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fix compile time syntax errors in ws-cp.pl #23

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fix compile time syntax errors in ws-cp.pl #23

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faaefa1
fixed compile error
brettinanl Jul 9, 2015
45a6613
Committing new testing framework, which permits the coding of tests f…
cshenry Jul 28, 2015
765194d
Fixing tests with all tests now passing
cshenry Jul 28, 2015
f07491f
Merge branch 'master' of https://github.com/PATRIC3/Workspace
cshenry Jul 28, 2015
feeab85
Fixing bug in client tests
cshenry Jul 29, 2015
22f4d46
Removing automatic calls to type compiler from make file. I do not th…
cshenry Jul 29, 2015
eb59903
Removing doc deploy too
cshenry Jul 29, 2015
e562630
Merge branch 'master' of https://github.com/brettin/Workspace-1
brettinanl Aug 7, 2015
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4 changes: 2 additions & 2 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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-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
Expand Down
22 changes: 13 additions & 9 deletions lib/Bio/P3/Workspace/ScriptHelpers.pm
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Expand Up @@ -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;
Expand All @@ -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;
}

Expand Down
13 changes: 12 additions & 1 deletion lib/Bio/P3/Workspace/WorkspaceImpl.pm
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Expand Up @@ -622,7 +622,6 @@ 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->[$i]->[1] ne "folder") {
#Workspace must be a folder
Expand Down Expand Up @@ -711,13 +710,19 @@ sub _delete_validated_object_set {
#Delete the specified workspace and all the objects it contains**
sub _delete_workspace {
my ($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 => $wsobj->{uuid}});
}
#Delete the specified object**
sub _delete_object {
my ($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($obj->{name}) || length($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}; $i++) {
Expand Down Expand Up @@ -800,6 +805,8 @@ sub _create {
#This function creates workspaces**
sub _create_workspace {
my ($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
Expand Down Expand Up @@ -829,6 +836,7 @@ 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};
Expand All @@ -855,6 +863,9 @@ 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->{name}) || length($object->{name}) == 0) {$self->_error("Name not specified in creation!");}
if ($specs->{type} eq "folder") {
#Creating folder on file system
$object->{autometadata} = {};
Expand Down
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