diff --git a/db/patches/0530_gcmd.sql b/db/patches/0530_gcmd.sql
new file mode 100644
index 00000000..f31969e3
--- /dev/null
+++ b/db/patches/0530_gcmd.sql
@@ -0,0 +1,41 @@
+create table gcmd_keyword (
+ identifier varchar not null primary key,
+ parent_identifier varchar constraint fk_parent
+ references gcmd_keyword(identifier)
+ deferrable initially deferred,
+ label varchar,
+ definition varchar
+);
+
+create view vw_gcmd_keyword as
+select
+ coalesce(level4.identifier,
+ level3.identifier,
+ level2.identifier,
+ level1.identifier,
+ term.identifier,
+ topic.identifier,
+ category.identifier) as identifier,
+ category.label as category,
+ topic.label as topic,
+ term.label as term,
+ level1.label as level1,
+ level2.label as level2,
+ level3.label as level3,
+ level4.label as level4
+from gcmd_keyword wrapper left join gcmd_keyword category on category.parent_identifier = wrapper.identifier
+ left join gcmd_keyword topic on topic.parent_identifier = category.identifier
+ left join gcmd_keyword term on term.parent_identifier = topic.identifier
+ left join gcmd_keyword level1 on level1.parent_identifier = term.identifier
+ left join gcmd_keyword level2 on level2.parent_identifier = level1.identifier
+ left join gcmd_keyword level3 on level3.parent_identifier = level2.identifier
+ left join gcmd_keyword level4 on level4.parent_identifier = level3.identifier
+where
+ wrapper.identifier='1eb0ea0a-312c-4d74-8d42-6f1ad758f999' and wrapper.label='Science Keywords';
+
+create table publication_gcmd_keyword_map (
+ publication_id integer not null references publication(id) on delete cascade on update cascade,
+ gcmd_keyword_identifier varchar not null references gcmd_keyword(identifier) on delete cascade on update cascade,
+ primary key (publication_id, gcmd_keyword_identifier)
+);
+
diff --git a/db/patches/0540_gcmd_view.sql b/db/patches/0540_gcmd_view.sql
new file mode 100644
index 00000000..37438155
--- /dev/null
+++ b/db/patches/0540_gcmd_view.sql
@@ -0,0 +1,125 @@
+create view vw_gcmd_keyword as
+select
+ coalesce(level4.identifier,
+ level3.identifier,
+ level2.identifier,
+ level1.identifier,
+ term.identifier,
+ topic.identifier,
+ category.identifier) as identifier,
+ category.label as category,
+ topic.label as topic,
+ term.label as term,
+ level1.label as level1,
+ level2.label as level2,
+ level3.label as level3,
+ level4.label as level4
+from gcmd_keyword wrapper inner join gcmd_keyword category on category.parent_identifier = wrapper.identifier
+ inner join gcmd_keyword topic on topic.parent_identifier = category.identifier
+ inner join gcmd_keyword term on term.parent_identifier = topic.identifier
+ inner join gcmd_keyword level1 on level1.parent_identifier = term.identifier
+ inner join gcmd_keyword level2 on level2.parent_identifier = level1.identifier
+ inner join gcmd_keyword level3 on level3.parent_identifier = level2.identifier
+ inner join gcmd_keyword level4 on level4.parent_identifier = level3.identifier
+where
+ wrapper.identifier='1eb0ea0a-312c-4d74-8d42-6f1ad758f999' and wrapper.label='Science Keywords'
+UNION
+select
+ coalesce(
+ level3.identifier,
+ level2.identifier,
+ level1.identifier,
+ term.identifier,
+ topic.identifier,
+ category.identifier) as identifier,
+ category.label as category,
+ topic.label as topic,
+ term.label as term,
+ level1.label as level1,
+ level2.label as level2,
+ level3.label as level3,
+ NULL as level4
+from gcmd_keyword wrapper inner join gcmd_keyword category on category.parent_identifier = wrapper.identifier
+ inner join gcmd_keyword topic on topic.parent_identifier = category.identifier
+ inner join gcmd_keyword term on term.parent_identifier = topic.identifier
+ inner join gcmd_keyword level1 on level1.parent_identifier = term.identifier
+ inner join gcmd_keyword level2 on level2.parent_identifier = level1.identifier
+ inner join gcmd_keyword level3 on level3.parent_identifier = level2.identifier
+where
+ wrapper.identifier='1eb0ea0a-312c-4d74-8d42-6f1ad758f999' and wrapper.label='Science Keywords'
+UNION
+select
+ coalesce(
+ level2.identifier,
+ level1.identifier,
+ term.identifier,
+ topic.identifier,
+ category.identifier) as identifier,
+ category.label as category,
+ topic.label as topic,
+ term.label as term,
+ level1.label as level1,
+ level2.label as level2,
+ NULL as level3,
+ NULL as level4
+from gcmd_keyword wrapper inner join gcmd_keyword category on category.parent_identifier = wrapper.identifier
+ inner join gcmd_keyword topic on topic.parent_identifier = category.identifier
+ inner join gcmd_keyword term on term.parent_identifier = topic.identifier
+ inner join gcmd_keyword level1 on level1.parent_identifier = term.identifier
+ inner join gcmd_keyword level2 on level2.parent_identifier = level1.identifier
+where
+ wrapper.identifier='1eb0ea0a-312c-4d74-8d42-6f1ad758f999' and wrapper.label='Science Keywords'
+UNION
+select
+ coalesce(
+ level1.identifier,
+ term.identifier,
+ topic.identifier,
+ category.identifier) as identifier,
+ category.label as category,
+ topic.label as topic,
+ term.label as term,
+ level1.label as level1,
+NULL as level2, NULL as level3, NULL as level4
+from gcmd_keyword wrapper inner join gcmd_keyword category on category.parent_identifier = wrapper.identifier
+ inner join gcmd_keyword topic on topic.parent_identifier = category.identifier
+ inner join gcmd_keyword term on term.parent_identifier = topic.identifier
+ inner join gcmd_keyword level1 on level1.parent_identifier = term.identifier
+where
+ wrapper.identifier='1eb0ea0a-312c-4d74-8d42-6f1ad758f999' and wrapper.label='Science Keywords'
+UNION
+select
+ coalesce(
+ term.identifier,
+ topic.identifier,
+ category.identifier) as identifier,
+ category.label as category,
+ topic.label as topic,
+ term.label as term,
+NULL as level1, NULL as level2, NULL as level3, NULL as level4
+from gcmd_keyword wrapper inner join gcmd_keyword category on category.parent_identifier = wrapper.identifier
+ inner join gcmd_keyword topic on topic.parent_identifier = category.identifier
+ inner join gcmd_keyword term on term.parent_identifier = topic.identifier
+where
+ wrapper.identifier='1eb0ea0a-312c-4d74-8d42-6f1ad758f999' and wrapper.label='Science Keywords'
+union
+select
+ coalesce(
+ topic.identifier,
+ category.identifier) as identifier,
+ category.label as category,
+ topic.label as topic,
+NULL as term, NULL as level1, NULL as level2, NULL as level3, NULL as level4
+from gcmd_keyword wrapper inner join gcmd_keyword category on category.parent_identifier = wrapper.identifier
+ inner join gcmd_keyword topic on topic.parent_identifier = category.identifier
+where
+ wrapper.identifier='1eb0ea0a-312c-4d74-8d42-6f1ad758f999' and wrapper.label='Science Keywords'
+union
+select
+ coalesce( category.identifier) as identifier,
+ category.label as category,
+NULL as topic, NULL as term, NULL as level1, NULL as level2, NULL as level3, NULL as level4
+from gcmd_keyword wrapper inner join gcmd_keyword category on category.parent_identifier = wrapper.identifier
+where
+ wrapper.identifier='1eb0ea0a-312c-4d74-8d42-6f1ad758f999' and wrapper.label='Science Keywords'
+;
diff --git a/eg/import_gcmd_keywords b/eg/import_gcmd_keywords
new file mode 100755
index 00000000..ca96c80e
--- /dev/null
+++ b/eg/import_gcmd_keywords
@@ -0,0 +1,47 @@
+#!/usr/bin/env perl
+
+use Mojo::UserAgent;
+use Tuba::DB::Objects qw/-nicknames -autoconnect/;
+use HTML::Entities qw/decode_entities/;
+use v5.14;
+
+my $me = $ENV{USER} || 'unknown';
+my $ua = Mojo::UserAgent->new();
+my $tx = $ua->get(q[http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.rdf]);
+
+# http://gcmdservices.gsfc.nasa.gov/static/kms/concept/536a86bd-3dd1-4f4a-9b4a-222a12746db5
+my $changes = 0;
+
+my $db = GcmdKeyword->meta->db;
+
+$db->do_transaction(sub {
+ $db->dbh->do('set constraints all deferred;');
+ $tx->res->dom->find('rdf\:RDF > skos\:Concept')->each(sub {
+ my $dom = shift;
+ my $identifier = $dom->attr('rdf:about');
+ my $label = [ $dom->find('skos\:prefLabel')->each ]->[0]->text;
+ my @broader = $dom->find('skos\:broader')->each;
+ die "not a tree" if @broader > 1;
+ my $parent;
+ if ($parent = $broader[0]) {
+ $parent = $parent->attr('rdf:resource');
+ my $gk = GcmdKeyword->new(identifier => $parent);
+ unless ($gk->load(speculative => 1)) {
+ $gk->save(audit_user => $me) or die $gk->error;
+ }
+ }
+ my @definition = $dom->find('skos\:definition')->each;
+ my $definition = $definition[0]->text if @definition;
+
+ my $kw = GcmdKeyword->new( identifier => $identifier );
+ $kw->load(speculative => 1);
+ $kw->parent($parent);
+ $kw->label($label || undef);
+ $definition =~ s/ / /g;
+ $kw->definition($definition);
+ $kw->save(audit_user => $me) or die $definition;
+ });
+});
+
+
+
diff --git a/eg/import_keywords b/eg/import_keywords
index 34e13324..374c06c1 100755
--- a/eg/import_keywords
+++ b/eg/import_keywords
@@ -8,6 +8,8 @@ use Smart::Comments;
use Tuba::DB::Objects qw/-nicknames -autoconnect/;
+# TODO use http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.rdf
+
my $me = $ENV{USER} || 'unknown';
my $ua = Mojo::UserAgent->new();
my $content = $ua->get(q[http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csv])->res->body;
diff --git a/lib/Tuba.pm b/lib/Tuba.pm
index e9af054f..81a9fa60 100644
--- a/lib/Tuba.pm
+++ b/lib/Tuba.pm
@@ -307,7 +307,15 @@ sub startup {
my @restrict = $opts->{restrict_identifier} ? ( $identifier => $opts->{restrict_identifier} ) : ();
my %defaults = $opts->{defaults} ? %{ $opts->{defaults} } : ();
if ($opts->{wildcard}) {
- my $reserved = q[^(?:form/update(?:_prov|_rel|_files)?|form/create|update(?:_rel|files|prov)?|put_files|history/)];
+ my $reserved = qr[^(?:form/update
+ (?:_prov|_rel|_files)?
+ |form/create
+ |update
+ (?:_prov|_rel|_files)?
+ |put_files
+ |history
+ )
+ ]x;
for my $format (@supported_formats) {
$resource->get("*$identifier.$format" => \@restrict => { format => $format } )
->over(not_match => { $identifier => $reserved })
@@ -330,6 +338,7 @@ sub startup {
$authed->get("/form/update/*$identifier" => \%defaults) ->to("$cname#update_form")->name("update_form_$name");
$authed->get("/form/update_prov/*$identifier" => \%defaults) ->to("$cname#update_prov_form")->name("update_prov_form_$name");
$authed->get("/form/update_rel/*$identifier" => \%defaults) ->to("$cname#update_rel_form")->name("update_rel_form_$name");
+ $authed->get("/form/update_keywords/*$identifier" => \%defaults) ->to("$cname#update_keywords_form")->name("update_keywords_form_$name");
$authed->get("/form/update_files/*$identifier" => \%defaults)->to("$cname#update_files_form")->name("update_files_form_$name");
$authed->get("/history/*$identifier" => \%defaults) ->to("$cname#history") ->name("history_$name");
$authed->delete("*$identifier" => \%defaults) ->to("$cname#remove") ->name("remove_$name");
@@ -337,6 +346,7 @@ sub startup {
->to("$cname#update") ->name("update_$name");
$authed->post("/prov/*$identifier") ->to("$cname#update_prov")->name("update_prov_$name");
$authed->post("/rel/*$identifier") ->to("$cname#update_rel")->name("update_rel_$name");
+ $authed->post("/keywords/*$identifier") ->to("$cname#update_keywords")->name("update_keywords_$name");
$authed->post("/files/*$identifier") ->to("$cname#update_files")->name("update_files_$name");
$authed->put("/files/*$identifier/#filename") # a default filename for PUTs would be ambiguous.
->to("$cname#put_files")->name("put_files_$name");
@@ -344,12 +354,14 @@ sub startup {
$authed->get("/form/update/:$identifier") ->to("$cname#update_form")->name("update_form_$name");
$authed->get("/form/update_prov/:$identifier" => \%defaults) ->to("$cname#update_prov_form")->name("update_prov_form_$name");
$authed->get("/form/update_rel/:$identifier" => \%defaults) ->to("$cname#update_rel_form")->name("update_rel_form_$name");
+ $authed->get("/form/update_keywords/:$identifier" => \%defaults) ->to("$cname#update_keywords_form")->name("update_keywords_form_$name");
$authed->get("/form/update_files/:$identifier" => \%defaults)->to("$cname#update_files_form")->name("update_files_form_$name");
$authed->get("/history/:$identifier" => \%defaults) ->to("$cname#history") ->name("history_$name");
$authed->delete(":$identifier" => \%defaults) ->to("$cname#remove") ->name("remove_$name");
$authed->post(":$identifier" => \%defaults) ->to("$cname#update") ->name("update_$name");
$authed->post("/prov/:$identifier" => \%defaults) ->to("$cname#update_prov")->name("update_prov_$name");
$authed->post("/rel/:$identifier" => \%defaults) ->to("$cname#update_rel")->name("update_rel_$name");
+ $authed->post("/keywords/:$identifier" => \%defaults) ->to("$cname#update_keywords")->name("update_keywords_$name");
$authed->post("/files/:$identifier" => \%defaults) ->to("$cname#update_files")->name("update_files_$name");
$authed->put("/files/:$identifier/#filename" => {filename => 'unnamed', %defaults })
->to("$cname#put_files")->name("put_files_$name");
@@ -430,6 +442,9 @@ sub startup {
$r->resource(person => { restrict_identifier => qr/\d+/ } );
$r->get('/person/:name')->to('person#redirect_by_name');
+ # GcmdKeyword
+ $r->resource('gcmd_keyword');
+
# Others, some of which aren't yet implemented.
$r->resource($_) for qw/dataset model software algorithm activity
instrument platform
diff --git a/lib/Tuba/Controller.pm b/lib/Tuba/Controller.pm
index 625e4d94..47ef4dbc 100644
--- a/lib/Tuba/Controller.pm
+++ b/lib/Tuba/Controller.pm
@@ -527,6 +527,43 @@ sub put_files {
$c->render(text => "ok");
}
+=head2 update_keywords
+
+Assign GCMD keywords to a resource.
+
+=cut
+
+sub update_keywords {
+ my $c = shift;
+ my $obj = $c->_this_object or return $c->render_not_found;
+ my $pub = $obj->get_publication(autocreate => 1);
+ $pub->save(audit => $c->user) unless $pub->id;
+ if (my $json = $c->req->json) {
+ my $delete_extra = delete $json->{_delete_extra};
+ $json = [ $json ] if ref($json) eq 'HASH';
+ my %to_delete = map { ($_->identifier => 1) } @{ $pub->gcmd_keywords };
+
+ for my $k (@$json) {
+ ref $k eq 'HASH' or return $c->render(json => { error => { data => $k, msg => "not a hash" }} );
+ my $kw = exists $k->{identifier} ? GcmdKeyword->new(%$k) : GcmdKeyword->new_from_flat(%$k);
+ $kw->load(speculative => 1) or return $c->render(json => { error => { data => $k, msg => 'not found' }} );
+ $pub->add_gcmd_keywords($kw);
+ delete $to_delete{$kw->identifier};
+ }
+ $pub->save(audit_user => $c->user);
+ if ($delete_extra) {
+ for my $extra (keys %to_delete) {
+ PublicationGcmdKeywordMap->new(
+ publication => $pub->id,
+ gcmd_keyword_identifier => $extra
+ )->delete;
+ }
+ }
+ return $c->render(json => 'ok');
+ }
+ return $c->render(text => "html not implemented"); # TODO
+}
+
=head2 update_rel
Update the relationships.
diff --git a/lib/Tuba/DB/Mixin/Object/GcmdKeyword.pm b/lib/Tuba/DB/Mixin/Object/GcmdKeyword.pm
new file mode 100644
index 00000000..bf82c027
--- /dev/null
+++ b/lib/Tuba/DB/Mixin/Object/GcmdKeyword.pm
@@ -0,0 +1,46 @@
+package Tuba::DB::Object::GcmdKeyword;
+use Tuba::Log;
+use Data::Dumper;
+# Tuba::DB::Mixin::Object::GcmdKeyword;
+
+sub stringify {
+ my $self = shift;
+ my %args = @_;
+ if ($args{short}) {
+ return $self->label;
+ }
+ if (my $parent = $self->parent) {
+ return join '>', $self->parent->label, $self->label;
+ }
+ return $self->label;
+}
+
+sub new_from_flat {
+ my $c = shift;
+ my %h = @_;
+ # Example :
+ # {
+ # 'id' => '5286',
+ # 'category' => 'EARTH SCIENCE',
+ # 'topic' => 'HUMAN DIMENSIONS',
+ # 'term' => 'ENVIRONMENTAL IMPACTS',
+ # 'level1' => 'FOSSIL FUEL BURNING'
+ # 'level2' => undef,
+ # 'level3' => undef,
+ # };
+ my $new;
+ my @cols = qw/category topic term level1 level2 level3/;
+ my %cols;
+ @cols{@cols} = @h{@cols};
+ my $ds = DBIx::Simple->new(Tuba::Plugin::Db->connection->dbh);
+ my @rows = $ds->select('vw_gcmd_keyword', '*', \%cols )->hashes;
+ return unless @rows > 0;
+ unless (@rows==1) {
+ logger()->warn("we got ".@rows." rows for ".dumpit(\%h));
+ }
+ my $identifier = $rows[0]->{identifier};
+ return $c->new(identifier => $identifier);
+}
+
+1;
+
diff --git a/lib/Tuba/DB/Object.pm b/lib/Tuba/DB/Object.pm
index f69cac36..dd263415 100644
--- a/lib/Tuba/DB/Object.pm
+++ b/lib/Tuba/DB/Object.pm
@@ -230,6 +230,7 @@ information :
- a list of parent publications
- a list of files
+ - a list of gcmd keywords
The parameter 'c' should have a controller object
(so that we can look up a URL for an object).
@@ -257,6 +258,7 @@ sub as_tree {
};
}
$tree->{files} = [ map $_->as_tree(@_), $pub->files ];
+ $tree->{gcmd_keywords} = [ map $_->as_tree(@_), $pub->gcmd_keywords ];
}
$tree->{uri} //= $s->uri($c);
}
diff --git a/lib/Tuba/Gcmdkeyword.pm b/lib/Tuba/Gcmdkeyword.pm
new file mode 100644
index 00000000..132c3ac4
--- /dev/null
+++ b/lib/Tuba/Gcmdkeyword.pm
@@ -0,0 +1,32 @@
+=head1 NAME
+
+Tuba::GcmdKeyword : Controller class for files.
+
+=cut
+
+package Tuba::Gcmdkeyword;
+use Mojo::Base qw/Tuba::Controller/;
+use Tuba::DB::Objects qw/-nicknames/;
+
+sub list {
+ my $c = shift;
+ $c->stash(objects => GcmdKeywords->get_objects(with_objects => 'publications', page => $c->page));
+ my $count = GcmdKeywords->get_objects_count;
+ $c->stash(extra_cols => [qw/label/]);
+ $c->set_pages($count);
+ $c->SUPER::list(@_);
+}
+
+sub show {
+ my $c = shift;
+ my $kw = $c->_this_object or $c->render_not_found;
+ $c->stash(object => $kw);
+ $c->SUPER::show(@_);
+}
+
+sub _guess_object_class {
+ return 'Tuba::DB::Object::GcmdKeyword';
+}
+
+1;
+
diff --git a/lib/Tuba/Log.pm b/lib/Tuba/Log.pm
index f9ec7d24..699f5b43 100644
--- a/lib/Tuba/Log.pm
+++ b/lib/Tuba/Log.pm
@@ -12,8 +12,8 @@ In the main app :
Someplace else
use Tuba::Log;
- loggger->info("hi!");
- loggger->info("hi!",dumpit($var));
+ logger->info("hi!");
+ logger->info("hi!",dumpit($var));
=head1 DESCRIPTION
diff --git a/lib/Tuba/files/templates/gcmd_keyword/fields.html.ep b/lib/Tuba/files/templates/gcmd_keyword/fields.html.ep
new file mode 100644
index 00000000..89524dd7
--- /dev/null
+++ b/lib/Tuba/files/templates/gcmd_keyword/fields.html.ep
@@ -0,0 +1,46 @@
+
+Fields
+
+% for my $col (sort {$a->name cmp $b->name} $meta->columns) {
+% next if $col->name =~ /^_/;
+% my $k = $col->accessor_method_name;
+% my $val = $object->$k;
+
+ | <%= $k %> |
+
+ % if (!$val) {
+
+ % } elsif ($k eq 'doi') {
+ %= link_to "http://dx.doi.org/$val" => target => "_blank" => begin
+ <%= $val %>
+ %= end
+ % } elsif ($k =~ /issn/ && $val) {
+ %= link_to "http://www.worldcat.org/issn/$val" => target => "_blank" => begin
+ <%= $val %>
+ %= end
+ % } elsif ($k eq 'url') {
+ %= link_to $val => target => "_blank" => begin
+ <%= $val %>
+ %= end
+ % } elsif (ref($val) eq 'ARRAY') {
+ %= include 'view_array', val => $val, header_rows => ($object->can('rows_in_header') ? $object->rows_in_header : 0)
+ % } else {
+ <%= $val %>
+ % }
+ |
+
+% }
+
+ |
+ GCMD Metadata
+ |
+
+ %= link_to q[http://gcmdservices.gsfc.nasa.gov/static/kms/concept/].$object->identifier => target => "_blank" => begin
+ <%= $object->identifier %>
+ %= end
+ |
+
+
+
+
+
diff --git a/lib/Tuba/files/templates/gcmd_keyword/object.html.ep b/lib/Tuba/files/templates/gcmd_keyword/object.html.ep
new file mode 100644
index 00000000..1e5abf64
--- /dev/null
+++ b/lib/Tuba/files/templates/gcmd_keyword/object.html.ep
@@ -0,0 +1,36 @@
+
+% layout 'default';
+
+
+<%= $object->meta->table %> : <%= $object->stringify %>
+
+
+%= include 'history_modal';
+
+% if ($object->can('identifier') && user_can('update')) {
+
+ <%= link_to $object->uri($self,{ tab => 'update_form' }) => class => "btn" => begin %>edit<%= end %>
+ history
+
+% }
+
+
+<%= include 'other_formats'; =%>
+<%= include 'db_meta'; =%>
+
+
+% if (my $pub = $object->get_publication) {
+Files
+
+
+%= include 'pub_thumbnails', pub => $pub, files => 1;
+
+
+ | GCMD Keywords |
+
+
+ %= include 'collapsible', row_content => begin
+ %= include 'obj_thumbnails', objs => scalar $pub->gcmd_keywords
+ %= end
+
+ |
+
+% }
+