def msiAVUs2BisqueTags(avuXml, bisqueTags, rei):
avuXml = avuXml.parseForStr()
print "msiAVUs2BisqueTags: avuXml:\n", avuXml
indoc = libxml2.parseDoc(avuXml)
outdoc = AVUs2BisqueTagsStyle.applyStylesheet(indoc, None)
print "msiAVUs2BisqueTags: outdoc:\n", outdoc
outdoc = str(outdoc)
print "msiAVUs2BisqueTags: outdoc:\n", outdoc
irods.fillStrInMsParam(bisqueTags, outdoc)
def msiIsReadyHcsColl(inStr, resStr, rei):
res = ''
coll = inStr.parseForStr()
print "msiIsReadyHcsColl: " + coll
# irods connection
conn = rei.getRsComm()
# select statement
i1 = inxIvalPair_t()
i1.addInxIval(COL_D_CREATE_TIME, 0)
# sort results
i1.addInxIval(COL_D_CREATE_TIME, ORDER_BY_DESC)
# condition statement
i2 = inxValPair_t()
i2.addInxVal(COL_COLL_NAME, " like '" + coll + "%'")
# create query
genQueryInp = genQueryInp_t()
genQueryInp.setSelectInp(i1)
genQueryInp.setSqlCondInp(i2)
genQueryInp.setMaxRows(2)
genQueryInp.setContinueInx(0)
# execute query
print 'msiIsReadyHcsColl: before query'
genQueryOut, status = rsGenQuery(conn, genQueryInp)
if status !=0:
res += "msiIsReadyLeicaColl: ERROR " + str(status) + '\n'
if status == CAT_NO_ROWS_FOUND:
res += "msiIsReadyLeicaColl: ERROR " + str(status) + '\n'
# read the times
for sqlRes in genQueryOut.getSqlResult():
for time in sqlRes.getValues():
res += "time " + str(time) + '\n'
res += "ready tai not\n"
genQueryOut.free()
print 'msiIsReadyHcsColl: after query'
res = 'test msiIsReadyHcsColl ' + str(coll) + '\n'
res = 'READY, query done\n'
print res
irods.fillStrInMsParam(resStr, res)
print 'msiIsReadyHcsColl: exiting'
def msiXSLTransform(inxml, xsl, outxml, rei):
inxml = inxml.parseForStr()
xsl = xsl.parseForStr()
print 'msiXSLTransform: inxml', inxml
print 'msiXSLTransform: xsl', xsl
doc = libxml2.parseDoc(inxml)
styledoc = libxml2.parseDoc(xsl)
style = libxslt.parseStylesheetDoc(styledoc)
result = style.applyStylesheet(doc, None)
result = str(result)
print 'msiXSLTransform: result', result
irods.fillStrInMsParam(outxml, result)
def msiAVUs2BisqueTags_OLD(path, tagsOut, rei):
# tags = '\''
tags = '<resource>'
conn = rei.getRsComm()
f = iRodsOpen(rei.getRsComm(), path.parseForStr(), 'w')
avus = f.getUserMetadata()
f.close()
print 'msiAVUs2BisqueTags', avus
for avu in avus:
(a, v, u) = avu
#tag = '<tag name="%s" value="%s"/>' % (a, v)
tag = '<tag name=\"%s\" value=\"%s\"/>' % (a, v)
tags += tag
tags += '</resource>'
print 'msiAVUs2BisqueTags', tags
irods.fillStrInMsParam(tagsOut, str(tags))
def msiIsReadyHcsColl0(inStr, resStr, rei):
inStr = inStr.parseForStr()
res = 'test msiIsReadyHcsColl0 ' + str(inStr) + '\n'
print res
irods.fillStrInMsParam(resStr, res)
def msiLeica2FlatDir(inputColl, outputColl, resStr, rei):
res = ''
inputColl = inputColl.parseForStr()
outputColl = outputColl.parseForStr()
print 'msiLeica2FlatDir: ', inputColl, outputColl
# irods connection
conn = rei.getRsComm()
# get directory handles
c = irodsCollection(conn)
res += c.getCollName() + '\n'
# experiment
experiment = findBasename(inputColl)
plateCode = createPlateCode(experiment)
c.openCollection(outputColl)
c.createCollection(experiment + '_flatdir')
outputColl += '/' + experiment + '_flatdir/'
c.openCollection(inputColl)
res += c.getCollName() + '\n'
# plate
c.openCollection('slide--S00')
wells = c.getSubCollections()
for w in wells:
# well
c.openCollection(w)
res += 'WELL ' + c.getCollName() + '\n'
wellCode = createWellCode(w)
fields = c.getSubCollections()
(xmax, ymax) = findFieldIndexRange(fields)
for f in fields:
c.openCollection(f)
res += 'FIELD ' + c.getCollName() + '\n'
fieldCode = createFieldCode(xmax, ymax, f)
for dataObj in c.getObjects():
image = dataObj[0]
resc = dataObj[1]
print image
stackName = plateCode + '_'+ wellCode + 'f' + fieldCode + '.tif'
print stackName
f = c.open(image, 'r', resc)
f.addUserMetadata('leica.experiment', experiment)
f.addUserMetadata('leica2flatdir.collection', outputColl)
f.addUserMetadata('leica2flatdir.plateId', plateCode)
f.addUserMetadata('leica2flatdir.stackName', stackName)
f.addUserMetadata('leica2flatdir.dataObject', outputColl + stackName)
f.close()
res += image + ' '+ stackName + '\n'
c.upCollection()
res += '\n'
c.upCollection()
irods.fillStrInMsParam(resStr, str(res))
def msiBase64Encode(inStr, outStr, rei):
input = inStr.parseForStr()
output = base64.encodestring(input).strip()
irods.fillStrInMsParam(outStr, str(output))
def msiUrlEncode(inParam, inValue, outStr, rei):
param = inParam.parseForStr()
value = inValue.parseForStr()
output = urllib.urlencode( { param: value })
irods.fillStrInMsParam(outStr, str(output))
def msiGetMatrixScreenerField(image, resStr, rei):
res = ''
image = image.parseForStr()
res += createFieldIndex(image)
print 'msiGetMatrixScreenerField', res
irods.fillStrInMsParam(resStr, str(res))
def msiGetMatrixScreenerWell(image, resStr, rei):
res = ''
image = image.parseForStr()
res += createWellCode(image)
print 'msiGetMatrixScreenerWell', res
irods.fillStrInMsParam(resStr, str(res))
def msiGetMatrixScreenerExperiment(image, resStr, rei):
res = ''
image = image.parseForStr()
res += createExperiment(image)
print 'msiGetMatrixScreenerExperiment', res
irods.fillStrInMsParam(resStr, str(res))
def testH2(inStr, resStr, rei):
inStr = inStr.parseForStr()
res = 'testH2 kukkuu ' + str(inStr) + '\n'
print res
irods.fillStrInMsParam(resStr, res)
def testH1(resStr, rei):
irods.fillStrInMsParam(resStr, 'testH1 kukkuu')