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added make target to build api docs #303

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merged 3 commits into from
May 3, 2013
Merged

added make target to build api docs #303

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ac86d45
Merge branch 'develop' of git@github.com:MG-RAST/MG-RAST into develop
May 3, 2013
114362c
fixed wrong api resource name
May 3, 2013
2200fb5
added make target to build api docs
May 3, 2013
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6 changes: 4 additions & 2 deletions Makefile
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Expand Up @@ -53,7 +53,7 @@ OVERRIDES = \
# if you change all: make sure all: in standard.mk is consistent. # if you change all: make sure all: in standard.mk is consistent.


all: installdirs $(TOOL_HDR) lib all: installdirs $(TOOL_HDR) lib

# Use the PACKAGES macro to transform lib, bin, etc., targets # Use the PACKAGES macro to transform lib, bin, etc., targets
# into package level dependencies, e.g., lib -> PkgA.lib, PkgB.lib # into package level dependencies, e.g., lib -> PkgA.lib, PkgB.lib
# Rules below then cause PkgA.lib to do a make in PkgaA on lib: # Rules below then cause PkgA.lib to do a make in PkgaA on lib:
Expand All @@ -66,6 +66,8 @@ clean: Makefile purge
purge: purge:
rm -rf $(TARGET) bin/*.r rm -rf $(TARGET) bin/*.r


api-doc:
perl src/WebApplication/scripts/api2html.pl -url http://api.metagenomics.anl.gov -outfile site/CGI/Html/api.cgi


## ##
# Targets to setup the expected directory structure for the # Targets to setup the expected directory structure for the
Expand Down Expand Up @@ -93,7 +95,7 @@ $(libdir)/%.installdirs:
$(tmpdir): $(tmpdir):
- mkdir -p $(tmpdir) - mkdir -p $(tmpdir)
- chmod a+w $(tmpdir) - chmod a+w $(tmpdir)

$(bindir): $(bindir):
- mkdir -p $(bindir) - mkdir -p $(bindir)


Expand Down
8 changes: 5 additions & 3 deletions src/MGRAST/lib/resources2/annotations.pm
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Expand Up @@ -16,9 +16,11 @@ sub new {
my $self = $class->SUPER::new(@args); my $self = $class->SUPER::new(@args);


# Add name / attributes # Add name / attributes
$self->{name} = "sequences"; $self->{name} = "annotations";
$self->{attributes} = { "id" => [ 'string', 'unique object identifier' ], $self->{attributes} = { "id" => [ 'string', 'unique object identifier' ],
"data" => [ 'hash', 'annotations names pointing to list of md5s' ], "data" => [ 'hash', [ { 'key' => ['string', 'annotation text'],
'value' => ['list', ['string', 'md5sum of hit protein']] },
'annotation to md5s' ]],
"version" => [ 'integer', 'version of the object' ], "version" => [ 'integer', 'version of the object' ],
"url" => [ 'uri', 'resource location of this object instance' ] }; "url" => [ 'uri', 'resource location of this object instance' ] };
return $self; return $self;
Expand Down Expand Up @@ -48,7 +50,7 @@ sub info {
'description' => "Returns a single data object.", 'description' => "Returns a single data object.",
'method' => "GET" , 'method' => "GET" ,
'type' => "synchronous" , 'type' => "synchronous" ,
'attributes' => $self->attributes, 'attributes' => $self->{attributes},
'parameters' => { 'required' => { "id" => [ "string", "unique metagenome identifier" ] }, 'parameters' => { 'required' => { "id" => [ "string", "unique metagenome identifier" ] },
'options' => { "type" => [ "cv", [[ "organism", "return organism data" ], 'options' => { "type" => [ "cv", [[ "organism", "return organism data" ],
[ "function", "return function data" ], [ "function", "return function data" ],
Expand Down
48 changes: 26 additions & 22 deletions src/MGRAST/lib/resources2/m5nr.pm
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Expand Up @@ -18,27 +18,31 @@ sub new {
# Add name / attributes # Add name / attributes
$self->{name} = "m5nr"; $self->{name} = "m5nr";
$self->{hierarchy} = { taxonomy => [ ['species', 'taxonomy level'], $self->{hierarchy} = { taxonomy => [ ['species', 'taxonomy level'],
['genus', 'taxonomy level'], ['genus', 'taxonomy level'],
['family', 'taxonomy level'], ['family', 'taxonomy level'],
['order', ' taxonomy level'], ['order', ' taxonomy level'],
['class', ' taxonomy level'], ['class', ' taxonomy level'],
['phylum', 'taxonomy level'], ['phylum', 'taxonomy level'],
['domain', 'top taxonomy level'] ], ['domain', 'top taxonomy level'] ],
ontology => [ ['function', 'bottom ontology level'], ontology => [ ['function', 'bottom ontology level'],
['level3', 'ontology level' ], ['level3', 'ontology level' ],
['level2', 'ontology level' ], ['level2', 'ontology level' ],
['level1', 'top ontology level'] ] ['level1', 'top ontology level'] ]
}; };
$self->{attributes} = { taxonomy => [ 'list', ['list', 'requested taxonomy levels, from highest to lowest'] ], $self->{attributes} = { taxonomy => { id => [ 'string', 'unique object identifier' ],
ontology => [ 'list', ['list', 'requested ontology levels, from highest to lowest'] ], data => [ 'list', ['list', 'requested taxonomy levels, from highest to lowest'] ],
sources => [ 'hash', [['key', ['string', 'source name']], version => [ 'integer', 'version of the object' ],
['value', ['object', [ { 'name' => ['string', 'source name'], url => [ 'uri', 'resource location of this object instance' ] },
'description' => ['string', 'description of source'], ontology => { id => [ 'string', 'unique object identifier' ],
'type' => ['string', 'type of source'], data => [ 'list', ['list', 'requested ontology levels, from highest to lowest'] ],
'link' => ['string', 'link for source id'] }, version => [ 'integer', 'version of the object' ],
'information about source' ]]] url => [ 'uri', 'resource location of this object instance' ] },
]] sources => { id => [ 'string', 'unique object identifier' ],
}; data => [ 'hash', [{'key' => ['string', 'source name'],
'value' => ['object', 'source object']}, 'source object hash'] ],
version => [ 'integer', 'version of the object' ],
url => [ 'uri', 'resource location of this object instance' ] }
};
return $self; return $self;
} }


Expand Down Expand Up @@ -67,7 +71,7 @@ sub info {
'description' => "", 'description' => "",
'method' => "GET", 'method' => "GET",
'type' => "synchronous", 'type' => "synchronous",
'attributes' => $self->attributes->{ontology}, 'attributes' => $self->{attributes}{ontology},
'parameters' => { 'options' => { 'source' => ['cv', [ ['Subsystems', 'returns 4 level SEED-Subsystems ontology' ], 'parameters' => { 'options' => { 'source' => ['cv', [ ['Subsystems', 'returns 4 level SEED-Subsystems ontology' ],
['COG', 'returns 3 level COG ontology'], ['COG', 'returns 3 level COG ontology'],
['NOG', 'returns 3 level NOG ontology'], ['NOG', 'returns 3 level NOG ontology'],
Expand All @@ -84,7 +88,7 @@ sub info {
'description' => "", 'description' => "",
'method' => "GET", 'method' => "GET",
'type' => "synchronous", 'type' => "synchronous",
'attributes' => $self->attributes->{taxonomy}, 'attributes' => $self->{attributes}{taxonomy},
'parameters' => { 'options' => { 'min_level' => ['cv', $self->{hierarchy}{taxonomy}], 'parameters' => { 'options' => { 'min_level' => ['cv', $self->{hierarchy}{taxonomy}],
'id_map' => ['boolean', 'if true overrides other options and returns a map { NCBI tax ID: [taxonomy levels] }'], 'id_map' => ['boolean', 'if true overrides other options and returns a map { NCBI tax ID: [taxonomy levels] }'],
'min_level' => ['cv', $self->{hierarchy}{taxonomy}], 'min_level' => ['cv', $self->{hierarchy}{taxonomy}],
Expand All @@ -98,7 +102,7 @@ sub info {
'description' => "", 'description' => "",
'method' => "GET", 'method' => "GET",
'type' => "synchronous", 'type' => "synchronous",
'attributes' => $self->attributes->{sources}, 'attributes' => $self->{attributes}{sources},
'parameters' => { 'options' => {}, 'parameters' => { 'options' => {},
'required' => {}, 'required' => {},
'body' => {} } 'body' => {} }
Expand Down
53 changes: 23 additions & 30 deletions src/MGRAST/lib/resources2/metadata.pm
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Expand Up @@ -16,36 +16,29 @@ sub new {
my $self = $class->SUPER::new(@args); my $self = $class->SUPER::new(@args);


# Add name / attributes # Add name / attributes
my %rights = $self->user ? map {$_, 1} @{$self->user->has_right_to(undef, 'view', 'project')} : (); my %rights = $self->user ? map {$_, 1} @{$self->user->has_right_to(undef, 'view', 'project')} : ();
my $metadata = [ 'hash', [['key', ['string', 'metadata label']], $self->{name} = "metadata";
['value', ['object', [ { 'type' => ['string', 'value type: text, int, float, select, ontology'], $self->{rights} = \%rights;
'definition' => ['string', 'definition of label'], $self->{attributes} = { "template" => { "project" => [ 'hash', [{'key' => ['string', 'project type'],
'required' => ['boolean', 'is a required label'], 'value' => ['hash', 'hash of metadata objects by label']}, 'projects and their metadata'] ],
'mixs' => ['boolean', 'is a MIxS label'], "sample" => [ 'hash', [{'key' => ['string', 'sample type'],
'aliases' => ['list', ['string', 'alternative name for label']] 'value' => ['hash', 'hash of metadata objects by label']}, 'samples and their metadata'] ],
}, 'information about metadata keyword' ]]] ] "library" => [ 'hash', [{'key' => ['string', 'library type'],
]; 'value' => ['hash', 'hash of metadata objects by label']}, 'libraries and their metadata'] ],
$self->{name} = "metadata"; "ep" => [ 'hash', [{'key' => ['string', 'enviromental package type'],
$self->{rights} = \%rights; 'value' => ['hash', 'hash of metadata objects by label']}, 'eps and their metadata'] ] },
$self->{attributes} = { "template" => { "project" => [ 'hash', ['key', ['string', 'project type']], "cv" => { "ontology" => [ 'hash', [{'key' => ['string', 'metadata label'],
['value', ['object', [$metadata, 'available metadata for this project type']]] ], 'value' => ['int', 'bioportal ontology ID']}, 'ontology IDs for metadata'] ],
"sample" => [ 'hash', ['key', ['string', 'sample type']], "ont_id" => [ 'hash', [{'key' => ['string', 'metadata label'],
['value', ['object', [$metadata, 'available metadata for this sample type']]] ], 'value' => ['int', 'bioportal term ID']}, 'term IDs for metadata'] ],
"library" => [ 'hash', ['key', ['string', 'library type']], "select" => [ 'hash', [{'key' => ['string', 'metadata label'],
['value', ['object', [$metadata, 'available metadata for this library type']]] ], 'value' => ['list', ['string', 'CV term']]}, 'list of CV terms for metadata'] ] },
"ep" => [ 'hash', ['key', ['string', 'enviromental package type']], "export" => { "id" => [ 'string', 'unique object identifier' ],
['value', ['object', [$metadata, 'available metadata for this ep type']]] ] }, "name" => [ 'string', 'human readable identifier' ],
"cv" => { "ontology" => [ 'hash', ['key', ['string', 'metadata label']], "samples" => [ 'list', [ 'object', 'sample object containing sample metadata, sample libraries, sample envPackage' ] ],
['value', ['int', 'bioportal ontology ID']] ], "sampleNum" => [ 'int', 'number of samples in project' ],
"ont_id" => [ 'hash', ['key', ['string', 'metadata label']], "data" => [ 'hash', [{'key' => ['string', 'metadata label'],
['value', ['int', 'bioportal term ID']] ], 'value' => ['object', 'project metadata objects']}, 'hash of metadata by label'] ] },
"select" => [ 'hash', ['key', ['string', 'metadata label']],
['value', ['int', 'list of available CV terms']] ] },
"export" => { "id" => [],
"name" => [],
"samples" => [],
"sampleNum" => [],
"data" => [] },
"validate_post" => { 'is_valid' => [ 'boolean', 'the inputed value is valid for the given category and label' ], "validate_post" => { 'is_valid' => [ 'boolean', 'the inputed value is valid for the given category and label' ],
'metadata' => [ 'object', 'valid metadata object for project and its samples and libraries' ] }, 'metadata' => [ 'object', 'valid metadata object for project and its samples and libraries' ] },
"validate_get" => { 'is_valid' => [ 'boolean', 'the inputed value is valid for the given category and label' ], "validate_get" => { 'is_valid' => [ 'boolean', 'the inputed value is valid for the given category and label' ],
Expand Down
2 changes: 1 addition & 1 deletion src/MGRAST/lib/resources2/metagenome.pm
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Expand Up @@ -28,7 +28,7 @@ sub new {
"version" => [ 'integer', 'version of the object' ], "version" => [ 'integer', 'version of the object' ],
"url" => [ 'uri', 'resource location of this object instance' ], "url" => [ 'uri', 'resource location of this object instance' ],
"status" => [ 'cv', [ ['public', 'object is public'], "status" => [ 'cv', [ ['public', 'object is public'],
['private', 'object is private'] ] ], ['private', 'object is private'] ] ],
"sequence_type" => [ 'string', 'sequencing type' ] "sequence_type" => [ 'string', 'sequencing type' ]
}; };
return $self; return $self;
Expand Down
44 changes: 11 additions & 33 deletions src/MGRAST/lib/resources2/metagenome_statistics.pm
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Expand Up @@ -22,39 +22,17 @@ sub new {
$self->{mgdb} = undef; $self->{mgdb} = undef;
$self->{attributes} = { $self->{attributes} = {
"id" => [ 'string', 'unique metagenome id' ], "id" => [ 'string', 'unique metagenome id' ],
"length_histogram" => { "length_histogram" => [ 'hash', [{'key' => ['string', 'pipeline stage'],
"upload" => [ 'list', 'length distribution of uploaded sequences' ], 'value' => ['list', 'length distribution of sequences in pipeline stage']}, 'length histograms for pipeline stages'] ],
"post_qc" => [ 'list', 'length distribution of post-qc sequences' ] "gc_histogram" => [ 'hash', [{'key' => ['string', 'pipeline stage'],
}, 'value' => ['list', 'gc % distribution of sequences in pipeline stage']}, 'gc % histograms for pipeline stages'] ],
"gc_histogram" => { "qc" => [ 'hash', [{'key' => ['string', 'QC type'],
"upload" => [ 'list', 'gc % distribution of uploaded sequences' ], 'value' => ['object', 'QC statistics object']}, 'set of QC statistics'] ],
"post_qc" => [ 'list', 'gc % distribution of post-qc sequences' ]
},
"qc" => {
"kmer" => { "6_mer" => {"columns" => ['list', 'names of columns'], "data" => ['list', 'kmer 6 counts']},
"15_mer" => {"columns" => ['list', 'names of columns'], "data" => ['list', 'kmer 15 counts']} },
"drisee" => { "counts" => {"columns" => ['list', 'names of columns'], "data" => ['list', 'drisee count profile']},
"percents" => {"columns" => ['list', 'names of columns'], "data" => ['list', 'drisee percent profile']},
"summary" => {"columns" => ['list', 'names of columns'], "data" => ['list', 'drisee summary stats']} },
"bp_profile" => { "counts" => {"columns" => ['list', 'names of columns'], "data" => ['list', 'nucleotide count profile']},
"percents" => {"columns" => ['list', 'names of columns'], "data" => ['list', 'nucleotide percent profile']} }
},
"sequence_stats" => [ 'hash', 'statistics on sequence files of all pipeline stages' ], "sequence_stats" => [ 'hash', 'statistics on sequence files of all pipeline stages' ],
"taxonomy" => { "taxonomy" => [ 'hash', [{'key' => ['string', 'taxonomic level'],
"species" => [ 'list', 'species counts' ], 'value' => ['list', ['tuple', 'taxanomic name and abundance']]}, 'set of abundaces per taxonomic levels'] ],
"genus" => [ 'list', 'genus counts' ], "ontology" => [ 'hash', [{'key' => ['string', 'ontology source'],
"family" => [ 'list', 'family counts' ], 'value' => ['list', ['tuple', 'ontology name and abundance']]}, 'set of abundaces per ontology group'] ],
"order" => [ 'list', 'order counts' ],
"class" => [ 'list', 'class counts' ],
"phylum" => [ 'list', 'phylum counts' ],
"domain" => [ 'list', 'domain counts' ]
},
"ontology" => {
"COG" => [ 'list', 'COG counts' ],
"KO" => [ 'list', 'KO counts' ],
"NOG" => [ 'list', 'NOG counts' ],
"Subsystems" => [ 'list', 'Subsystem counts' ]
},
"source" => [ 'hash', 'evalue and % identity counts per source' ], "source" => [ 'hash', 'evalue and % identity counts per source' ],
"rarefaction" => [ 'list', 'rarefaction coordinate data' ] "rarefaction" => [ 'list', 'rarefaction coordinate data' ]
}; };
Expand Down Expand Up @@ -84,7 +62,7 @@ sub info {
'description' => "Returns a JSON structure of statistical information.", 'description' => "Returns a JSON structure of statistical information.",
'method' => "GET" , 'method' => "GET" ,
'type' => "synchronous" , 'type' => "synchronous" ,
'attributes' => $self->attributes, 'attributes' => $self->{attributes},
'parameters' => { 'options' => { 'verbosity' => ['cv', 'parameters' => { 'options' => { 'verbosity' => ['cv',
[['minimal','returns only sequence_stats attribute'], [['minimal','returns only sequence_stats attribute'],
['verbose','returns all but qc attribute'], ['verbose','returns all but qc attribute'],
Expand Down
6 changes: 3 additions & 3 deletions src/MGRAST/lib/resources2/project.pm
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Expand Up @@ -21,8 +21,8 @@ sub new {
$self->{attributes} = { "id" => [ 'string', 'unique object identifier' ], $self->{attributes} = { "id" => [ 'string', 'unique object identifier' ],
"name" => [ 'string', 'human readable identifier' ], "name" => [ 'string', 'human readable identifier' ],
"libraries" => [ 'list', [ 'reference library', 'a list of references to the related library objects' ] ], "libraries" => [ 'list', [ 'reference library', 'a list of references to the related library objects' ] ],
"samples" => [ 'list', [ 'reference sample', 'a list of references to the related sample objects' ] ], "samples" => [ 'list', [ 'reference sample', 'a list of references to the related sample objects' ] ],
"analyzed" => [ 'list', [ 'reference metagenome', 'a list of references to the related metagenome objects' ] ], "analyzed" => [ 'list', [ 'reference metagenome', 'a list of references to the related metagenome objects' ] ],
"description" => [ 'string', 'a short, comprehensive description of the project' ], "description" => [ 'string', 'a short, comprehensive description of the project' ],
"funding_source" => [ 'string', 'the official name of the source of funding of this project' ], "funding_source" => [ 'string', 'the official name of the source of funding of this project' ],
"pi" => [ 'string', 'the first and last name of the principal investigator of the project' ], "pi" => [ 'string', 'the first and last name of the principal investigator of the project' ],
Expand All @@ -31,7 +31,7 @@ sub new {
"version" => [ 'integer', 'version of the object' ], "version" => [ 'integer', 'version of the object' ],
"url" => [ 'uri', 'resource location of this object instance' ], "url" => [ 'uri', 'resource location of this object instance' ],
"status" => [ 'cv', [ ['public', 'object is public'], "status" => [ 'cv', [ ['public', 'object is public'],
['private', 'object is private'] ] ] ['private', 'object is private'] ] ]
}; };
return $self; return $self;
} }
Expand Down
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