if xml is not None:
self.set_elements(xml)
+ def _get_runfolder_name(self):
+ """Return runfolder name"""
+ if self.tree is None:
+ raise ValueError("Can't query an empty run")
+ runfolder = self.tree.xpath('RunParameters/Runfolder')
+ return runfolder
+ runfolder_name = property(_get_runfolder)
+
def _get_software(self):
"""Return software name"""
if self.tree is None:
return path_fields[-1]
def _get_runfolder_name(self):
- if self.gerald is None:
- return None
- else:
+ if self.gerald:
return self.gerald.runfolder_name
+ elif hasattr(self.image_analysis, 'runfolder_name'):
+ return self.image_analysis.runfolder_name
+ else:
+ return None
runfolder_name = property(_get_runfolder_name)
def _get_run_dirname(self):
temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
flowcell_id = '4286GAAXX'
- runfolder_dir = os.path.join(
- temp_dir,
- '090608_HWI-EAS229_0117_{0}'.format(flowcell_id))
+ runfolder = '090608_HWI-EAS229_0117_{0}'.format(flowcell_id)
+ runfolder_dir = os.path.join(temp_dir, runfolder)
os.mkdir(runfolder_dir)
data_dir = os.path.join(runfolder_dir, 'Data')
if obj is not None:
obj.flowcell_id = flowcell_id
obj.temp_dir = temp_dir
+ obj.runfolder = runfolder
obj.runfolder_dir = runfolder_dir
obj.data_dir = data_dir
obj.image_analysis_dir = intensities_dir
# do we get the flowcell id from the filename?
self.failUnlessEqual(len(runs), 1)
- name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+ name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
self.failUnlessEqual(runs[0].serialization_filename, name)
+ self.assertEqual(runs[0].runfolder_name, '090220_HWI-EAS229_0093_30VR0AAXX')
# do we get the flowcell id from the FlowcellId.xml file
make_flowcell_id(self.runfolder_dir, '207BTAAXY')
name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
self.failUnlessEqual(runs[0].serialization_filename, name)
+
r1 = runs[0]
xml = r1.get_elements()
xml_str = ElementTree.tostring(xml)
import logging
import os
+from pprint import pformat
import string
import re
stripNamespace, \
submissionOntology
from htsworkflow.util.url import parse_ssh_url
+from htsworkflow.util.ucsc import bigWigInfo
from django.conf import settings
from django.template import Context, loader
track_name = self.make_track_name(track)
track_subgroup = self.make_track_subgroups(subgroups, track)
+ track_type = self.make_track_type(track)
if 'file_label' in track:
track_label = self.sanitize_name(track['file_label'])
else:
track_label = track_name
- newtrack = Track(
- name=track_name,
- tracktype = str(track['file_type']),
- url= hub_url + str(track['relative_path']),
- short_label=str(track['library_id']),
- long_label=str(track_label),
- subgroups=track_subgroup,
- )
+ attributes = {
+ 'name': track_name,
+ 'tracktype': track_type,
+ 'url': hub_url + str(track['relative_path']),
+ 'short_label': str(track['library_id']),
+ 'long_label': str(track_label),
+ 'subgroups': track_subgroup,
+ }
+
+ LOGGER.debug('track attributes: %s', pformat(attributes))
+ newtrack = Track(**attributes)
view.add_tracks([newtrack])
results = hub.render()
"""
current_view_type = str(track['output_type'])
if not view or current_view_type != view.name:
- view = ViewTrack(
- name=current_view_type,
- view=current_view_type,
- visibility='squish',
- short_label=current_view_type,
- tracktype=str(track['file_type']),
- )
+ attributes = {
+ 'name': current_view_type,
+ 'view': current_view_type,
+ 'visibility': str(track.get('visibility', 'squish')),
+ 'short_label': current_view_type,
+ 'tracktype': str(track['file_type'])
+ }
+ maxHeightPixels = track.get('maxHeightPixels')
+ if maxHeightPixels:
+ attributes['maxHeightPixels'] = str(maxHeightPixels)
+ autoScale = track.get('autoScale')
+ if autoScale:
+ attributes['autoScale'] = str(autoScale)
+ view = ViewTrack(**attributes)
composite.add_view(view)
view_type = current_view_type
return view
value = self.sanitize_name(track[k])
track_subgroups[k] = value
return track_subgroups
+
+ def make_track_type(self, track):
+ """Further annotate tracktype.
+
+ bigWig files can have additional information. Add it if we can
+ """
+ track_type = track['file_type']
+ if track_type.lower() == 'bigwig':
+ # something we can enhance
+ info = bigWigInfo(track['relative_path'])
+ if info.min is not None and info.max is not None:
+ track_type = '{} {} {}'.format(track_type, int(info.min), int(info.max))
+
+ LOGGER.debug("track_type: %s", track_type)
+ return str(track_type)
def add_subgroups(self, composite):
"""Add subgroups to composite track"""
-#file_name format output_type experiment replicate enriched_in ucsc_db replaces replace_reason{% for r in files %}
-{{ r.relative_path }} {{ r.file_format }} {{ r.output_type }} {{ r.dataset_id }} {{ r.replicate }} {{ r.enriched_in }} {{ r.ucsc_db }} {{ r.replaces_accession|default_if_none:"" }} {{ r.replace_reason|default_if_none:"" }}{% endfor %}
+#version 1.7
+#file_name format output_type experiment replicate enriched_in ucsc_db paired_end technical_replicate{% for r in files %}
+{{ r.relative_path }} {{ r.file_format }} {{ r.output_type }} {{ r.dataset_id }} {{ r.replicate }} {{ r.enriched_in }} {{ r.ucsc_db }} {{ r.paired_end|default_if_none:"n/a" }} {{ r.technical_replicate|default_if_none:"n/a"}}{% endfor %}
PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
PREFIX cells: <http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#>
-select distinct ?name ?filename ?relative_path ?file_format ?output_type ?dataset_id ?replicate ?enriched_in ?ucsc_db ?replaces_accession ?replace_reason
+select distinct ?name ?filename ?relative_path ?file_format ?output_type ?dataset_id ?replicate ?enriched_in ?ucsc_db ?paired_end ?technical_replicate ?replaces ?replace_reason
WHERE {
<{{submission}}> a submissionOntology:submission ;
submissionOntology:name ?name ;
?fileClass geoSoft:fileTypeLabel ?file_format ;
ucscDaf:output_type ?output_type .
+ OPTIONAL { ?fileClass ucscDaf:paired_end ?paired_end . }
+ OPTIONAL { ?fileClass ucscDaf:technical_replicate ?technical_replicate . }
+
?library htswlib:replicate ?replicate ;
ucscDaf:enriched_in ?enriched_in;
PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
+PREFIX trackdb: <http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#>
PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
PREFIX cells: <http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#>
PREFIX encode3: <http://jumpgate.caltech.edu/wiki/Encode3#>
-select distinct ?lab_library_id ?library_id ?filename ?relative_path ?output_type ?file_type ?cell ?replicate ?assay ?rna_type ?protocol ?file_label
+select distinct ?lab_library_id ?library_id ?filename ?relative_path ?output_type ?file_type ?cell ?replicate ?assay ?rna_type ?protocol ?file_label ?autoScale ?maxHeightPixels ?visibility
WHERE {
- ?trackType geoSoft:fileTypeLabel ?file_type ;
+ ?trackType trackdb:type ?file_type ;
ucscDaf:output_type ?output_type .
+ OPTIONAL { ?trackType trackdb:autoScale ?autoScale . }
+ OPTIONAL { ?trackType trackdb:maxHeightPixels ?maxHeightPixels . }
+ OPTIONAL { ?trackType trackdb:visibility ?visibility . }
?file ucscDaf:filename ?filename ;
ucscDaf:relative_path ?relative_path ;
htswlib:library ?library ;
statements = []
retries = 3
+ succeeded = False
while retries > 0:
try:
retries -= 1
statements = rdf_parser.parse_as_stream(url, ns)
retries = 0
+ succeeded = True
except RDF.RedlandError, e:
errmsg = "RDF.RedlandError: {0} {1} tries remaining"
logger.error(errmsg.format(str(e), retries))
-
+
+ if not succeeded:
+ logger.warn("Unable to download %s", url)
+
for s in statements:
conditionally_add_statement(model, s, ns)
import logging
import os
+import sys
from subprocess import Popen, PIPE
LOGGER = logging.getLogger(__name__)
def scan_file(self, filename):
cmd = ['bigWigInfo',
filename]
- p = Popen(cmd, stdout=PIPE)
- stdout, _ = p.communicate()
- for line in stdout.split(os.linesep):
- if len(line) > 0:
- term, value = line.split(': ')
- if term in ('isCompressed', 'isSwapped'):
- value = parseBoolean(value)
- else:
- value = parseNumber(value)
- LOGGER.debug('%s: %s', term, str(value))
- setattr(self, term, value)
+ try:
+ p = Popen(cmd, stdout=PIPE)
+ stdout, _ = p.communicate()
+ for line in stdout.split(os.linesep):
+ if len(line) > 0:
+ term, value = line.split(': ')
+ if term in ('isCompressed', 'isSwapped'):
+ value = parseBoolean(value)
+ else:
+ value = parseNumber(value)
+ LOGGER.debug('%s: %s', term, str(value))
+ setattr(self, term, value)
+ except OSError as e:
+ LOGGER.error("Exception %s trying to run: %s", str(e), ' '.join(cmd))
+ sys.exit(-1)
+
projects / htsworkflow.git / commitdiff