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0,"def show_slug_with_level(context, page, lang=None, fallback=True):
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""""""Display slug with level by language.""""""
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if not lang:
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lang = context.get('lang', pages_settings.PAGE_DEFAULT_LANGUAGE)
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page = get_page_from_string_or_id(page, lang)
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if not page:
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return ''
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return {'content': page.slug_with_level(lang)}"
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1,"def show_revisions(context, page, content_type, lang=None):
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""""""Render the last 10 revisions of a page content with a list using
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the ``pages/revisions.html`` template""""""
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if not pages_settings.PAGE_CONTENT_REVISION:
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return {'revisions': None}
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revisions = Content.objects.filter(page=page, language=lang,
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type=content_type).order_by('-creation_date')
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if len(revisions) < 2:
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return {'revisions': None}
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return {'revisions': revisions[0:10]}"
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2,"def do_videoplaceholder(parser, token):
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""""""
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Method that parse the imageplaceholder template tag.
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""""""
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name, params = parse_placeholder(parser, token)
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return VideoPlaceholderNode(name, **params)"
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3,"def do_get_pages_with_tag(parser, token):
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""""""
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Return Pages with given tag
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Syntax::
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{% get_pages_with_tag <tag name> as <varname> %}
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Example use:
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{% get_pages_with_tag ""footer"" as pages %}
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""""""
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bits = token.split_contents()
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if 4 != len(bits):
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raise TemplateSyntaxError('%r expects 2 arguments' % bits[0])
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if bits[-2] != 'as':
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raise TemplateSyntaxError(
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'%r expects ""as"" as the second last argument' % bits[0])
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varname = bits[-1]
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tag = parser.compile_filter(bits[1])
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varname = bits[-1]
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return GetPagesWithTagNode(tag, varname)"
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4,"def parserunstats(self):
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""""""Parses the XML run statistics file (GenerateFASTQRunStatistics.xml). In some cases, the file is not
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available. Equivalent data can be pulled from Basespace.Generate a text file name indexingQC.txt containing
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the copied tables from the Indexing QC tab of the run on Basespace""""""
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# metadata = GenObject()
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# If the default file GenerateFASTQRunStatistics.xml is present, parse it
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if os.path.isfile(os.path.join(self.path, ""GenerateFASTQRunStatistics.xml"")):
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# Create a list of keys for which values are to be extracted
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datalist = [""SampleNumber"", ""SampleID"", ""SampleName"", ""NumberOfClustersPF""]
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# Load the file as an xml ElementTree object
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runstatistics = ElementTree.ElementTree(file=os.path.join(self.path, ""GenerateFASTQRunStatistics.xml""))
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# Iterate through all the elements in the object
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# .iterfind() allow for the matching and iterating though matches
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# This is stored as a float to allow subsequent calculations
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tclusterspf = [float(element.text) for element in runstatistics.iterfind(""RunStats/NumberOfClustersPF"")][0]
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# Iterate through all the elements (strains) in the OverallSamples/SummarizedSampleStatistics category
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for element in runstatistics.iterfind(""OverallSamples/SummarizedSampleStatistics""):
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# List comprehension. Essentially iterate through each element for each category in datalist:
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# (element.iter(category) and pull out the value for nestedelement
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straindata = [nestedelement.text for category in datalist for nestedelement in element.iter(category)]
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# Try and replicate the Illumina rules to create file names from ""Sample_Name""
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samplename = samplenamer(straindata, 1)
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# Calculate the percentage of clusters associated with each strain
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# noinspection PyTypeChecker
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percentperstrain = ""{:.2f}"".format((float(straindata[3]) / tclusterspf * 100))
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try:
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# Use the sample number -1 as the index in the list of objects created in parsesamplesheet
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strainindex = int(straindata[0]) - 1
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# Set run to the .run object of self.samples[index]
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run = self.samples[strainindex].run
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# An assertion that compares the sample computer above to the previously entered sample name
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# to ensure that the samples are the same
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assert self.samples[strainindex].name == samplename, \
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""Sample name does not match object name {0!r:s}"".format(straindata[1])
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# Add the appropriate values to the strain metadata object
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run.SampleNumber = straindata[0]
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run.NumberofClustersPF = straindata[3]
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run.TotalClustersinRun = tclusterspf
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run.PercentOfClusters = percentperstrain
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run.flowcell = self.flowcell
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run.instrument = self.instrument
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except IndexError:
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pass
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elif os.path.isfile(os.path.join(self.path, 'indexingQC.txt')):
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# Grab the first element from the second line in the file
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tclusterspf = float(getline(os.path.join(self.path, ""indexingQC.txt""), 2).split(""\t"")[0])
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# Open the file and extract the relevant data
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with open(os.path.join(""indexingQC.txt"")) as indexqc:
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# Iterate through the file
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for line in indexqc:
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# Once ""Index"" is encountered, iterate through the rest of the file
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if ""Index"" in line:
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