0000000..ad2e234 --- /dev/null +++ b/t/server-tests/fba @@ -0,0 +1 @@ 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genome."},"start_time":1432783583,"hostname":"https://p3.theseed.org/services/ProbModelSEED","elapsed_time":7,"parameters":{"template_model":null,"fulldb":"0","output_file":"TestModel","media":"/chenry/public/modelsupport/media/Complete","output_path":"/chenry/models","genome":"/chenry/genomes/test/.Buchnera_aphidicola/Buchnera_aphidicola.genome"},"job_output":"","end_time":1432783590,"id":0,"output_files":[["/chenry/models/TestModel"]]},"gapgens":[],"id":"TestModel","type":"GenomeScale","gapfillings":[]} diff --git a/t/server-tests/tests.t b/t/server-tests/tests.t new file mode 100644 index 0000000..2f6bb7d --- /dev/null +++ b/t/server-tests/tests.t @@ -0,0 +1,5 @@ +use FindBin qw($Bin); +use Bio::ModelSEED::ProbModelSEED::ProbModelSEEDTests; + +my $tester = Bio::P3::Workspace::WorkspaceTests->new($bin); +$tester->run_tests(); \ No newline at end of file diff --git a/t/server-tests/testserver.cfg b/t/server-tests/testserver.cfg new file mode 100644 index 0000000..2a1f914 --- /dev/null +++ b/t/server-tests/testserver.cfg @@ -0,0 +1,27 @@ +[auth] +globus-token-url = http://rast.nmpdr.org/goauth/token?grant_type=client_credentials +globus-profile-url = http://rast.nmpdr.org/users + +[Workspace] + +# these are compile time configs used by auto-deploy +service-url = http://p3.theseed.org/services/Workspace +service-host = localhost +service-port = 7125 + +# these are runtime configs used by the service impl +shock-url = http://p3.theseed.org/services/shock_api +#shock-url = http://140.221.85.54:7445 +#db-path = /disks/p3/workspace +db-path = /Users/chenry/P3WSDB/ +mongodb-database = WorkspaceBuild +mongodb-host = localhost +mongodb-user = null +mongodb-pwd = null +wsuser = reviewer +wspassword = reviewer +adminlist = chenry +update-interval = 1800 +job-directory = /Users/chenry/temp/wsjobs/ +script-path = /Users/chenry/code/Workspace/internal-scripts/ +types-file = /Users/chenry/code/Workspace/typeslist.txt \ No newline at end of file diff --git a/t/server-tests/workspace-test.t b/t/server-tests/workspace-test.t deleted file mode 100644 index 5aa46b4..0000000 --- a/t/server-tests/workspace-test.t +++ /dev/null @@ -1,547 +0,0 @@ -use FindBin qw($Bin); -use Test::More; -use Config::Simple; -use JSON; -use Data::Dumper; -use Bio::P3::Workspace::WorkspaceImpl; -use Bio::KBase::AuthToken; -use File::Path; -use REST::Client; -use LWP::UserAgent; -use JSON::XS; -use HTTP::Request::Common; -my $test_count = 39; - -BEGIN { - use_ok( Bio::P3::Workspace::WorkspaceImpl ); -} - -#if (!defined $ENV{KB_DEPLOYMENT_CONFIG} || !-e $ENV{KB_DEPLOYMENT_CONFIG}) { - $ENV{KB_DEPLOYMENT_CONFIG}=$Bin."/../../configs/test.cfg"; -#} -print "Loading server with this config: ".$ENV{KB_DEPLOYMENT_CONFIG}."\n"; - -my $testuserone = "reviewer"; -my $tokenObj = Bio::KBase::AuthToken->new( - user_id => $testuserone, password => 'reviewer',ignore_authrc => 1 -); -my $testusertwo = "chenry"; -#Setting context to authenticated user one -$Bio::P3::Workspace::Service::CallContext = undef; -setcontext(2); -my $ws = Bio::P3::Workspace::WorkspaceImpl->new(); - -#Clearing out previous test results -my $output = $ws->ls({ - paths => [""], - adminmode => 1 -}); -if (defined($output->{""})) { - my $hash = {}; - for (my $i=0; $i < @{$output->{""}}; $i++) { - my $item = $output->{""}->[$i]; - print $item->[2].$item->[0]."\n"; - $hash->{$item->[2].$item->[0]} = 1; - } - if (defined($hash->{"/chenry/TestWorkspace"})) { - $output = $ws->delete({ - objects => ["/chenry/TestWorkspace"], - force => 1, - deleteDirectories => 1, - adminmode => 1 - }); - } - if (defined($hash->{"/reviewer/TestWorkspace"})) { - $output = $ws->delete({ - objects => ["/reviewer/TestWorkspace"], - force => 1, - deleteDirectories => 1, - adminmode => 1 - }); - } - if (defined($hash->{"/reviewer/TestAdminWorkspace"})) { - $output = $ws->delete({ - objects => ["/reviewer/TestAdminWorkspace"], - force => 1, - deleteDirectories => 1, - adminmode => 1 - }); - } -} - -#Setting context to authenticated user one -can_ok("Bio::P3::Workspace::WorkspaceImpl", qw( - create - get - ls - copy - delete - set_permissions - list_permissions - version - ) -); - -#Creating a private workspace as "$testuserone" -setcontext(1); -my $output = $ws->create({ - objects => [["/reviewer/TestWorkspace","folder",{description => "My first workspace!"},undef]], - permission => "n" -}); -ok defined($output), "Successfully created a top level directory!"; -print "create output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Creating a public workspace as "$testusertwo" -setcontext(2); -$output = $ws->create({ - objects => [["/chenry/TestWorkspace","folder",{description => "My first workspace!"},undef]], - permission => "r" -}); -ok defined($output), "Successfully created a top level directory!"; -print "create output:\n".Data::Dumper->Dump($output)."\n\n"; -#Testing testusertwo acting as an adminitrator -setcontext(2); -$output = $ws->create({ - objects => [["/reviewer/TestAdminWorkspace","folder",{description => "My first admin workspace!"},undef,0]], - permission => "r", - adminmode => 1, - setowner => "reviewer" -}); -ok defined($output), "Successfully created a top level directory!"; -print "create output:\n".Data::Dumper->Dump($output)."\n\n"; -#Attempting to make a workspace for another user -setcontext(2); -$output = undef; -eval { - print Data::Dumper->Dump([$Bio::P3::Workspace::Service::CallContext])."\n"; - $output = $ws->create({ - objects => [["/reviewer/OtherTestWorkspace","folder",{description => "My second workspace!"},undef]], - permission => "r" - }); -}; -ok !defined($output), "Creating a top level directory for another user should fail!"; -#Getting workspace metadata -setcontext(2); -$output = $ws->get({ - metadata_only => 1, - objects => ["/chenry/TestWorkspace"] -}); -ok defined($output), "Successfully ran get function to retrieve workspace metadata!"; -print "get output:\n".Data::Dumper->Dump($output)."\n\n"; -#Listing workspaces as "$testusertwo" -setcontext(2); -$output = $ws->ls({ - paths => [""] -}); -delete $ctxtwo->{_wscache}; -delete $ctxone->{_wscache}; -ok defined($output->{""}->[0]) && !defined($output->{""}->[2]), "Successfully ran ls function on got one workspace back!"; -print "list_workspaces output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Listing workspaces as "$testuserone" -setcontext(1); -$output = $ws->ls({ - paths => [""] -}); -ok defined($output->{""}->[2]), "Successfully ran ls function on got three workspaces back!"; -print "ls output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Listing workspaces as "$testuserone" but restricting to owned only -setcontext(1); -$output = $ws->ls({ - paths => ["/$testuserone/"] -}); -ok defined($output->{"/$testuserone/"}->[1]) && !defined($output->{"/$testuserone/"}->[2]), "Successfully ran ls function and got two workspace back!"; -print "list_workspaces output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Saving an object -open ( my $fh, "<", $Bin."/testmodel"); -my $data = ""; -while (my $line = <$fh>) { - $data .= $line; -} -close($fh); -setcontext(1); -$output = $ws->create({ - objects => [["/$testuserone/TestWorkspace/models/testmodel","model",{"Description" => "My first object!"},$data]] -}); -ok defined($output->[0]), "Successfully ran save_objects action!"; -print "save_objects output:\n".Data::Dumper->Dump($output)."\n\n"; -open ( my $fh, "<", $Bin."/fba"); -$data = ""; -while (my $line = <$fh>) { - $data .= $line; -} -close($fh); -sleep(10); -$output = $ws->ls({ - paths => ["/$testuserone/TestWorkspace/models/"] -}); -print "ls of uploaded objects:\n".Data::Dumper->Dump($output->{"/$testuserone/TestWorkspace/models/"})."\n\n"; -exit; -setcontext(1); -$output = $ws->create({ - objects => [["/$testuserone/TestWorkspace/models/fba","fba",{"Description" => "My first object!"},$data]] -}); -ok defined($output->[0]), "Successfully ran save_objects action!"; -print "save_objects output:\n".Data::Dumper->Dump($output)."\n\n"; -open ( my $fh, "<", $Bin."/gf"); -$data = ""; -while (my $line = <$fh>) { - $data .= $line; -} -close($fh); -setcontext(1); -$output = $ws->create({ - objects => [["/$testuserone/TestWorkspace/models/gf","fba",{"Description" => "My first object!"},$data]] -}); -ok defined($output->[0]), "Successfully ran save_objects action!"; -print "save_objects output:\n".Data::Dumper->Dump($output)."\n\n"; -#Testing overwrite -setcontext(1); -$output = $ws->create({ - objects => [["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/testobj","genome",{"Description" => "My first object!"},{ - id => "83333.1", - scientific_name => "Escherichia coli", - domain => "Bacteria", - dna_size => 4000000, - num_contigs => 1, - gc_content => 0.5, - taxonomy => "Bacteria", - features => [{}] - }]], - overwrite => 1 -}); -ok defined($output->[0]), "Successfully ran save_objects action!"; -print "save_objects output:\n".Data::Dumper->Dump($output)."\n\n"; -#Testing overwrite -setcontext(1); -$output = $ws->create({ - objects => [["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/testobj","genome",{"Description" => "My first object!"},{ - id => "83333.1", - scientific_name => "Escherichia coli", - domain => "Bacteria", - dna_size => 4000000, - num_contigs => 1, - gc_content => 0.5, - taxonomy => "Bacteria", - features => [{}] - }]], - overwrite => 1 -}); -ok defined($output->[0]), "Successfully ran save_objects action!"; -print "save_objects output:\n".Data::Dumper->Dump($output)."\n\n"; -#Listing workspaces as "$testuserone" but restricting to owned only -setcontext(1); -$output = $ws->ls({ - paths => ["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/"] -}); -ok defined($output->{"/$testuserone/TestWorkspace/testdir/testdir2/testdir3/"}->[0]) && !defined($output->{"/$testuserone/TestWorkspace/testdir/testdir2/testdir3/"}->[1]), "Successfully ran ls function and got two workspace back!"; -print "list_workspaces output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Recreating an existing folder -setcontext(1); -$output = $ws->create({ - objects => [["/$testuserone/TestWorkspace/testdir","folder",{"Description" => "My recreated folder!"},undef]] -}); -ok !defined($output->[0]), "Successfully ran save_objects action!"; - -#Saving contigs -setcontext(1); -$output = $ws->create({ - objects => [["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/contigs","contigs",{"Description" => "My first contigs!"},">gi|284931009|gb|CP001873.1| Mycoplasma gallisepticum str. F, complete genome -TTTTTATTATTAACCATGAGAATTGTTGATAAATCTGTGGATAACTCTAAAAAAATTCCGGATTTATAAA -AGTACATTAAAATATTTATATTTTAATGTAAATATTATATCACTTTTTCACAAAAACGTGTATTATATAT -AAGGAGTTTTGTAAATTATTTAACTATATTACTATGTAATATAGTTATTATATCAAAACAAACTAAAACA -GTAGAGCAACCTTTAAAAATTAACTAAAAACTAAATACAAATTTGTTTATAGACGAAAGTTTTTCTATTA -ATATCCCCACATTAACTCTATCAAAACCCCTATACTAAAAAAAACACACTCTGAATACATAACTTGTATG -TAAAGTTTGAGTGAAGTTAAATCGCTTTAATATTGTAACAATATTGTTTGTAAAAATATTTATTTAATAT -GAAAAAAATATTGTGATTTTTATCGGAAATATTGTGATTTTCTAATTCAGGCCAATTAAAAATATCAAAA -CTAATTACTTAAATAAAAATATCAATAAATAAATTAAAAAACTTATTAACATTTCTACTAAGAGAGTTCG -TATTTGGAAATAATATTAAAGTAATACACAATATTAAAAAAATATTATTAGTATTTAAACGATTAAGTAC -TTTTTCATTCTTTTGTCTATCTGTAAAAGACACTAGGTAAGGATTACTTTATTAACAAGATAAAGAGAAA -AGAATTTATTTTTAATAATACGATTTTAATATTTTTAAAATATTATTCAATTTACGTTGTTTTATTACCA -AAAATAGAATATTAAAACAATATTTATAAGTTAATTAAAATTAATACTTTTTAAAACAAAACAACAATAT -TATTTCAATATGGTCACAGTAGTCACAATAAAGTTGATAATATTTAAATAATATTAATTAAATATTTATT -CAAGAATTTATTATTCTTGAATAACAGCAAAAAACTTTTATAGAACTGAAGAGCATTCTTAAAAAAGAAA -AAACCTAATGCTAACGGCATCAGAACTAACTAATACGAAAATAATATTTGATTACAAGAGAAGCAAATAA -TATTGTTAAGGGATCAATATTGTAATAATATTAAAATCATATCATAGAAGGTTAATGCTTACCAGTAATA -CTACTAACAGATAGTTTAATGTAGATGTATTAATATTGTAATAATATTAAAGTCATATTGTAAAAAGTTT -ATCTTTAGCAAAAAATACTACTAAACGGAGAATTTAATATAGATATATCATTAATATTTAAATAATATTA -CTTCATAAGGAAGCAATAATAACAAATATTCTTAACTTATAAATAAGCAATATATTAATAATATGGTAAC -AATATTGTTTTAATACTACATTCGTAATAAAGCTAGTTTAAGAGAATATTAAAATAATATTGGTTTGAAA -CTGTTAAAAATTATCTTTCTTAACAATATTGCCAAATCCGATTTTGCTTTACTTCAACGGGAATAAGTTT -TTAACTAAACTTTGCACTCTAATTACTAAAATATAAAAACAAACTTAGGACTAAAAAGATTTGAAATGAT -TAGCGTAAGGCTGAGGTTTTAGTTTAAATATACAAAGTAAAGTATTTTTTATTTAAAACAAGTTTTAAAA -ATACCAAAATGATATTTTATTAATATTGTTATCTATATCAAGATTTATAATATGTTTTCTTGAGCACTTT -TTTTCAAGATTGCCTAATAATAATATATTTTTAATATTTAATTACTAGGAAAATAATATTGCGAAAATTA"]] -}); -ok defined($output->[0]), "Successfully ran save_objects action!"; -print "save_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Querying multiple objects -$output = $ws->ls({ - paths => ["/$testuserone/TestWorkspace/"], - query => {type => ["genome","contigs"]}, - recursive => 1 -}); -ok defined($output->{"/$testuserone/TestWorkspace/"}->[0]), "Successfully ran ls with multiple types!"; -print "ls output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Creating shock nodes -setcontext(1); -$output = $ws->create({ - objects => [["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/shockobj","genome",{"Description" => "My first shock object!"}]], - createUploadNodes => 1 -}); -ok defined($output->[0]), "Successfully ran create_upload_node action!"; -print "create_upload_node output:\n".Data::Dumper->Dump($output)."\n\n"; -#Uploading file to newly created shock node -print "Filename:".$Bin."/testdata.txt\n"; -my $req = HTTP::Request::Common::POST($output->[0]->[11],Authorization => "OAuth ".$ctxone->{token},Content_Type => 'multipart/form-data',Content => [upload => [$Bin."/testdata.txt"]]); -$req->method('PUT'); -my $ua = LWP::UserAgent->new(); -my $res = $ua->request($req); -print "File uploaded:\n".Data::Dumper->Dump([$res])."\n\n"; -$output = $ws->update_auto_meta({objects => ["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/shockobj"]}); -print "update_auto_meta output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Updating metadata -setcontext(2); -$output = $ws->update_metadata({ - objects => [["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/shockobj",undef,undef,0]], - autometadata => 0, - adminmode => 1 -}); -ok defined($output->[0]), "Successfully ran update_metadata action!"; -print "update_metadata output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Retrieving shock object through workspace API -setcontext(1); -$output = $ws->get({ - objects => ["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/shockobj"] -}); -ok defined($output->[0]), "Successfully ran get function!"; -print "get_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Listing objects -setcontext(1); -$output = $ws->ls({ - paths => ["/$testuserone/TestWorkspace/testdir/testdir2"], - excludeDirectories => 0, - excludeObjects => 0, - recursive => 1 -}); -ok defined($output->{"/$testuserone/TestWorkspace/testdir/testdir2"}), "Successfully listed all workspace contents!"; -print "ls output:\n".Data::Dumper->Dump([$output])."\n\n"; -setcontext(1); -$output = $ws->ls({ - paths => ["/$testuserone/TestWorkspace"], - excludeDirectories => 0, - excludeObjects => 0, - recursive => 0 -}); -ok defined($output->{"/$testuserone/TestWorkspace"}->[0]) && !defined($output->{"/$testuserone/TestWorkspace"}->[1]), "Successfuly listed workspace contents nonrecursively!"; -print "list_workspace_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; -setcontext(1); -$output = $ws->ls({ - paths => ["/$testuserone/TestWorkspace"], - excludeDirectories => 1, - excludeObjects => 0, - recursive => 1 -}); -ok defined($output->{"/$testuserone/TestWorkspace"}->[0]) && !defined($output->{"/$testuserone/TestWorkspace"}->[3]), "Successfully listed workspace contents without directories!"; -print "list_workspace_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; -setcontext(1); -$output = $ws->ls({ - paths => ["/$testuserone/TestWorkspace"], - excludeDirectories => 0, - excludeObjects => 1, - recursive => 1 -}); -ok defined($output->{"/$testuserone/TestWorkspace"}->[2]) && !defined($output->{"/$testuserone/TestWorkspace"}->[3]), "Successfully listed workspace contents without objects!"; -print "list_workspace_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Listing objects hierarchically -setcontext(1); -$output = $ws->ls({ - paths => ["/$testuserone/TestWorkspace"], - excludeDirectories => 0, - excludeObjects => 0, - recursive => 1, - fullHierachicalOutput => 1 -}); -ok defined($output->{"/$testuserone/TestWorkspace"}) && defined($output->{"/$testuserone/TestWorkspace/testdir"}), "Successfully listed workspace contents hierarchically!"; -print "list_workspace_hierarchical_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Copying workspace object -setcontext(1); -$output = undef; -eval { -$output = $ws->copy({ - objects => [["/$testuserone/TestWorkspace/testdir","/$testusertwo/TestWorkspace/copydir"]], - recursive => 1 -}); -}; -ok !defined($output), "Copying to a read only workspace fails!"; - -#Changing workspace permissions -setcontext(2); -$output = $ws->set_permissions({ - path => "/$testusertwo/TestWorkspace", - permissions => [[$testuserone,"w"]] -}); -ok defined($output), "Successfully ran set_workspace_permissions function!"; -print "set_workspace_permissions output:\n".Data::Dumper->Dump($output)."\n\n"; -#Listing workspace permission -setcontext(2); -$output = $ws->list_permissions({ - objects => ["/$testusertwo/TestWorkspace"] -}); -ok defined($output->{"/$testusertwo/TestWorkspace"}->[0]), "Successfully ran list_workspace_permissions function!"; -print "list_workspace_permissions output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Copying workspace object -setcontext(1); -$output = $ws->copy({ - objects => [["/$testuserone/TestWorkspace/testdir","/$testusertwo/TestWorkspace/copydir"]], - recursive => 1 -}); -ok defined($output), "Successfully ran copy_objects function!"; -print "copy_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Listing contents of workspace with copied objects -setcontext(1); -$output = $ws->ls({ - paths => ["/$testusertwo/TestWorkspace"], - excludeDirectories => 0, - excludeObjects => 0, - recursive => 1 -}); -ok defined($output->{"/$testusertwo/TestWorkspace"}->[0]), "Successfully listed workspace contents!"; -print "list_workspace_contents output:\n".Data::Dumper->Dump([$output])."\n\n"; - -#Changing global workspace permissions -setcontext(1); -$output = $ws->set_permissions({ - path => "/$testuserone/TestWorkspace", - new_global_permission => "w" -}); -ok defined($output), "Successfully changed global permissions!"; -print "reset_global_permission output:\n".Data::Dumper->Dump($output)."\n\n"; - - -#Moving objects -setcontext(2); -$output = $ws->copy({ - objects => [["/$testusertwo/TestWorkspace/copydir","/$testuserone/TestWorkspace/movedir"]], - recursive => 1, - move => 1 -}); -ok defined($output), "Successfully ran copy to move objects!"; -print "move_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Deleting an object -setcontext(1); -$output = $ws->delete({ - objects => ["/$testuserone/TestWorkspace/movedir/testdir2/testdir3/testobj","/$testuserone/TestWorkspace/movedir/testdir2/testdir3/shockobj"] -}); -ok defined($output), "Successfully ran delete_objects function on object!"; -print "delete_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -setcontext(1); -$output = $ws->delete({ - objects => ["/$testuserone/TestWorkspace/movedir/testdir2/testdir3"], - force => 1, - deleteDirectories => 1 -}); -ok defined($output), "Successfully ran delete_objects function on directory!"; -print "delete_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Deleting a directory -setcontext(1); -$output = $ws->delete({ - objects => ["/$testuserone/TestWorkspace/movedir"], - force => 1, - deleteDirectories => 1 -}); -ok defined($output), "Successfully ran delete_workspace_directory function!"; -print "delete_workspace_directory output:\n".Data::Dumper->Dump($output)."\n\n"; -#Creating a directory -setcontext(1); -$output = $ws->create({ - objects => [["/$testuserone/TestWorkspace/emptydir","folder",{},undef]] -}); -ok defined($output), "Successfully ran create_workspace_directory function!"; -print "create_workspace_directory output:\n".Data::Dumper->Dump($output)."\n\n"; -#Getting an object -setcontext(1); -$output = $ws->get({ - objects => ["/$testuserone/TestWorkspace/testdir/testdir2/testdir3/testobj"] -}); -ok defined($output->[0]->[1]), "Successfully ran get_objects function!"; -print "get_objects output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Getting an object by reference -setcontext(1); -$output = $ws->get({ - objects => [$output->[0]->[0]->[4]] -}); -ok defined($output->[0]->[1]), "Successfully ran get_objects_by_reference function!"; -print "get_objects_by_reference output:\n".Data::Dumper->Dump($output)."\n\n"; - -#Deleting workspaces -setcontext(1); -$output = $ws->delete({ - objects => ["/$testuserone/TestWorkspace"], - force => 1, - deleteDirectories => 1 -}); -ok defined($output), "Successfully ran delete_workspace function!"; -print "delete_workspace output:\n".Data::Dumper->Dump($output)."\n\n"; -#Setting context to authenticated user one -setcontext(2); -$output = $ws->delete({ - objects => ["/$testusertwo/TestWorkspace"], - force => 1, - deleteDirectories => 1 -}); -ok defined($output), "Successfully ran delete_workspace function!"; -print "delete_workspace output:\n".Data::Dumper->Dump($output)."\n\n"; - -done_testing($test_count); - -sub setcontext { - my($context) = @_; - if ($context == 1) { - $Bio::P3::Workspace::Service::CallContext = Bio::P3::Workspace::ServiceContext->new($tokenObj->token(),"test",$testuserone); - } else { - $Bio::P3::Workspace::Service::CallContext = Bio::P3::Workspace::ServiceContext->new("un=chenry|tokenid=03B0C858-7A70-11E4-9DE6-FDA042A49C03|expiry=1449094224|client_id=chenry|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|sig=085255b952c8db3ddd7e051ac4a729f719f22e531ddbc0a3edd86a895da851faa93249a7347c75324dc025b977e9ac7c4e02fb4c966ec6003ecf90d3148e35160265dbcdd235658deeed0ec4e0c030efee923fda1a55e8cc6f116bcd632fa6a576d7bf4a794554d2d914b54856e1e7ac2b071f81a8841d142123095f6af957cc","test",$testusertwo); - } -} - -package Bio::P3::Workspace::ServiceContext; - -use strict; - -sub new { - my($class,$token,$method,$user) = @_; - my $self = { - token => $token, - method => $method, - user_id => $user - }; - return bless $self, $class; -} -sub user_id { - my($self) = @_; - return $self->{user_id}; -} -sub token { - my($self) = @_; - return $self->{token}; -} -sub method { - my($self) = @_; - return $self->{method}; -} \ No newline at end of file From 765194dcf4c0448113697ff3fbdfea4abf337319 Mon Sep 17 00:00:00 2001 From: non Date: Tue, 28 Jul 2015 00:26:18 -0500 Subject: [PATCH 3/6] Fixing tests with all tests now passing --- lib/Bio/P3/Workspace/WorkspaceImpl.pm | 3 -- lib/Bio/P3/Workspace/WorkspaceTests.pm | 50 +++++++++++++++----------- t/client-tests/test.cfg | 1 + t/client-tests/tests.t | 2 +- t/server-tests/test.cfg | 1 + t/server-tests/tests.t | 2 +- 6 files changed, 33 insertions(+), 26 deletions(-) diff --git a/lib/Bio/P3/Workspace/WorkspaceImpl.pm b/lib/Bio/P3/Workspace/WorkspaceImpl.pm index beaa88f..fad8184 100644 --- a/lib/Bio/P3/Workspace/WorkspaceImpl.pm +++ b/lib/Bio/P3/Workspace/WorkspaceImpl.pm @@ -621,7 +621,6 @@ sub _validate_save_objects_before_saving { } } elsif ($user ne $self->_getUsername() && $self->_adminmode() == 0) { #Users can only create their own workspaces - print STDERR "user=$user username=" . $self->_getUsername() . "\n"; $self->_error("Insufficient permissions to create ".$objects->[$i]->[0]); } elsif ($objects->[$i]->[1] ne "folder") { #Workspace must be a folder @@ -722,7 +721,6 @@ sub _delete_object { #Ensuring all parts of object path have nonzero length if (!defined($obj->{wsobj}->{owner}) || length($obj->{wsobj}->{owner}) == 0) {$self->_error("Owner not specified in deletion!");} if (!defined($obj->{wsobj}->{name}) || length($obj->{wsobj}->{name}) == 0) {$self->_error("Top directory not specified in deletion!");} - if (!defined($obj->{path}) || length($obj->{path}) == 0) {$self->_error("Path not specified in deletion!");} if (!defined($obj->{name}) || length($obj->{name}) == 0) {$self->_error("Name not specified in deletion!");} if ($obj->{folder} == 1) { my $objs = $self->_get_directory_contents($obj,0); @@ -866,7 +864,6 @@ sub _create_object { } if (!defined($object->{wsobj}->{owner}) || length($object->{wsobj}->{owner}) == 0) {$self->_error("Owner not specified in creation!");} if (!defined($object->{wsobj}->{name}) || length($object->{wsobj}->{name}) == 0) {$self->_error("Top directory not specified in creation!");} - if (!defined($object->{path}) || length($object->{path}) == 0) {$self->_error("Path not specified in creation!");} if (!defined($object->{name}) || length($object->{name}) == 0) {$self->_error("Name not specified in creation!");} if ($specs->{type} eq "folder") { #Creating folder on file system diff --git a/lib/Bio/P3/Workspace/WorkspaceTests.pm b/lib/Bio/P3/Workspace/WorkspaceTests.pm index 89e497b..a5fd46b 100644 --- a/lib/Bio/P3/Workspace/WorkspaceTests.pm +++ b/lib/Bio/P3/Workspace/WorkspaceTests.pm @@ -10,10 +10,11 @@ sub new { my($class,$bin) = @_; my $c = Config::Simple->new(); - $c->read($bin."/test.cfg"); + $c->read($bin."test.cfg"); my $self = { testcount => 0, - dumpoutput => 0, + dumpoutput => $c->param("WorkspaceTest.dumpoutput"), + showerrors => $c->param("WorkspaceTest.showerrors"), user => $c->param("WorkspaceTest.user"), password => $c->param("WorkspaceTest.password"), usertwo => $c->param("WorkspaceTest.adminuser"), @@ -31,10 +32,7 @@ }); $ENV{KB_INTERACTIVE} = 1; if (defined($c->param("WorkspaceTest.serverconfig"))) { - $ENV{KB_DEPLOYMENT_CONFIG} = $c->param("WorkspaceTest.serverconfig"); - } - if (defined($c->param("WorkspaceTest.dumpoutput"))) { - $self->{dumpoutput} = $c->param("WorkspaceTest.dumpoutput"); + $ENV{KB_DEPLOYMENT_CONFIG} = $bin.$c->param("WorkspaceTest.serverconfig"); } if (!defined($self->{url}) || $self->{url} eq "impl") { print "Loading server with this config: ".$ENV{KB_DEPLOYMENT_CONFIG}."\n"; @@ -95,6 +93,10 @@ $output = $self->{obj}->$function(); } }; + my $errors; + if ($@) { + $errors = $@; + } $self->{completetestcount}++; if (defined($output)) { $self->{testoutput}->{$name}->{output} = $output; @@ -119,12 +121,15 @@ $self->{testoutput}->{$name}->{function} = 0; if (defined($fail_to_pass) && $fail_to_pass == 1) { $self->{testoutput}->{$name}->{pass} = 1; - $self->{testoutput}->{$name}->{status} = "Command failed as expected!"; + $self->{testoutput}->{$name}->{status} = $name." failed as expected!"; } else { $self->{testoutput}->{$name}->{pass} = 0; - $self->{testoutput}->{$name}->{status} = "Command failed to function at all!"; + $self->{testoutput}->{$name}->{status} = $name." failed to function at all!"; } ok $self->{testoutput}->{$name}->{pass} == 1, $self->{testoutput}->{$name}->{status}; + if ($self->{showerrors} && $self->{testoutput}->{$name}->{pass} == 0 && defined($errors)) { + print "Errors:\n".$errors."\n"; + } } if ($self->{dumpoutput}) { print "$function output:\n".Data::Dumper->Dump([$output])."\n\n"; @@ -134,9 +139,6 @@ sub run_tests { my($self) = @_; - ok(system("curl -h > /dev/null 2>&1") == 0, "curl is installed"); - ok(system("curl $url > /dev/null 2>&1") == 0, "$url is reachable"); - $self->{completetestcount} += 2; #Clearing out previous test results my $output = $self->test_harness("ls",{ @@ -202,7 +204,7 @@ permission => "r", adminmode => 1, setowner => $self->{user} - },"Creating top level TestAdminWorkspace for ".$self->{user}." as ".$self->{usertwo}." as admin",[],0,undef,2); + },"Creating top level TestAdminWorkspace for ".$self->{user}." with ".$self->{usertwo}." as admin",[],0,undef,2); #Attempting to make a workspace for another user $output = $self->test_harness("create",{ @@ -213,18 +215,24 @@ #Listing workspaces as user one $output = $self->test_harness("ls",{ paths => ["/".$self->{user}] - },"Using ls function as user one",["\$output->{\"/".$self->{user}."\"}->[0]->[5] eq ".$self->{user}],0,undef,1); + },"Using ls function as ".$self->{user},[ + ["\$output->{\"/".$self->{user}."\"}->[0]->[5] eq \"".$self->{user}."\"","First workspace returned is owned by ".$self->{user}] + ],0,undef,1); #Listing workspaces as user two $output = $self->test_harness("ls",{ paths => ["/".$self->{usertwo}] - },"Using ls function as user two",["\$output->{\"/".$self->{usertwo}."\"}->[0]->[5] eq \"".$self->{usertwo}."\""],0,undef,2); + },"Using ls function as ".$self->{usertwo},[ + ["\$output->{\"/".$self->{usertwo}."\"}->[0]->[5] eq \"".$self->{usertwo}."\"","First workspace returned is owned by ".$self->{usertwo}] + ],0,undef,2); #Getting workspace metadata $output = $self->test_harness("get",{ metadata_only => 1, objects => ["/".$self->{usertwo}."/TestWorkspace"] - },"Using get function to retrieve TestWorkspace metadata only",[["defined(\$output->[0]->[0])","Metadata for object contained in output"]],0,undef,2); + },"Using get function to retrieve TestWorkspace metadata only",[ + ["defined(\$output->[0]->[0])","Metadata for object contained in output"] + ],0,undef,2); #Saving an object $output = $self->test_harness("create",{ @@ -239,8 +247,8 @@ features => [{}] }]] },"Creating a genome object",[ - ["defined(\$output->[0])","Getting metadata for created object back"], - ["\$output->[0]->[1] eq \"genome\"","Object has type genome"] + ["defined(\$output->[3])","Getting metadata for created objects back"], + ["\$output->[3]->[1] eq \"genome\"","Object has type genome"] ],0,undef,1); #Recreating an existing folder @@ -294,8 +302,8 @@ ],0,undef,1); #Uploading file to newly created shock node - print "Filename:".$self->{bin}."/testdata.txt\n"; - my $req = HTTP::Request::Common::POST($output->[0]->[11],Authorization => "OAuth ".$self->{token},Content_Type => 'multipart/form-data',Content => [upload => [$self->{bin}."/testdata.txt"]]); + print "Filename:".$self->{bin}."testdata.txt\n"; + my $req = HTTP::Request::Common::POST($output->[0]->[11],Authorization => "OAuth ".$self->{token},Content_Type => 'multipart/form-data',Content => [upload => [$self->{bin}."testdata.txt"]]); $req->method('PUT'); my $ua = LWP::UserAgent->new(); my $res = $ua->request($req); @@ -344,7 +352,7 @@ excludeObjects => 0, recursive => 1 },"Running ls on workspace recursively with directories excluded",[ - ["defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[0]) && !defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[2])","Returns contents with only two items"] + ["defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[2]) && !defined(\$output->{\"/".$self->{user}."/TestWorkspace\"}->[3])","Returns contents with only three items"] ],0,undef,1); $output = $self->test_harness("ls",{ @@ -374,7 +382,7 @@ },"Copying to read only workspace fails",[],1,undef,1); #Changing workspace permissions - $output = $self->test_harness("copy",{ + $output = $self->test_harness("set_permissions",{ path => "/".$self->{usertwo}."/TestWorkspace", permissions => [[$self->{user},"w"]] },"Resetting permissions on workspace",[],0,undef,2); diff --git a/t/client-tests/test.cfg b/t/client-tests/test.cfg index fab0d05..2c9058f 100644 --- a/t/client-tests/test.cfg +++ b/t/client-tests/test.cfg @@ -5,4 +5,5 @@ adminuser=chenry adminpassword= url=http://p3.theseed.org/services/Workspace dumpoutput=0 +showerrors=1 serverconfig=testserver.cfg \ No newline at end of file diff --git a/t/client-tests/tests.t b/t/client-tests/tests.t index 2f6bb7d..1bbcdb1 100644 --- a/t/client-tests/tests.t +++ b/t/client-tests/tests.t @@ -1,5 +1,5 @@ use FindBin qw($Bin); -use Bio::ModelSEED::ProbModelSEED::ProbModelSEEDTests; +use Bio::P3::Workspace::WorkspaceTests; my $tester = Bio::P3::Workspace::WorkspaceTests->new($bin); $tester->run_tests(); \ No newline at end of file diff --git a/t/server-tests/test.cfg b/t/server-tests/test.cfg index 8467604..7ea4f2a 100644 --- a/t/server-tests/test.cfg +++ b/t/server-tests/test.cfg @@ -5,4 +5,5 @@ adminuser=chenry adminpassword= url=impl dumpoutput=0 +showerrors=1 serverconfig=testserver.cfg \ No newline at end of file diff --git a/t/server-tests/tests.t b/t/server-tests/tests.t index 2f6bb7d..1bbcdb1 100644 --- a/t/server-tests/tests.t +++ b/t/server-tests/tests.t @@ -1,5 +1,5 @@ use FindBin qw($Bin); -use Bio::ModelSEED::ProbModelSEED::ProbModelSEEDTests; +use Bio::P3::Workspace::WorkspaceTests; my $tester = Bio::P3::Workspace::WorkspaceTests->new($bin); $tester->run_tests(); \ No newline at end of file From feeab853833ca5334fec1843a939a2c7e64d3735 Mon Sep 17 00:00:00 2001 From: non Date: Tue, 28 Jul 2015 23:16:40 -0500 Subject: [PATCH 4/6] Fixing bug in client tests --- lib/Bio/P3/Workspace/WorkspaceTests.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/Bio/P3/Workspace/WorkspaceTests.pm b/lib/Bio/P3/Workspace/WorkspaceTests.pm index a5fd46b..1cd4a41 100644 --- a/lib/Bio/P3/Workspace/WorkspaceTests.pm +++ b/lib/Bio/P3/Workspace/WorkspaceTests.pm @@ -28,7 +28,7 @@ user_id => $self->{user}, password => $self->{password},tokenonly => 1 }); $self->{tokentwo} = Bio::P3::Workspace::ScriptHelpers::login({ - user_id => $self->{adminuser}, password => $self->{adminpassword},tokenonly => 1 + user_id => $self->{usertwo}, password => $self->{passwordtwo},tokenonly => 1 }); $ENV{KB_INTERACTIVE} = 1; if (defined($c->param("WorkspaceTest.serverconfig"))) { From 22f4d466b0b212e3e1a0ba71f84e98563a6e0a99 Mon Sep 17 00:00:00 2001 From: non Date: Tue, 28 Jul 2015 23:40:03 -0500 Subject: [PATCH 5/6] Removing automatic calls to type compiler from make file. I do not think the type compiler should be automatically called. It should be manually called as needed by the developer. --- Makefile | 4 ++-- quick_deploy.sh | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Makefile b/Makefile index b0f72fb..eddda4b 100644 --- a/Makefile +++ b/Makefile @@ -42,7 +42,7 @@ TPAGE_ARGS = --define kb_top=$(TARGET) \ TESTS = $(wildcard t/client-tests/*.t) -all: bin compile-typespec service +all: bin service jarfile: gen_java_client $(SERVER_SPEC) org.patricbrc.Workspace java @@ -84,7 +84,7 @@ bin: $(BIN_PERL) $(BIN_SERVICE_PERL) deploy: deploy-client deploy-service deploy-all: deploy-client deploy-service -deploy-client: compile-typespec deploy-docs deploy-libs deploy-scripts +deploy-client: deploy-docs deploy-libs deploy-scripts deploy-service: deploy-dir deploy-monit deploy-libs deploy-service-scripts $(TPAGE) $(TPAGE_ARGS) service/start_service.tt > $(TARGET)/services/$(SERVICE)/start_service diff --git a/quick_deploy.sh b/quick_deploy.sh index a0256f2..43f9d61 100755 --- a/quick_deploy.sh +++ b/quick_deploy.sh @@ -44,7 +44,7 @@ pushd modules/$SERVICE source /disks/p3/deployment/user-env.sh -perl t/client-tests/workspace-full-api-test.t +perl t/client-tests/tests.t if [ $? -ne 0 ] ; then echo "BUILD ERROR: problem running make test" exit 1 From eb599035e8706c6bd74a0b2ab0fa5f9884024e6d Mon Sep 17 00:00:00 2001 From: non Date: Tue, 28 Jul 2015 23:45:49 -0500 Subject: [PATCH 6/6] Removing doc deploy too --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index eddda4b..806887f 100644 --- a/Makefile +++ b/Makefile @@ -84,7 +84,7 @@ bin: $(BIN_PERL) $(BIN_SERVICE_PERL) deploy: deploy-client deploy-service deploy-all: deploy-client deploy-service -deploy-client: deploy-docs deploy-libs deploy-scripts +deploy-client: deploy-libs deploy-scripts deploy-service: deploy-dir deploy-monit deploy-libs deploy-service-scripts $(TPAGE) $(TPAGE_ARGS) service/start_service.tt > $(TARGET)/services/$(SERVICE)/start_service