def sync(self, conflictResolution='raise', readOnly=False):
"""
Two-way sync with the pickled file object on disk. Supports syncing contents of objects implementing an
'update()' method (e.g. dicts). Only reads the stored file if its modification time has been changed.
:param conflictResolution: One of 'raise', 'local', 'remote'. A conflict happens if both the local object and
the file stored object has changed and is not equal. If 'raise`, a SyncConflictError is raised, if
'local', the locally stored object replaces the object stored in the file, and if 'remote', the object
stored in the file replaces the locally stored object.
:param readOnly: If True, only syncs and remote changes into the local state (according to conflimtResolution)
but the local state is not written to the file until the next time sync is called with readOnly=False.
:return: None
"""
self._checkIfClosed()
assert conflictResolution in ['raise', 'local', 'remote']
assert readOnly in [False, True]
ensurePathExists(self._fn)
fileModTime = self._getFileModTime()
fileDirty = fileModTime != self._prevFileModTime
if fileDirty or self._dirty() or self._postponeWrite:
with FileLock(self._fn, 'w' if self._dirty() else 'r'):
if fileDirty:
self._readFileAndSyncWithLocalObject(fileModTime, conflictResolution)
if self._dirty() or self._postponeWrite:
if readOnly:
self._cleanEditHistory(postponeWrite=True)
else:
self._writeSyncedObjectToFile(fileModTime)
self._cleanEditHistory()
def __enter__(self):
if self._mode == 'r':
lockflags = LOCK_SH | LOCK_NB
else:
lockflags = LOCK_EX
ensurePathExists(self._lockFilePath)
# os.open with os.O_SHLOCK instead?
self._lckFile = open(self._lockFilePath, self._mode)
fcntl.flock(self._lckFile.fileno(), lockflags)
def getDiskPath(self, ensurePath=False, relativeToBase=False):
path = self._galaxyFn
if relativeToBase:
if path.startswith(GALAXY_BASE_DIR):
path = path[len(GALAXY_BASE_DIR):]
fn = getGalaxyFilesFilename(path, self._relativeId)
#fn = os.sep.join([GALAXY_FILE_PATH] + [self._id[1], 'dataset_'+self._id[2]+'_files'] + self._id[3:])
if ensurePath:
ensurePathExists(fn)
return fn
def _produceTableWithGsuiteButton(core,
gsuiteFn=None,
gsuiteHistElementName=None,
origProduceTableCallbackFunc=None,
**kwArgsToCallback):
assert gsuiteFn is not None
from proto.CommonFunctions import ensurePathExists
ensurePathExists(gsuiteFn)
core.importFileToHistoryButton("Import GSuite with results to history",
gsuiteFn, 'gsuite',
gsuiteHistElementName)
return origProduceTableCallbackFunc(core, **kwArgsToCallback)
def _compute(self):
ensurePathExists(self._trackFilePath)
outputFile = open(self._trackFilePath, 'a')
trackView = self._children[0].getResult()
starts = trackView.startsAsNumpyArray()
ends = trackView.endsAsNumpyArray()
for segmentIndex in range(0, len(starts)):
outputFile.write('\t'.join([
self._region.chr,
str(starts[segmentIndex]),
str(ends[segmentIndex])
]) + '\n')
outputFile.close()
# this return is not entirely necessary, as the filenames have already been added to the trackstructure
return quote(self._trackFilePath)
def tableWithTabularImportButton(self,
tabularFn=None,
tabularHistElementName='Raw table',
produceTableCallbackFunc=None,
**kwArgsToCallback):
assert produceTableCallbackFunc is not None
assert tabularFn is not None
textCore = self._getTextCoreCls()()
textCore = produceTableCallbackFunc(textCore, **kwArgsToCallback)
from proto.CommonFunctions import ensurePathExists
ensurePathExists(tabularFn)
open(tabularFn, 'w').write(str(textCore))
self.importFileToHistoryButton("Import table to history (tabular)",
tabularFn, 'tabular',
tabularHistElementName)
return produceTableCallbackFunc(self, **kwArgsToCallback)
def getDiskPath(self, ensurePath=False, relativeToBase=False):
path = self.STATIC_DIR if relativeToBase else self.STATIC_PATH
fn = os.sep.join([path] + self._id)
if ensurePath:
ensurePathExists(fn)
return fn
def execute(cls, choices, galaxyFn=None, username=''):
genome = choices.genome
from quick.multitrack.MultiTrackCommon import getGSuiteDataFromGalaxyTN
trackTitles, refTrackNameList, genome = getGSuiteDataFromGalaxyTN(choices.gsuite)
queryTrackName = ExternalTrackManager.extractFnFromGalaxyTN(choices.targetTrack)
if choices.isBasic:
suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(choices.targetTrack, False)
regSpec = suffix
binSpec = queryTrackName
else:
regSpec, binSpec = UserBinMixin.getRegsAndBinsSpec(choices)
#targetTrack = choices.targetTrack.split(':')
#targetTrackTitle = targetTrack[-1]
#print targetTrackTitle
#
#binSpec = targetTrackTitle
#Phenotype and disease associations:Assorted experiments:Virus integration, HPV specific, Kraus and Schmitz, including 50kb flanks
from gold.gsuite.GSuiteConstants import TITLE_COL
from gold.gsuite.GSuite import GSuite
from proto.hyperbrowser.StaticFile import GalaxyRunSpecificFile
from gold.gsuite.GSuiteEditor import selectColumnsFromGSuite
staticFile=[]
results = []
for refTrack in refTrackNameList:
analysisDef = '-> ProportionCountStat' #ProportionCountStat #CountStat
res = GalaxyInterface.runManual([refTrack], analysisDef, regSpec, binSpec, genome, username=username, galaxyFn=galaxyFn, printRunDescription=False, printResults=False, printProgress=False)
segCoverageProp = [res[seg]['Result'] for seg in res.getAllRegionKeys()]
results.append(segCoverageProp)
regFileNamer = GalaxyRunSpecificFile(refTrack, galaxyFn)
staticFile.append([regFileNamer.getLink('Download bed-file'), regFileNamer.getLoadToHistoryLink('Download bed-file to History')])
refGSuite = getGSuiteFromGalaxyTN(choices.gsuite)
if TITLE_COL == choices.selectColumns:
selected = trackTitles
else:
selected = refGSuite.getAttributeValueList(choices.selectColumns)
yAxisNameOverMouse=[]
metadataAll =[]
for x in range(0, len(selected)):
if selected[x] == None:
yAxisNameOverMouse.append(str(trackTitles[x]) + ' --- ' + 'None')
else:
if TITLE_COL == choices.selectColumns:
yAxisNameOverMouse.append(selected[x].replace('\'', '').replace('"', ''))
else:
metadata = str(selected[x].replace('\'', '').replace('"', ''))
yAxisNameOverMouse.append(str(trackTitles[x]) + ' --- ' + metadata)
metadataAll.append(metadata)
colorListForYAxisNameOverMouse = []
if len(metadataAll) > 0:
import quick.webtools.restricted.visualization.visualizationGraphs as vg
cList = vg.colorList().fullColorList()
uniqueCList = list(set(metadataAll))
for m in metadataAll:
colorListForYAxisNameOverMouse.append(cList[uniqueCList.index(m)])
#startEnd - order in res
startEndInterval = []
startEnd = []
i=0
extraX=[]
rowLabel = []
for ch in res.getAllRegionKeys():
rowLabel.append(str(ch.chr) + ":" + str(ch.start) + "-" + str(ch.end) + str(' (Pos)' if ch.strand else ' (Neg)'))
if not i==0 and not i==len(res.getAllRegionKeys())-1:
start = ch.start
if start-end > 0:
startEnd.append(start-end)
else:
startEnd.append('null')
extraX.append("""{ color: 'orange', width: 5, value: '""" + str(i-0.5) + """' }""")
startEndInterval.append(ch.end - ch.start)
else:
startEndInterval.append(ch.end - ch.start)
end = ch.end
i+=1
extraXAxis='plotLines: [ '
extraXAxis = extraXAxis + ",".join(extraX)
extraXAxis = extraXAxis + """ ], """
#rowLabel = res.getAllRegionKeys()
#rowLabel = [str(x) for x in rowLabel]
import quick.webtools.restricted.visualization.visualizationPlots as vp
htmlCore = HtmlCore()
htmlCore.begin()
htmlCore.divBegin(divId='results-page')
htmlCore.divBegin(divClass='results-section')
htmlCore.divBegin('plotDiv')
htmlCore.line(vp.addJSlibs())
htmlCore.line(vp.useThemePlot())
htmlCore.line(vp.addJSlibsExport())
htmlCore.line(vp.axaddJSlibsOverMouseAxisisPopup())
#vp.addGuideline(htmlCore)
htmlCore.line(vp._addGuidelineV1())
htmlCore.line(vp.addJSlibsHeatmap())
from config.Config import DATA_FILES_PATH
from proto.StaticFile import StaticFile, GalaxyRunSpecificFile
#sf = GalaxyRunSpecificFile(['result.txt'], galaxyFn)
#outFile = sf.getDiskPath(ensurePath=True)
htmlCore.divBegin()
writeFile = open(
cls.makeHistElement(galaxyExt='tabular',
title='result'), 'w')
# htmlCore.link('Get all results', sf.getURL())
htmlCore.divEnd()
i = 0
writeFile.write('Track' + '\t' + '\t'.join(rowLabel)+ '\n')
for rList in results:
writeFile.write(str(yAxisNameOverMouse[i]) + '\t' + '\t'.join([str(r) for r in rList]) + '\n')
i+=1
fileOutput = GalaxyRunSpecificFile(['heatmap.png'],
galaxyFn)
ensurePathExists(fileOutput.getDiskPath())
fileOutputPdf = GalaxyRunSpecificFile(['heatmap.pdf'],
galaxyFn)
ensurePathExists(fileOutputPdf.getDiskPath())
cls.generateStaticRPlot(results, colorListForYAxisNameOverMouse, rowLabel, yAxisNameOverMouse,
colorMaps[choices.colorMapSelectList],
fileOutput.getDiskPath(), fileOutputPdf.getDiskPath())
htmlCore.divBegin(divId='heatmap', style="padding: 10px 0 px 10 px 0px;margin: 10px 0 px 10 px 0px")
htmlCore.link('Download heatmap image', fileOutputPdf.getURL())
htmlCore.divEnd()
if len(results) * len(results[1]) >= 10000:
htmlCore.image(fileOutput.getURL())
else:
min = 1000000000
max = -1000000000
for rList in results:
for r in rList:
if min > r:
min = r
if max < r:
max = r
if max-min != 0:
resultNormalised = []
for rList in results:
resultNormalisedPart = []
for r in rList:
resultNormalisedPart.append((r-min)/(max-min))
resultNormalised.append(resultNormalisedPart)
addText = '(normalised to [0, 1])'
else:
resultNormalised = results
addText = ''
hm, heatmapPlotNumber, heatmapPlot = vp.drawHeatMap(
resultNormalised,
colorMaps[choices.colorMapSelectList],
label='this.series.xAxis.categories[this.point.x] + ' + "'<br >'" + ' + yAxisNameOverMouse[this.point.y] + ' + "'<br>Overlap proportion" + str(addText) + ": <b>'" + ' + this.point.value + ' + "'</b>'",
yAxisTitle= 'Reference tracks',
categories=rowLabel,
tickInterval=1,
plotNumber=3,
interaction=True,
otherPlotNumber=1,
titleText='Overlap with reference tracks for each local region',
otherPlotData=[startEnd, startEndInterval],
overMouseAxisX=True,
overMouseAxisY=True,
yAxisNameOverMouse=yAxisNameOverMouse,
overMouseLabelY=" + 'Track: '" + ' + this.value + ' + "' '" + ' + yAxisNameOverMouse[this.value] + ',
overMouseLabelX = ' + this.value.substring(0, 20) +',
extrOp = staticFile
)
htmlCore.line(hm)
htmlCore.line(vp.drawChartInteractionWithHeatmap(
[startEndInterval, startEnd],
tickInterval=1,
type='line',
categories=[rowLabel, rowLabel],
seriesType=['line', 'column'],
minWidth=300,
height=500,
lineWidth=3,
titleText=['Lengths of segments (local regions)','Gaps between consecutive segments'],
label=['<b>Length: </b>{point.y}<br/>', '<b>Gap length: </b>{point.y}<br/>'],
subtitleText=['',''],
yAxisTitle=['Lengths','Gap lengths'],
seriesName=['Lengths','Gap lengths'],
xAxisRotation=90,
legend=False,
extraXAxis=extraXAxis,
heatmapPlot=heatmapPlot,
heatmapPlotNumber=heatmapPlotNumber,
overMouseAxisX=True,
overMouseLabelX = ' + this.value.substring(0, 20) +'
))
htmlCore.divEnd()
htmlCore.divEnd()
htmlCore.divEnd()
htmlCore.end()
htmlCore.hideToggle(styleClass='debug')
print htmlCore