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