Of course to use the ontology I had to make one first.
Unsurprisingly implementing it touched a bunch of code & templates.
I tried to be more consisten with using mixed-case names for
classes and lower_case names for properties.
There's some inconsistencies. like i use the term notes & comments
in different areas. Also, should I be using my own terms or
do better at reusing more standard ontologies?
import encode_find
from htsworkflow.submission.ucsc import submission_view_url
-from htsworkflow.util.rdfhelp import dump_model, get_model, fromTypedNode
+from htsworkflow.util.rdfhelp import add_default_schemas, \
+ dump_model, get_model, fromTypedNode
+from htsworkflow.util.rdfinfer import Infer
SOURCE_PATH = os.path.split(os.path.abspath(__file__))[0]
print SOURCE_PATH
class TestEncodeFind(unittest.TestCase):
+ def setUp(self):
+ self.model = get_model()
+ add_default_schemas(self.model)
+ self.inference = Infer(self.model)
+
def test_create_status_node_with_uri(self):
subURL = submission_view_url('5136')
submissionUri = RDF.Uri(subURL)
test_file = os.path.join(SOURCE_PATH, 'testdata', '5136SubDetail.html')
from lxml.html import parse
tree = parse(test_file)
- model = get_model()
- dates = encode_find.get_creation_dates(model, subNode)
+ dates = encode_find.get_creation_dates(self.model, subNode)
self.assertEqual(len(dates), 0)
- encode_find.parse_submission_page(model, tree, subNode)
- dates = encode_find.get_creation_dates(model, subNode)
+ encode_find.parse_submission_page(self.model, tree, subNode)
+ dates = encode_find.get_creation_dates(self.model, subNode)
self.assertEqual(len(dates), 1)
object_date = fromTypedNode(dates[0].object)
self.assertEqual(object_date, datetime(2011,12,7,15,23,0))
libns:total_unique_locations 5789938 .
''', 'http://jumpgate.caltech.edu/library/')
+ errmsgs = list(self.inference.run_validation())
+ self.assertEqual(len(errmsgs), 0)
urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/lane/1232'))
encode_find.delete_lane(model, urn)
self.failUnlessEqual(len(model), 0)
def test_delete_lane_with_mapping(self):
- model = get_model()
+ ontology_size = len(self.model)
parser = RDF.Parser(name='turtle')
- parser.parse_string_into_model(model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+ parser.parse_string_into_model(self.model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix : <http://www.w3.org/1999/xhtml> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
+<http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> a libns:IlluminaFlowcell .
<http://jumpgate.caltech.edu/lane/1232>
libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
libns:has_mappings _:bnode110110 ;
- libns:total_unique_locations 5789938 .
+ libns:total_unique_locations 5789938 ;
+ a libns:IlluminaLane .
_:bnode110110
+ a libns:MappedCount ;
libns:mapped_to "newcontam_UK.fa"@en ;
libns:reads 42473 .
''', 'http://jumpgate.caltech.edu/library/')
- self.failUnlessEqual(len(model), 5)
+ errmsgs = list(self.inference.run_validation())
+ self.assertEqual(len(errmsgs), 0)
+ self.failUnlessEqual(len(self.model), 8 + ontology_size)
urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/lane/1232'))
- encode_find.delete_lane(model, urn)
- self.failUnlessEqual(len(model), 0)
+ encode_find.delete_lane(self.model, urn)
+ self.failUnlessEqual(len(self.model), 1 + ontology_size)
+ # the flowcell triple wasn't deleted.
def test_delete_library(self):
- model = get_model()
parser = RDF.Parser(name='turtle')
- parser.parse_string_into_model(model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+ parser.parse_string_into_model(self.model, '''@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix : <http://www.w3.org/1999/xhtml> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
+<http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> a libns:IlluminaFlowcell .
+<http://jumpgate.caltech.edu/flowcell/62WCKAAXX/> a libns:IlluminaFlowcell .
+
<http://jumpgate.caltech.edu/lane/1232>
+ a libns:IlluminaLane ;
libns:flowcell <http://jumpgate.caltech.edu/flowcell/42JV5AAXX/> ;
libns:has_mappings _:bnode110110 ;
libns:total_unique_locations 5789938 .
libns:has_lane <http://jumpgate.caltech.edu/lane/1232> ;
libns:library_id "11011"@en ;
libns:library_type "None"@en ;
- a "libns:library"@en ;
+ a libns:Library ;
<http://www.w3.org/1999/xhtml/vocab#stylesheet> <http://jumpgate.caltech.edu/static/css/app.css>, <http://jumpgate.caltech.edu/static/css/data-browse-index.css> .
_:bnode110110
+ a libns:MappedCount ;
libns:mapped_to "newcontam_UK.fa"@en ;
libns:reads 42473 .
<http://jumpgate.caltech.edu/lane/1903>
+ a libns:IlluminaLane ;
libns:flowcell <http://jumpgate.caltech.edu/flowcell/62WCKAAXX/> ;
libns:has_mappings _:bnode120970 ;
libns:total_unique_locations 39172114 .
libns:has_lane <http://jumpgate.caltech.edu/lane/1903> ;
libns:library_id "12097"@en ;
libns:library_type "Paired End (non-multiplexed)"@en ;
- a "libns:library"@en .
+ a libns:Library .
_:bnode120970
+ a libns:MappedCount ;
libns:mapped_to "newcontam_UK.fa"@en ;
libns:reads 64 .
''', 'http://jumpgate.caltech.edu/library')
+ errmsgs = list(self.inference.run_validation())
+ self.assertEqual(len(errmsgs), 0)
urn = RDF.Node(RDF.Uri('http://jumpgate.caltech.edu/library/11011/'))
- encode_find.delete_library(model, urn)
+ encode_find.delete_library(self.model, urn)
q = RDF.Statement(None, encode_find.libraryOntology['reads'], None)
- stmts = list(model.find_statements(q))
+ stmts = list(self.model.find_statements(q))
self.failUnlessEqual(len(stmts), 1)
self.failUnlessEqual(fromTypedNode(stmts[0].object),
64)
q = RDF.Statement(None, encode_find.libraryOntology['library_id'], None)
- stmts = list(model.find_statements(q))
+ stmts = list(self.model.find_statements(q))
self.failUnlessEqual(len(stmts), 1)
self.failUnlessEqual(fromTypedNode(stmts[0].object),
'12097')
failed_fc_span = flowcell_spans[0]
failed_fc_a = failed_fc_span.getparent()
# make sure some of our RDF made it.
- self.assertEqual(failed_fc_a.get('rel'), 'libns:flowcell')
+ self.assertEqual(failed_fc_a.get('typeof'), 'libns:IlluminaFlowcell')
self.assertEqual(failed_fc_a.get('href'), '/flowcell/30012AAXX/')
fc_response = self.client.get(failed_fc_a.get('href'))
self.assertEqual(fc_response.status_code, 200)
select ?flowcell ?flowcell_id ?lane_id ?library_id
where {
- ?flowcell a libns:illumina_flowcell ;
+ ?flowcell a libns:IlluminaFlowcell ;
libns:flowcell_id ?flowcell_id ;
libns:has_lane ?lane .
?lane libns:lane_number ?lane_id ;
def test_rdf(self):
response = self.client.get('/flowcell/FC12150/', apidata)
tree = fromstring(response.content)
- divs = tree.xpath('//div[@rel="libns:sequenced_by"]',
- namespaces=NSMAP)
- self.assertEqual(len(divs), 1)
- self.assertEqual(divs[0].attrib['rel'], 'libns:sequenced_by')
- self.assertEqual(divs[0].attrib['resource'], '/sequencer/2')
-
- name = divs[0].xpath('./span[@property="libns:sequencer_name"]')
+ seq_by = tree.xpath('//div[@rel="libns:sequenced_by"]',
+ namespaces=NSMAP)
+ self.assertEqual(len(seq_by), 1)
+ self.assertEqual(seq_by[0].attrib['rel'], 'libns:sequenced_by')
+ seq = seq_by[0].getchildren()
+ self.assertEqual(len(seq), 1)
+ self.assertEqual(seq[0].attrib['about'], '/sequencer/2')
+ self.assertEqual(seq[0].attrib['typeof'], 'libns:Sequencer')
+
+ name = seq[0].xpath('./span[@property="libns:sequencer_name"]')
self.assertEqual(len(name), 1)
self.assertEqual(name[0].text, 'Tardigrade')
- instrument = divs[0].xpath(
+ instrument = seq[0].xpath(
'./span[@property="libns:sequencer_instrument"]')
self.assertEqual(len(instrument), 1)
self.assertEqual(instrument[0].text, 'ILLUMINA-EC5D15')
- model = divs[0].xpath(
+ model = seq[0].xpath(
'./span[@property="libns:sequencer_model"]')
self.assertEqual(len(model), 1)
self.assertEqual(model[0].text, 'Illumina Genome Analyzer IIx')
</thead>
<tbody>
{% for lane in lanes %}
- <tr rel="libns:has_lane" resource="{{lane.get_absolute_url}}" >
- <td><a href="{{lane.get_absolute_url}}">
- <span property="libns:lane_number" datatype="xsd:decimal">{{lane.lane_number}}</span></a></td>
- <td><a href="{{lane.library.get_absolute_url}}"
- rel="libns:library"><span property="libns:library_id"
- >{{lane.library.id}}</span></a>
+ <tr rel="libns:has_lane">
+ <div typeof="libns:IlluminaLane" about="{{lane.get_absolute_url}}">
+ <td>
+ <a href="{{lane.get_absolute_url}}">
+ <span property="libns:lane_number" datatype="xsd:decimal"
+ >{{lane.lane_number}}</span>
+ </a>
+ </td>
+ <div rel="libns:library">
+ <div typeof="libns:Library" about="{{lane.library.get_absolute_url}}">
+ <td>
+ <a href="{{lane.library.get_absolute_url}}">
+ <span property="libns:library_id"
+ >{{lane.library.id}}</span></a>
{% if user.is_staff %}
<a href="{{lane.library.get_admin_url}}">
<img class="icon_button"
src="/media/img/admin/icon_changelink.gif"/>
</a>{% endif %}
</td>
- <td><a href="{{lane.library.get_absolute_url}}" rel="libns:library"><span property="libns:name">{{lane.library.library_name}}</span></a></td>
- <td><a href="{{lane.library.library_species.get_absolute_url}}" rel="libns:species">
+ <td><a href="{{lane.library.get_absolute_url}}">
+ <span property="libns:name">{{lane.library.library_name}}</span>
+ </a></td>
+ <td rel="libns:species">
+ <a href="{{lane.library.library_species.get_absolute_url}}"
+ typeof="libns:Species">
<span property="libns:species_name">{{ lane.library.library_species.scientific_name }}</span></a></td>
+ </div> <!-- end library class -->
+ </div> <!-- end library relation -->
<td><span property="libns:comment">{{lane.comment}}</span></td>
+ </div> <!-- end lane -->
</tr>
{% endfor %}
</tbody>
<h2>About this Flowcell</h2>
<b>Flowcell</b>:
<a href="{{flowcell.get_absolute_url}}" property="libns:flowcell_id">{{flowcell.flowcell_id}}</a>{% if user.is_staff %}<a href="{{flowcell.get_admin_url}}"><img class="icon_button" src="/media/img/admin/icon_changelink.gif" alt="Edit"/></a>{% endif%}
- <br rel="rdf:type" resource="http://jumpgate.caltech.edu/wiki/LibraryOntology#illumina_flowcell"/>
- <div rel="libns:sequenced_by"
- resource="{{flowcell.sequencer.get_absolute_url}}">
+ <br rel="rdf:type" resource="http://jumpgate.caltech.edu/wiki/LibraryOntology#IlluminaFlowcell"/>
+ <div rel="libns:sequenced_by">
+ <div typeof="libns:Sequencer"
+ about="{{flowcell.sequencer.get_absolute_url}}">
<b>Instrument</b>:
<span property="libns:sequencer_name">{{ flowcell.sequencer.name }}</span>
{% if flowcell.sequencer.instrument_name %}
<span property="libns:sequencer_model">{{flowcell.sequencer.model}}</span>
<br/>
</div>
+ </div>
{% for datarun in flowcell.datarun_set.all %}
<b>Image Analysis</b>:
<span property="libns:image_software">{{datarun.image_software}}</span>
<!-- App Stuff -->
<link type="text/css" rel="stylesheet" href="/static/css/app.css" />
<script type="text/javascript" src="/static/js/jquery.min.js"></script>
-
+
{% block additional_javascript %}
{% endblock %}
{% endblock %}
{% block content %}
-<div id="lane_detail" class="htswdetail">
+<div id="lane_detail" class="htswdetail" rel="rdf:type" resource="libns:IlluminaLane">
<div rel="libns:flowcell" resource="{{flowcell.get_absolute_url}}">
{% include "experiments/flowcell_header.html" %}
<div class="flowcell_lane_detail">
<h2>About this lane</h2>
- <b>Lane</b>:
+ <b>Lane</b>:
<span property="libns:lane_number" datatype="xsd:decimal">{{lane.lane_number}}</span><br/>
<b>pM</b>:
<span property="libns:pM" datatype="xsd:decimal">{{ lane.pM }}</span><br/>
<b>Cluster Estimate</b>:
<span property="libns:cluster_estimate" datatype="xsd:decimal"
content="{{lane.cluster_estimate}}">{{ lane.cluster_estimate|intcomma }}</span><br/>
- <b>Lane Status</b>:
+ <b>Lane Status</b>:
<span property="libns:status">{{ lane.status }}</span><br/>
- <b>Comments</b>:
+ <b>Comments</b>:
<span property="libns:comment">{{ lane.comment }}</span><br/>
</div>
<hr/>
</td>
</tr>
{% endif %}
- {% endfor %}
+ {% endfor %}
</tbody>
</table>
{% endfor %}
-<div id="librarydetail" about="{{lib.get_absolute_url}}" typeof="libns:library">
+<div id="librarydetail"
+ about="{{lib.get_absolute_url}}"
+ typeof="libns:Library">
<div class="library_identity">
<h2>Library Name</h2>
<b>Library ID</b>:
<tbody>
{% for lane in lib.lane_set.all %}
<tr rel="libns:has_lane" resource="{{lane.get_absolute_url}}">
- <td><a href="{{lane.flowcell.get_absolute_url}}" rel="libns:flowcell"
- ><span property="libns:flowcell_id">{{ lane.flowcell.flowcell_id }}</span></a>
+ <td>
+ <a typeof="libns:IlluminaFlowcell" href="{{lane.flowcell.get_absolute_url}}">
+ <span property="libns:flowcell_id"
+ >{{lane.flowcell.flowcell_id}}</span></a>
{% if user.is_staff %}
<a href="{{lane.flowcell.get_admin_url}}">
<img class="icon_button"
</a>
{% endif%}
</td>
- <td><a href="{{lane.get_absolute_url}}">
+ <td typeof="libns:IlluminaLane" about="{{lane.get_absolute_url}}">
+ <span rel="libns:flowcell" resource="{{lane.flowcell.get_absolute_url}}"></span>
+ <a href="{{lane.get_absolute_url}}">
<span property="libns:lane_number" datatype="xsd:decimal"
- >{{ lane.lane_number }}</span></a></td>
+ >{{ lane.lane_number }}</span>
+ </a></td>
<td>{{ lane.comment }}</td>
</tr>
{% endfor %}
select ?library ?lane
where {{
<{flowcell}> libNS:has_lane ?lane ;
- a libNS:illumina_flowcell .
+ a libNS:IlluminaFlowcell .
?lane libNS:lane_number {lane_id} ;
libNS:library ?library .
}}
libns:has_lane <{base}/lane/1169>, <{base}/lane/1170>,
<{base}/lane/1171>, <{base}/lane/1172> ;
libns:read_length 75 ;
- a libns:illumina_flowcell .
+ a libns:IlluminaFlowcell .
<{base}/lane/1169>
libns:lane_number 1 ; libns:library <{base}/library/10923/> .
def import_library(self, library):
"""Import library data into our model if we don't have it already
"""
- q = RDF.Statement(library, rdfNS['type'], libraryOntology['library'])
+ q = RDF.Statement(library, rdfNS['type'], libraryOntology['Library'])
present = False
if not self.model.contains_statement(q):
present = True
select distinct ?flowcell ?flowcell_id
WHERE {
- ?library a libns:library ;
+ ?library a libns:Library ;
libns:has_lane ?lane .
?lane libns:flowcell ?flowcell .
?flowcell libns:flowcell_id ?flowcell_id .
LOGGER.debug("Flowcells = %s" %(unicode(flowcell_ids)))
flowcell_test = RDF.Statement(r['flowcell'],
rdfNS['type'],
- libraryOntology['illumina_flowcell'])
+ libraryOntology['IlluminaFlowcell'])
if not self.model.contains_statement(flowcell_test):
# we probably lack full information about the flowcell.
load_into_model(self.model, 'rdfa', r['flowcell'])
from htsworkflow.submission.condorfastq import CondorFastqExtract
from htsworkflow.submission.results import ResultMap
-from htsworkflow.util.rdfhelp import load_string_into_model, dump_model
+from htsworkflow.util.rdfhelp import \
+ add_default_schemas, load_string_into_model, dump_model
+from htsworkflow.util.rdfinfer import Infer
FCDIRS = [
'C02F9ACXX',
@prefix seqns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
@prefix invns: <http://jumpgate.caltech.edu/wiki/InventoryOntology#> .
+<http://localhost/library/10000/> a libns:Library .
+<http://localhost/library/1331/> a libns:Library .
+<http://localhost/library/1421/> a libns:Library .
+<http://localhost/library/1661/> a libns:Library .
+
<http://localhost/flowcell/30221AAXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 33 ;
libns:flowcell_type "Single"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "30221AAXX"@en .
<http://localhost/lane/3401>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
libns:lane_number 1 .
<http://localhost/lane/3402>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
libns:lane_number 2 .
<http://localhost/lane/3403>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
libns:lane_number 3 .
<http://localhost/lane/3404>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 4 .
# read_length 33;
# status "Unknown"@en .
<http://localhost/lane/3405>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
libns:lane_number 5 .
<http://localhost/lane/3406>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
libns:lane_number 6 .
<http://localhost/lane/3407>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
libns:lane_number 7 .
<http://localhost/lane/3408>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30221AAXX/> ;
libns:library <http://localhost/library/10000/> ;
libns:lane_number 8 .
<http://localhost/flowcell/42JUYAAXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 76 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "42JUYAAXX"@en .
<http://localhost/lane/4201>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
libns:lane_number 1 .
<http://localhost/lane/4202>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
libns:lane_number 2 .
<http://localhost/lane/4203>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
libns:lane_number 3 .
<http://localhost/lane/4204>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
libns:lane_number 4 .
<http://localhost/lane/4205>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 5 .
# read_length 76;
# status "Unknown"@en .
<http://localhost/lane/4206>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
libns:lane_number 6 .
<http://localhost/lane/4207>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
libns:lane_number 7 .
<http://localhost/lane/4208>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/42JUYAAXX/> ;
libns:library <http://localhost/library/1421/> ;
libns:lane_number 8 .
<http://localhost/flowcell/61MJTAAXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 76 ;
libns:flowcell_type "Single"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "61MJTAAXX"@en .
<http://localhost/lane/6601>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
libns:lane_number 1 .
<http://localhost/lane/6602>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
libns:lane_number 2 .
<http://localhost/lane/6603>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
libns:lane_number 3 .
<http://localhost/lane/6604>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
libns:lane_number 4 .
<http://localhost/lane/6605>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
libns:lane_number 5 .
<http://localhost/lane/6606>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 6 .
# read_length 76;
# status "Unknown"@en .
<http://localhost/lane/6607>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
libns:lane_number 7 .
<http://localhost/lane/6608>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/61MJTAAXX/> ;
libns:library <http://localhost/library/1661/> ;
libns:lane_number 8 .
<http://localhost/flowcell/30DY0AAXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 76 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "30DY0AAXX"@en .
<http://localhost/lane/3801>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
libns:lane_number 1 .
<http://localhost/lane/3802>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
libns:lane_number 2 .
<http://localhost/lane/3803>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
libns:lane_number 3 .
<http://localhost/lane/3804>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
libns:lane_number 4 .
<http://localhost/lane/3805>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
libns:lane_number 5 .
<http://localhost/lane/3806>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
libns:lane_number 6 .
<http://localhost/lane/3807>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/1331/> ;
libns:lane_number 7 .
<http://localhost/lane/3808>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/30DY0AAXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 8 .
# status "Unknown"@en .
<http://localhost/flowcell/C02F9ACXX/>
- a libns:illumina_flowcell ;
+ a libns:IlluminaFlowcell ;
libns:read_length 101 ;
libns:flowcell_type "Paired"@en ;
libns:date "2012-01-19T20:23:26"^^xsd:dateTime;
libns:flowcell_id "C02F9ACXX"@en .
<http://localhost/lane/12300>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/C02F9ACXX/> ;
libns:library <http://localhost/library/12345/> ;
libns:lane_number 3 .
# status "Unknown"@en .
<http://localhost/lane/12500>
+ a libns:IlluminaLane ;
libns:flowcell <http://localhost/flowcell/C02F9ACXX/> ;
libns:library <http://localhost/library/11154/> ;
libns:lane_number 3 .
# status "Unknown"@en .
<http://localhost/library/11154/>
- a libns:library ;
+ a libns:Library ;
libns:affiliation "TSR"@en;
libns:concentration "29.7";
libns:date "2012-12-28T00:00:00"^^xsd:dateTime ;
<http://localhost/library/12345/>
- a libns:library ;
+ a libns:Library ;
libns:affiliation "TSR"@en;
libns:concentration "12.345";
libns:cell_line "Unknown"@en ;
self.flowcelldir,
self.logdir)
load_string_into_model(self.extract.model, 'turtle', lib_turtle)
+ add_default_schemas(self.extract.model)
+ inference = Infer(self.extract.model)
+ errmsgs = list(inference.run_validation())
+ self.assertEqual(len(errmsgs), 0)
def tearDown(self):
shutil.rmtree(self.tempdir)
--- /dev/null
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix htswlib: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
+
+# I'm still learning how to do modeling & validation
+# this version is just using rdfs:Literal for
+# any literal node.
+
+<http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+ dc:title "HTS-Workflow ontology" ;
+ a owl:Ontology .
+
+htswlib:Class a rdfs:Class .
+
+htswlib:IlluminaFlowcell
+ a rdfs:Class, htswlib:Class ;
+ rdfs:comment "information about a illumina flowcell" ;
+ rdfs:label "Flowcell" .
+
+htswlib:IlluminaLane
+ a rdfs:Class, htswlib:Class ;
+ rdfs:comment "information specific to a lane in a flowcell" ;
+ rdfs:label "Lane" .
+
+htswlib:Library
+ a rdfs:Class, htswlib:Class ;
+ rdfs:comment "a biological library that can be run on a flowcell" ;
+ rdfs:label "library" .
+
+htswlib:Sequencer
+ a rdfs:Class, htswlib:Class;
+ rdfs:comment "an instrument that converts libraries into sequence reads" ;
+ rdfs:label "Sequencer" .
+
+htswlib:Species
+ a rdfs:Class, htswlib:Class ;
+ rdfs:comment "What 'species' was our sample created from." ;
+ rdfs:label "Species" .
+
+htswlib:MappedCount
+ a rdfs:Class, htswlib:Class ;
+ rdfs:comment "Count of reads with locations" ;
+ rdfs:label "Mapped locations" .
+
+# reused properties?
+htswlib:flowcell
+ a rdf:Property ;
+ rdfs:comment "link to our source flowcell" ;
+ rdfs:label "Flowcell" ;
+ rdfs:domain htswlib:IlluminaLane ;
+ rdfs:range htswlib:IlluminaFlowcell .
+
+htswlib:has_lane
+ a rdf:Property ;
+ rdfs:comment "which lanes are attached to a flowcell" ;
+ rdfs:label "lanes" ;
+ # cheating, only flowcells & libraries can have lanes
+ rdfs:domain htswlib:Library ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range htswlib:IlluminaLane .
+
+htswlib:date
+ a rdf:Property ;
+ rdfs:comment "Date thing was constructed" ;
+ rdfs:label "made on" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:total_unique_locations
+ a rdf:Property ;
+ rdfs:comment "How many reads mapped uniquely" ;
+ rdfs:label "Unique locations" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:domain htswlib:IlluminaLane ;
+ rdfs:range rdfs:Literal .
+
+htswlib:has_mappings
+ a rdf:Property ;
+ rdfs:comment "collection of counts against sequence collections" ;
+ rdfs:label "Has mapping" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:domain htswlib:IlluminaLane ;
+ rdfs:range htswlib:MappedCount .
+
+# flowcell properties
+htswlib:flowcell_id
+ a rdf:Property ;
+ rdfs:comment "Serial number of a flowcell, used as unique key" ;
+ rdfs:label "Flowcell ID" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:flowcell_notes
+ a rdf:Property ;
+ rdfs:comment "Comments about flowcell" ;
+ rdfs:label "Notes" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:control_lane
+ a rdf:Property ;
+ rdfs:comment "Control lane used for image analysis/base calling" ;
+ rdfs:label "Control Lane" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:read_length
+ a rdf:Property ;
+ rdfs:comment "How many cycles did we run the sequencer for" ;
+ rdfs:label "Read length" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:flowcell_type
+ a rdf:Property ;
+ rdfs:comment "What kind of flowcell, e.g. single, paired." ;
+ rdfs:label "Flowcell Type" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:image_software
+ a rdf:Property ;
+ rdfs:comment "Image analysis software name." ;
+ rdfs:label "Image processor" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:image_version
+ a rdf:Property ;
+ rdfs:comment "Image analysis software version identifier." ;
+ rdfs:label "Image processor version" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:basecall_software
+ a rdf:Property ;
+ rdfs:comment "Base caller software name." ;
+ rdfs:label "Basecaller" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:basecall_version
+ a rdf:Property ;
+ rdfs:comment "Base caller software version identifier." ;
+ rdfs:label "Basecaller Version" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:alignment_software
+ a rdf:Property ;
+ rdfs:comment "Alignment software name." ;
+ rdfs:label "Alignment software" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:alignment_version
+ a rdf:Property ;
+ rdfs:comment "Alignment software version identifier." ;
+ rdfs:label "Aligner" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range rdfs:Literal .
+
+htswlib:sequenced_by
+ a rdf:Property ;
+ rdfs:comment "Which sequencer sequenced this flowcell" ;
+ rdfs:label "Sequenced By" ;
+ rdfs:domain htswlib:IlluminaFlowcell ;
+ rdfs:range htswlib:Sequencer .
+
+htswlib:sequencer_model
+ a rdf:Property ;
+ rdfs:comment "What model of sequencer was this flowcell run on." ;
+ rdfs:label "Sequencer model" ;
+ rdfs:domain htswlib:Sequencer ;
+ rdfs:range rdfs:Literal .
+
+htswlib:sequencer_instrument
+ a rdf:Property ;
+ rdfs:comment "Sequencer instrument identifier." ;
+ rdfs:label "Instrument ID " ;
+ rdfs:domain htswlib:Sequencer ;
+ rdfs:range rdfs:Literal .
+
+htswlib:sequencer_name
+ a rdf:Property ;
+ rdfs:comment "Local name for sequencer." ;
+ rdfs:label "Sequencer name " ;
+ rdfs:domain htswlib:Sequencer ;
+ rdfs:range rdfs:Literal .
+
+
+# library only properties
+htswlib:library_id
+ a rdf:Property ;
+ rdfs:comment "Library unique identifier" ;
+ rdfs:label "Library ID" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:name
+ a rdf:Property ;
+ rdfs:comment "human readable name" ;
+ rdfs:label "Name" ;
+ rdfs:range rdfs:Literal .
+
+htswlib:library_type
+ a rdf:Property ;
+ rdfs:comment """what type of library are we, which is primarily
+ determined by the type of adaptors ligated onto
+ sequence fragments.""" ;
+ rdfs:label "Library Type" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:stopping_point
+ a rdf:Property ;
+ rdfs:comment "Protocol stopping point" ;
+ rdfs:label "Stopping Point" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:concentration
+ a rdf:Property ;
+ rdfs:comment "Concentration of sample in nanograms per microliter" ;
+ rdfs:label "Concentration" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:insert_size
+ a rdf:Property ;
+ rdfs:comment "The expected size of the sample sequence" ;
+ rdfs:label "Insert Size" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:gel_cut
+ a rdf:Property ;
+ rdfs:comment "The estimated fragment sizes cut from gel";
+ rdfs:label "Gel Cut" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:made_by
+ a rdf:Property ;
+ rdfs:comment "Name of person who created library" ;
+ rdfs:label "Made by" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:multiplex_index
+ a rdf:Property ;
+ rdfs:comment "multiplex sequence" ;
+ rdfs:label "index" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:cell_line
+ a rdf:Property ;
+ rdfs:comment "Description of source material" ;
+ rdfs:label "cell line" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:experiment_type
+ a rdf:Property ;
+ rdfs:comment "What type of sequencing is this. e.g. RNA-Seq, DeNovo etc." ;
+ rdfs:label "Experiment Type" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:affiliation
+ a rdf:Property ;
+ rdfs:comment "Entity associated with this sample" ;
+ rdfs:label "affiliation" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+htswlib:species
+ a rdf:Property ;
+ rdfs:comment "Scientific name of sample species" ;
+ rdfs:label "Species" ;
+ rdfs:domain htswlib:Library ;
+ #rdfs:domain htswlib:IlluminaLane;
+ rdfs:range htswlib:Species .
+
+htswlib:replicate
+ a rdf:Property ;
+ rdfs:comment "Which replicate this was" ;
+ rdfs:label "replicate" ;
+ rdfs:domain htswlib:Library ;
+ rdfs:range rdfs:Literal .
+
+# lane only properties
+htswlib:lane_number
+ a rdf:Property ;
+ rdfs:comment "Which lane were we run in" ;
+ rdfs:label "lane id" ;
+ rdfs:domain htswlib:IlluminaLane ;
+ rdfs:range rdfs:Literal .
+
+# FIXME: should this be note?
+htswlib:comment
+ a rdf:Property ;
+ rdfs:comment "Comment about an object" ;
+ rdfs:range rdfs:Literal .
+
+htswlib:library
+ a rdf:Property ;
+ rdfs:comment "which library was run on this lane." ;
+ rdfs:label "Library" ;
+ rdfs:domain htswlib:IlluminaLane ;
+ rdfs:range htswlib:Library .
+
+# species properites
+htswlib:species_name
+ a rdf:Property ;
+ rdfs:comment "Scientific name of species" ;
+ rdfs:label "Species" ;
+ rdfs:domain htswlib:Species ;
+ rdfs:range rdfs:Literal .
+
+# mapped count properties
+htswlib:mapped_to
+ a rdf:Property ;
+ rdfs:comment "A sequence collection, genome, chromosome, spike in, etc.";
+ rdfs:label "Mapped to" ;
+ rdfs:domain htswlib:MappedCount ;
+ rdfs:range rdfs:Literal .
+
+htswlib:reads
+ a rdf:Property ;
+ rdfs:comment "Number of read locations" ;
+ rdfs:label "Reads" ;
+ rdfs:domain htswlib:MappedCount ;
+ rdfs:range rdfs:Literal .
\ No newline at end of file
projects / htsworkflow.git / commitdiff