Bio::Das::ProServer::SourceAdaptor - base class for sources
$Revision: 554 $
A base class implementing stubs for all SourceAdaptors.
SourceAdaptor.pm generates XML and manages callouts for DAS request handling.
If you're extending ProServer, this class is probably what you need to inherit. The build_* methods are probably the ones you need to extend. build_features() in particular.
Roger Pettett <rmp@sanger.ac.uk>
Andy Jenkinson <andy.jenkinson@ebi.ac.uk>
my $oSourceAdaptor = Bio::Das::ProServer::SourceAdaptor::<implementation>->new({
'dsn' => q(),
'port' => q(),
'hostname' => q(),
'protocol' => q(),
'baseuri' => q(),
'config' => q(),
'debug' => 1,
});
Generally this would only be invoked on a subclass
$oSourceAdaptor->init();
my $sSegmentLength = $oSourceAdaptor->length('DYNA_CHICK');
By default returns 0
my $sMapMaster = $oSourceAdaptor->mapmaster(); By default returns configuration 'mapmaster' setting
my $sDescription = $oSourceAdaptor->description(); By default returns configuration 'description' setting or $self->title
my $sDocHref = $oSourceAdaptor->doc_href(); By default returns configuration 'doc_href' setting
my $title = $oSourceAdaptor->title(); By default returns configuration 'title' setting or $self->source_uri
my $uriS = $oSourceAdaptor->source_uri(); By default returns configuration 'source_uri' setting or $self->dsn
my $uriV = $oSourceAdaptor->version_uri(); By default returns configuration 'version_uri' setting or $self->source_uri
my $email = $oSourceAdaptor->maintainer(); By default returns configuration 'maintainer' setting, server setting or an empty string
my $strict = $oSourceAdaptor->strict_boundaries(); # boolean By default returns configuration 'strict_boundaries' setting, server setting or nothing (false)
This call is made by das_features(). It is passed one of:
{ 'segment' => $, 'start' => $, 'end' => $, 'types' => [$,$,...], 'maxbins' => $ }
{ 'feature_id' => $ }
{ 'group_id' => $, 'types' => [$,$,...], 'maxbins' => $ }
and is expected to return a reference to an array of hash references, i.e.
[{},{}...{}]
Each hash returned represents a single feature and should contain a subset of the following keys and types. For scalar types (i.e. numbers and strings) refer to the specification on biodas.org.
segment => $ # segment ID (if not provided)
id || feature_id => $ # feature ID
label || feature_label => $ # feature text label
start => $ # feature start position
end => $ # feature end position
ori => $ # feature strand
phase => $ # feature phase
type => $ # feature type ID
typetxt => $ # feature type text label
typecategory || type_category => $ # feature type category
typesubparts => $ # feature has subparts
typesuperparts => $ # feature has superparts
typereference => $ # feature is reference
method => $ # annotation method ID
method_label => $ # annotation method text label
score => $ # annotation score
note => $ or [$,$,$...] # feature text note
##########################################################################
# For one or more links:
link => $ or [$,$,$...] # feature link href
linktxt => $ or [$,$,$...] # feature link label
# For hash-based links:
link => {
$ => $, # href => label
...
}
###############################################################################
# For a single target:
target_id => $ # target ID
target_start => $ # target start position
target_stop => $ # target end position
targettxt => $ # target text label
# For multiple targets:
target => scalar or [{
id => $,
start => $,
stop => $,
targettxt => $,
},{}...]
###############################################################################
# For a single group:
group_id => $ # feature group ID
grouplabel => $ # feature group text label
grouptype => $ # feature group type ID
groupnote => $ # feature group text note
grouplink => $ # feature group ID
grouplinktxt => $ # feature group ID
# For multiple groups:
group => [{
grouplabel => $
grouptype => $
groupnote => $
grouplink => $
grouplinktxt => $
note => $ or [$,$,$...]
target => [{
id => $
start => $
stop => $
targettxt => $
}],
}, {}...]
This call is made by das_sequence() or das_dna(). It is passed:
{ 'segment' => $, 'start' => $, 'end' => $ }
It is expected to return a hash reference:
{
seq => $,
version => $, # can also be specified with the segment_version method
moltype => $,
}
For details of the data constraints refer to the specification on biodas.org.
This call is made by das_types(). If no specific segments are requested by the client, it is passed no arguments. Otherwise it is passed:
{ 'segment' => $, 'start' => $, 'end' => $ }
It is expected to return a reference to an array of hash references, i.e. [{},{}...{}]
Each hash returned represents a single type and should contain a subset of the following keys and values. For scalar types (i.e. numbers and strings) refer to the specification on biodas.org.
type => $ method => $ category => $ c_ontology => $ evidence => $ e_ontology => $ description => $ count => $
This call is made by das_entry_points(). It is not passed any args
and is expected to return a reference to an array of hash references, i.e. [{},{}...{}]
Each hash returned represents a single entry_point and should contain a subset of the following keys and values. For scalar types (i.e. numbers and strings) refer to the specification on biodas.org.
segment => $ length => $ subparts => $ start => $ stop => $ ori => $
This call is made by das_alignment(). It is passed these arguments:
( $, # query sequence $, # number of rows [ $, $ ], # subjects $ # subject coordinate system )
It is expected to return an array reference of alignment hash references:
[
{
name => $,
type => $,
max => $,
position => $,
alignObj => [
{
id => $, # internal object ID
version => $,
type => $,
dbSource => $,
dbVersion => $,
dbAccession => $,
dbCoordSys => $,
sequence => $,
aliObjectDetail => [
{
property => $,
value => $,
dbSource => $,
},
],
},
],
scores => [
{
method => $,
score => $,
},
],
blocks => [
{
blockOrder => $,
blockScore => $,
segments => [
{
id => $, # internal object ID
start => $,
end => $,
orientation => $, # + / - / undef
cigar => $,
},
],
],
geo3D => [
{
id
vector => {
x => $,
y => $,
z => $,
},
matrix => [
[$,$,$], # mat11, mat12, mat13
[$,$,$], # mat21, mat22, mat23
[$,$,$], # mat31, mat32, mat33
],
},
],
This call is made by das_interaction(). It is passed this structure:
# For request:
# /interaction?interactor=$;interactor=$;detail=property:$;detail=property:$,value:$
{
interactors => [$, $, ..],
details => {
$ => undef, # property exists
$ => $, # property has a certain value
},
}
It is expected to return a hash reference of interactions and interactors where all the requested interactors are part of the interaction:
{
interactors => [
{
id => $,
label || name => $,
dbSource => $,
dbSourceCvId => $, # controlled vocabulary ID
dbVersion => $,
dbAccession => $,
dbCoordSys => $, # co-ordinate system
sequence => $,
details => [
{
property => $,
value => $,
propertyCvId => $,
valueCvId => $,
start => $,
end => $,
startStatus => $,
endStatus => $,
startStatusCvId => $,
endStatusCvId => $,
},
..
],
},
..
],
interactions => [
{
label || name => $,
dbSource => $,
dbSourceCvId => $,
dbVersion => $,
dbAccession => $,
details => [
{
property => $,
value => $,
propertyCvId => $,
valueCvId => $,
},
..
],
participants => [
{
id => $,
details => [
{
property => $,
value => $,
propertyCvId => $,
valueCvId => $,
start => $,
end => $,
startStatus => $,
endStatus => $,
startStatusCvId => $,
endStatusCvId => $,
},
..
],
},
..
],
},
..
],
}
This call is made by das_volmap(). It is passed a single 'query' argument.
It is expected to return a hash reference for a single volume map:
{
id => $,
class => $,
type => $,
version => $,
link => $, # href for data
linktxt => $, # text
note => $ OR [ $, $, .. ]
}
By default - do nothing Not necessary for most circumstances, but useful for deciding on what sort of coordinate system you return the results if more than one type is available. $self->init_segments() is called inside das_features() before build_features().
my @aSegmentNames = $oSourceAdaptor->known_segments();
my $sVersion = $oSourceAdaptor->segment_version($sSegment);
my $sDSN = $oSourceAdaptor->dsn();
my $sDSNVersion = $oSourceAdaptor->dsnversion();
By default returns $self->{'dsnversion'}, configuration 'dsnversion' setting or '1.0'
# e.g. '2007-09-20T15:26:23Z' -- ISO 8601, Coordinated Universal Time
# e.g. '2007-09-20T16:26:23+01:00' -- ISO 8601, British Summer Time
# e.g. '2007-09-20 07:26:23 -08' -- indicating Pacific Standard Time
# e.g. 1190301983 -- UNIX
# e.g. '2007-09-20'
my $sDSNCreated = $oSourceAdaptor->dsncreated();
By default tries and returns the following:
1. $self->{'dsncreated'}
2. configuration 'dsncreated' setting
3. adaptor's 'last_modified' method (if it exists)
4. zero (epoch)
# e.g. 1190301983 my $sDSNCreated = $oSourceAdaptor->dsncreated_unix();
# e.g. '2007-09-20T15:26:23Z' my $sDSNCreated = $oSourceAdaptor->dsncreated_iso();
my $hCoords = $oSourceAdaptor->coordinates(); Hash contains a key-value pair for each coordinate system, the key being either the URI or description, and the value being a suitable test range. By default returns an empty hash reference
my $aCoords = $oSourceAdaptor->coordinates();
Returns the fully-annotated co-ordinates systems this adaptor supports, as an
array or array reference (depending on context):
[
{
'description' => 'NCBI_36,Chromosome,Homo sapiens',
'uri' => 'http://www.dasregistry.org/dasregistry/coordsys/CS_DS40',
'taxid' => '9606',
'authority' => 'NCBI',
'source' => 'Chromosome',
'version' => '36',
'test_range' => '1:11000000,12000000',
},
{
...
},
]
The co-ordinate system details are read in from disk by Bio::Das::ProServer.
By default returns an empty array.
my $hCapabilities = $oSourceAdaptor->capabilities();
Hash contains a key-value pair for each command, the key being the command
name, and the value being the implementation version.
By default returns: { 'dsn' => '1.0' }
my $hProps = $oSourceAdaptor->properties(); Hash contains key-scalar or key-array pairs for custom properties. By default returns an empty hash reference
my $sStart = $oSourceAdaptor->start('DYNA_CHICK');
By default returns 1
my $sEnd = $oSourceAdaptor->end('DYNA_CHICK');
By default returns $self->length
my $sUrl = $oSourceAdaptor->server_url();
my $sUrl = $oSourceAdaptor->source_url();
my $oHydra = $oSourceAdaptor->hydra();
my $oTransport = $oSourceAdaptor->transport();
OR
my $oTransport1 = $oSourceAdaptor->transport('foo');
my $oTransport2 = $oSourceAdaptor->transport('bar');
my $oAuthenticator = $oSourceAdaptor->authenticator(); Authenticators are built only if explicitly configured in the INI file, e.g.: [mysource] state = on adaptor = simple authenticator = ip See L<Bio::Das::ProServer::Authenticator> for more details.
$oSourceAdaptor->config($oConfig); my $oConfig = $oSourceAdaptor->config();
my $bIsImplemented = $oSourceAdaptor->implements($sDASCall); # e.g. $sDASCall = 'sequence'
my $sHTTPHeader = $oSourceAdaptor->das_capabilities();
my $sXMLResponse = $sa->unknown_segment(); Reference sources (i.e. those implementing the 'dna' or 'sequence' command) will return an <ERRORSEGMENT> element. Annotation sources will return an <UNKNOWNSEGMENT> element.
my $sXMLResponse = $sa->error_segment(); Returns an <ERRORSEGMENT> element.
my $sXMLResponse = $sa->error_feature();
my $sXMLResponse = $sa->das_features(); See the build_features method for details of custom implementations.
my $xml = $sa->das_dna(); See the sequence method for details of custom implementations.
my $sXMLResponse = $sa->das_sequence(); See the sequence method for details of custom implementations.
my $sXMLResponse = $sa->das_types(); See the build_types method for details of custom implementations.
my $sXMLResponse = $sa->das_entry_points(); See the build_entry_points method for details of custom implementations.
my $sXMLResponse = $sa->das_interaction(); See the build_interaction method for details of custom implementations.
my $sXMLResponse = $sa->das_volmap(); See the build_volmap method for details of custom implementations.
my $sXMLResponse = $sa->das_stylesheet();
my $sXMLResponse = $sa->das_sourcedata();
my $sHTMLResponse = $sa->das_homepage();
my $sXMLResponse = $sa->das_dsn();
my $sXSLResponse = $sa->das_xsl();
my $sXMLResponse = $sa->das_alignment(); See the build_alignment method for details of custom implementations. Example Response:
<alignment> <alignObject> <alignObjectDetail /> <sequence /> </alignObject> <score/> <block> <segment> <cigar /> </segment> </block> <geo3D> <vector /> <matrix mat11="float" mat12="float" mat13="float" mat21="float" mat22="float" mat23="float" mat31="float" mat32="float" mat33="float" /> </geo3D> </alignment>
Title : _gen_align_object_response Function : Formats alignment object into dasalignment xml Args : align data structure Returns : Das Response string encapuslating aliObject
Title : _gen_align_score_response Function: Formats input score data structure into dasalignment xml Args : score data structure Returns : Das Response string from alignment score
Title : _gen_align_block_response
Function: Formats an input block data structure into
: dasalignment xml
Args : block data structure
Returns : Das Response string from alignmentblock
Title : genAlignGeo3d Function : Formats geo3d data structure into alignment matrix xml Args : data structure containing the vector and matrix Returns : String containing the DAS response xml
Title : das_structure
Function : This produces the das repsonse for a pdb structure
Args : query options. Currently, this will that query, chain and modelnumber.
: The only part of the specification that this does not adhere to is the range argument.
: However, I think this argument is a potential can of worms!
returns : string containing Das repsonse for the pdb structure
comment : See http://www.efamily.org.uk/xml/das/documentation/structure.shtml for more information
: on the das structure specification.
Example Response:
<object dbAccessionId="1A4A" intObjectId="1A4A" objectVersion="29-APR-98" type="protein structure" dbSource="PDB" dbVersion="20040621" dbCoordSys="PDBresnum" />
<chain id="A" SwissprotId="null">
<group name="ALA" type="amino" groupID="1">
<atom atomID="1" atomName=" N " x="-19.031" y="16.695" z="3.708" />
<atom atomID="2" atomName=" CA " x="-20.282" y="16.902" z="4.404" />
<atom atomID="3" atomName=" C " x="-20.575" y="18.394" z="4.215" />
<atom atomID="4" atomName=" O " x="-20.436" y="19.194" z="5.133" />
<atom atomID="5" atomName=" CB " x="-20.077" y="16.548" z="5.883" />
<atom atomID="6" atomName="1H " x="-18.381" y="17.406" z="4.081" />
<atom atomID="7" atomName="2H " x="-18.579" y="15.781" z="3.874" />
<atom atomID="8" atomName="3H " x="-19.018" y="16.844" z="2.68" />
</group>
<group name="HOH" type="hetatm" groupID="219">
<atom atomID="3057" atomName=" O " x="-17.904" y="13.635" z="-7.538" />
<atom atomID="3058" atomName="1H " x="-18.717" y="14.098" z="-7.782" />
<atom atomID="3059" atomName="2H " x="-17.429" y="13.729" z="-8.371" />
</group>
</chain>
<connect atomSerial="26" type="bond">
<atomID atomID="25" />
<atomID atomID="242" />
</connect>
Title : _gen_object_response
Function : Formats the supplied structure object data structure into dasstructure xml
Args : object data structure
Returns : Das Response string encapuslating 'object'
Comment : The object response allows the details of the coordinates to be descriped. For example
: the fact that the coos are part of a pdb file.
Title : _gen_chain_response
Function : Formats the supplied chain object data structure into dasstructure xml
Args : chain data structure
Returns : Das Response string encapuslating 'chain'
Comment : Chain objects contain all of the atom positions (including hetatoms).
: The groups are typically residues or ligands.
Title : _gen_connect_response Function : Formats the supplied connect data structure into dasstructure xml Args : connect data structure Returns : Das Response string encapuslating "connect" Comment : Such objects are specified to enable groups of atoms to be connected together.
Used within Bio::Das::ProServer::Config, eg/proserver and of course all subclasses.
set $self->{'debug'} = 1
None reported
None reported
Copyright (c) 2008 The Sanger Institute
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
