def __call__(self):
header = _("Reference analysis QC")
subheader = _("Reference analysis quality control graphs ")
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = "<img src='" + self.portal_url + "/++resource++bika.lims.images/warning.png' height='9' width='9'/>"
error_icon = "<img src='" + self.portal_url + "/++resource++bika.lims.images/exclamation.png' height='9' width='9'/>"
self.parms = []
titles = []
sample_uid = self.request.form.get('ReferenceSampleUID', '')
sample = self.reference_catalog.lookupObject(sample_uid)
if not sample:
message = _("No reference sample was selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.parms.append({
'title': _("Reference Sample"),
'value': sample.Title()
})
titles.append(sample.Title())
service_uid = self.request.form.get('ReferenceServiceUID', '')
service = self.reference_catalog.lookupObject(service_uid)
if not service:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.contentFilter = {
'portal_type': 'ReferenceAnalysis',
'review_state': ['verified', 'published'],
'path': {
"query": "/".join(sample.getPhysicalPath()),
"level": 0
}
}
self.parms.append({
'title': _("Analysis Service"),
'value': service.Title()
})
titles.append(service.Title())
val = self.selection_macros.parse_daterange(self.request,
'getDateVerified',
'DateVerified')
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
self.parms.append(val['parms'])
titles.append(val['titles'])
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
# Compile a list with all relevant analysis data
analyses = []
out_of_range_count = 0
results = []
capture_dates = []
plotdata = ""
tabledata = []
for analysis in proxies:
analysis = analysis.getObject()
service = analysis.getService()
resultsrange = \
[x for x in sample.getReferenceResults() if x['uid'] == service_uid][
0]
try:
result = float(analysis.getResult())
results.append(result)
except:
result = analysis.getResult()
capture_dates.append(analysis.getResultCaptureDate())
if result < float(resultsrange['min']) or result > float(
resultsrange['max']):
out_of_range_count += 1
try:
precision = str(analysis.getPrecision())
except:
precision = "2"
try:
formatted_result = str("%." + precision + "f") % result
except:
formatted_result = result
tabledata.append({
_("Analysis"):
analysis.getId(),
_("Result"):
formatted_result,
_("Analyst"):
analysis.getAnalyst(),
_("Captured"):
analysis.getResultCaptureDate().strftime(self.date_format_long)
})
plotdata += "%s\t%s\t%s\t%s\n" % (
analysis.getResultCaptureDate().strftime(
self.date_format_long), result, resultsrange['min'],
resultsrange['max'])
plotdata.encode('utf-8')
result_values = [int(r) for r in results]
result_dates = [c for c in capture_dates]
self.parms += [
{
"title": _("Total analyses"),
"value": len(proxies)
},
]
# # This variable is output to the TAL
self.report_data = {
'header': header,
'subheader': subheader,
'parms': self.parms,
'tables': [],
'footnotes': [],
}
if MinimumResults <= len(proxies):
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set key off
#set logscale
set timefmt "%(timefmt)s"
set xdata time
set format x "%(xformat)s"
set xrange ["%(x_start)s":"%(x_end)s"]
set auto fix
set offsets graph 0, 0, 1, 1
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
f(x) = mean_y
fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y
stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1))
plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y with lines lc rgb '#ffffff' lw 3,\
"gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\
'' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\
'' using 1:4 with lines lc rgb '#000000' lw 1,\
'' using 1:5 with lines lc rgb '#000000' lw 1""" % \
{
'title': "",
'xlabel': "",
'ylabel': service.getUnit(),
'x_start': "%s" % min(result_dates).strftime(
self.date_format_short),
'x_end': "%s" % max(result_dates).strftime(
self.date_format_short),
'timefmt': r'%Y-%m-%d %H:%M',
'xformat': '%%Y-%%m-%%d\n%%H:%%M',
}
plot_png = plot(str(plotdata),
plotscript=str(plotscript),
usefifo=False)
# Temporary PNG data file
fh, data_fn = tempfile.mkstemp(suffix='.png')
os.write(fh, plot_png)
plot_url = data_fn
self.request['to_remove'].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
'title':
"%s: %s (%s)" %
(t(_("Analysis Service")), service.Title(), service.getKeyword()),
'columns':
[_('Analysis'),
_('Result'),
_('Analyst'),
_('Captured')],
'parms': [],
'data':
tabledata,
'plot_url':
plot_url,
}
self.report_data['tables'].append(table)
translate = self.context.translate
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
self.report_data['footnotes'].append("%s %s" %
(error_icon, t(msgid)))
self.report_data['parms'].append({
"title": _("Analyses out of range"),
"value": out_of_range_count
})
title = t(header)
if titles:
title += " (%s)" % " ".join(titles)
return {
'report_title': title,
'report_data': self.template(),
}
def plot(title,
xlabel,
ylabel,
xtics,
data,
width=1024,
height=768,
yunit='',
bare=False):
title, xlabel, ylabel = map(escape, (title, xlabel, ylabel))
xtics = ', '.join(
['"{}" {:d}'.format(escape(c), i) for i, c in enumerate(xtics)])
# this data must be well-formed
keys = sorted(data.keys())
colwise = [[data[k][i] for k in keys] for i in xrange(len(data[keys[0]]))]
ymax = math.ceil(max([max(d) for d in data.values()]))
ntics = 10
# might want svg
plotscript = '''
set terminal pngcairo transparent enhanced size {width:d},{height:d}
set title '{title}'
set xlabel '{xlabel}'
set ylabel '{ylabel}'
set key outside
set format y '%g{yunit}'
set yrange [0:]
set grid
set tics scale 0
set xtics nomirror rotate 90 font ", 8" ({xtics})
'''.format(**locals())
if bare:
plotscript += '''
set title '{title}' font ", 10" offset 0,-0.8
unset xlabel
unset ylabel
unset xtics
unset ytics
unset key
set bmargin 0.5
set lmargin 0.5
set rmargin 0.5
set tmargin 1
'''.format(**locals())
plotscript += 'plot ' + ', '.join([
'''"gpw_DATAFILE_gpw" using {:d} title '{}' with lines'''.format(
i + 1, escape(title)) for i, title in enumerate(keys)
])
plotdata = '\n'.join(
[' '.join(['{:f}'.format(n) for n in row]) for row in colwise]) + '\n'
if PY3:
plotscript = plotscript.encode()
plotout = gpw.plot(plotdata, plotscript=plotscript, usefifo=False)
return plotout
def __call__(self):
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = "<img " + \
"src='" + self.portal_url + "/++resource++bika.lims.images/warning.png' " + \
"height='9' width='9'/>"
error_icon = "<img " + \
"src='" + self.portal_url + "/++resource++bika.lims.images/exclamation.png' " + \
"height='9' width='9'/>"
header = _("Results per sample point")
subheader = _(
"Analysis results for per sample point and analysis service")
self.contentFilter = {'portal_type': 'Analysis',
'review_state': ['verified', 'published']}
parms = []
titles = []
val = self.selection_macros.parse_client(self.request)
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_samplepoint(self.request)
sp_uid = val
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_sampletype(self.request)
st_uid = val
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_analysisservice(self.request)
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
else:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
val = self.selection_macros.parse_daterange(self.request,
'getDateSampled',
'DateSampled')
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_state(self.request,
'bika_worksheetanalysis_workflow',
'worksheetanalysis_review_state',
'Worksheet state')
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
# Query the catalog and store analysis data in a dict
analyses = {}
out_of_range_count = 0
in_shoulder_range_count = 0
analysis_count = 0
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
# # Compile a list of dictionaries, with all relevant analysis data
for analysis in proxies:
analysis = analysis.getObject()
result = analysis.getResult()
client = analysis.aq_parent.aq_parent
uid = analysis.UID()
service = analysis.getService()
keyword = service.getKeyword()
service_title = "%s (%s)" % (service.Title(), keyword)
result_in_range = self.ResultOutOfRange(analysis)
if service_title not in analyses.keys():
analyses[service_title] = []
try:
result = float(analysis.getResult())
except:
# XXX Unfloatable analysis results should be indicated
continue
analyses[service_title].append({
'service': service,
'obj': analysis,
'Request ID': analysis.aq_parent.getId(),
'Analyst': analysis.getAnalyst(),
'Result': result,
'Sampled': analysis.getDateSampled(),
'Captured': analysis.getResultCaptureDate(),
'Uncertainty': analysis.getUncertainty(),
'result_in_range': result_in_range,
'Unit': service.getUnit(),
'Keyword': keyword,
'icons': '',
})
analysis_count += 1
keys = analyses.keys()
keys.sort()
parms += [
{"title": _("Total analyses"), "value": analysis_count},
]
## This variable is output to the TAL
self.report_data = {
'header': header,
'subheader': subheader,
'parms': parms,
'tables': [],
'footnotes': [],
}
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set key off
#set logscale
set timefmt "%(date_format_long)s"
set xdata time
set format x "%(date_format_short)s\\n%(time_format)s"
set xrange ["%(x_start)s":"%(x_end)s"]
set auto fix
set offsets graph 0, 0, 1, 1
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
f(x) = mean_y
fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y
stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1))
plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y with lines lc rgb '#ffffff' lw 3,\
"gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\
'' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\
'' using 1:4 with lines lc rgb '#000000' lw 1,\
'' using 1:5 with lines lc rgb '#000000' lw 1"""
## Compile plots and format data for display
for service_title in keys:
# used to calculate XY axis ranges
result_values = [int(o['Result']) for o in analyses[service_title]]
result_dates = [o['Sampled'] for o in analyses[service_title]]
parms = []
plotdata = str()
range_min = ''
range_max = ''
for a in analyses[service_title]:
a['Sampled'] = a['Sampled'].strftime(self.date_format_long) if a[
'Sampled'] else ''
a['Captured'] = a['Captured'].strftime(self.date_format_long) if \
a['Captured'] else ''
R = a['Result']
U = a['Uncertainty']
a['Result'] = a['obj'].getFormattedResult()
in_range = a['result_in_range']
# result out of range
if str(in_range[0]) == 'False':
out_of_range_count += 1
a['Result'] = "%s %s" % (a['Result'], error_icon)
# result almost out of range
if str(in_range[0]) == '1':
in_shoulder_range_count += 1
a['Result'] = "%s %s" % (a['Result'], warning_icon)
spec = {}
if hasattr(a["obj"], 'specification') and a["obj"].specification:
spec = a["obj"].specification
plotdata += "%s\t%s\t%s\t%s\t%s\n" % (
a['Sampled'],
R,
spec.get("min", ""),
spec.get("max", ""),
U and U or 0,
)
plotdata.encode('utf-8')
unit = analyses[service_title][0]['Unit']
if MinimumResults <= len(dict([(d, d) for d in result_dates])):
_plotscript = str(plotscript) % {
'title': "",
'xlabel': t(_("Date Sampled")),
'ylabel': unit and unit or '',
'x_start': "%s" % min(result_dates).strftime(
self.date_format_long),
'x_end': "%s" % max(result_dates).strftime(
self.date_format_long),
'date_format_long': self.date_format_long,
'date_format_short': self.date_format_short,
'time_format': self.time_format,
}
plot_png = plot(str(plotdata),
plotscript=str(_plotscript),
usefifo=False)
# Temporary PNG data file
fh, data_fn = tempfile.mkstemp(suffix='.png')
os.write(fh, plot_png)
plot_url = data_fn
self.request['to_remove'].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
'title': "%s: %s" % (
t(_("Analysis Service")),
service_title),
'parms': parms,
'columns': ['Request ID',
'Analyst',
'Result',
'Sampled',
'Captured'],
'data': analyses[service_title],
'plot_url': plot_url,
}
self.report_data['tables'].append(table)
translate = self.context.translate
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
self.report_data['footnotes'].append(
"%s %s" % (error_icon, t(msgid)))
if in_shoulder_range_count:
msgid = _("Analyses in error shoulder range")
self.report_data['footnotes'].append(
"%s %s" % (warning_icon, t(msgid)))
self.report_data['parms'].append(
{"title": _("Analyses out of range"),
"value": out_of_range_count})
self.report_data['parms'].append(
{"title": _("Analyses in error shoulder range"),
"value": in_shoulder_range_count})
title = t(header)
if titles:
title += " (%s)" % " ".join(titles)
return {
'report_title': title,
'report_data': self.template(),
}
def __call__(self):
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = "<img " + \
"src='" + self.portal_url + "/++resource++bika.lims.images/warning.png' " + \
"height='9' width='9'/>"
error_icon = "<img " + \
"src='" + self.portal_url + "/++resource++bika.lims.images/exclamation.png' " + \
"height='9' width='9'/>"
header = _("Results per sample point")
subheader = _(
"Analysis results for per sample point and analysis service")
self.contentFilter = {'portal_type': 'Analysis',
'review_state': ['verified', 'published']}
parms = []
titles = []
val = self.selection_macros.parse_client(self.request)
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_samplepoint(self.request)
sp_uid = val
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_sampletype(self.request)
st_uid = val
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_analysisservice(self.request)
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
else:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
val = self.selection_macros.parse_daterange(self.request,
'getDateSampled',
'DateSampled')
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_state(self.request,
'bika_worksheetanalysis_workflow',
'worksheetanalysis_review_state',
'Worksheet state')
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
# Query the catalog and store analysis data in a dict
analyses = {}
out_of_range_count = 0
in_shoulder_range_count = 0
analysis_count = 0
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
# # Compile a list of dictionaries, with all relevant analysis data
for analysis in proxies:
analysis = analysis.getObject()
result = analysis.getResult()
client = analysis.aq_parent.aq_parent
uid = analysis.UID()
keyword = analysis.getKeyword()
service_title = "%s (%s)" % (analysis.Title(), keyword)
result_in_range = self.ResultOutOfRange(analysis)
if service_title not in analyses.keys():
analyses[service_title] = []
try:
result = float(analysis.getResult())
except:
# XXX Unfloatable analysis results should be indicated
continue
analyses[service_title].append({
# The report should not mind taking 'analysis' in place of
# 'service' - the service field values are placed in analysis.
'service': analysis,
'obj': analysis,
'Request ID': analysis.aq_parent.getId(),
'Analyst': analysis.getAnalyst(),
'Result': result,
'Sampled': analysis.getDateSampled(),
'Captured': analysis.getResultCaptureDate(),
'Uncertainty': analysis.getUncertainty(),
'result_in_range': result_in_range,
'Unit': analysis.getUnit(),
'Keyword': keyword,
'icons': '',
})
analysis_count += 1
keys = analyses.keys()
keys.sort()
parms += [
{"title": _("Total analyses"), "value": analysis_count},
]
## This variable is output to the TAL
self.report_data = {
'header': header,
'subheader': subheader,
'parms': parms,
'tables': [],
'footnotes': [],
}
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set key off
#set logscale
set timefmt "%(date_format_long)s"
set xdata time
set format x "%(date_format_short)s\\n%(time_format)s"
set xrange ["%(x_start)s":"%(x_end)s"]
set auto fix
set offsets graph 0, 0, 1, 1
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
f(x) = mean_y
fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y
stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1))
plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y with lines lc rgb '#ffffff' lw 3,\
"gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\
'' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\
'' using 1:4 with lines lc rgb '#000000' lw 1,\
'' using 1:5 with lines lc rgb '#000000' lw 1"""
## Compile plots and format data for display
for service_title in keys:
# used to calculate XY axis ranges
result_values = [int(o['Result']) for o in analyses[service_title]]
result_dates = [o['Sampled'] for o in analyses[service_title]]
parms = []
plotdata = str()
range_min = ''
range_max = ''
for a in analyses[service_title]:
a['Sampled'] = a['Sampled'].strftime(self.date_format_long) if a[
'Sampled'] else ''
a['Captured'] = a['Captured'].strftime(self.date_format_long) if \
a['Captured'] else ''
R = a['Result']
U = a['Uncertainty']
a['Result'] = a['obj'].getFormattedResult()
in_range = a['result_in_range']
# result out of range
if str(in_range) == 'False':
out_of_range_count += 1
a['Result'] = "%s %s" % (a['Result'], error_icon)
# result almost out of range
if str(in_range) == '1':
in_shoulder_range_count += 1
a['Result'] = "%s %s" % (a['Result'], warning_icon)
spec = {}
if hasattr(a["obj"], 'specification') and a["obj"].specification:
spec = a["obj"].specification
plotdata += "%s\t%s\t%s\t%s\t%s\n" % (
a['Sampled'],
R,
spec.get("min", ""),
spec.get("max", ""),
U and U or 0,
)
plotdata.encode('utf-8')
unit = analyses[service_title][0]['Unit']
if MinimumResults <= len(dict([(d, d) for d in result_dates])):
_plotscript = str(plotscript) % {
'title': "",
'xlabel': t(_("Date Sampled")),
'ylabel': unit and unit or '',
'x_start': "%s" % min(result_dates).strftime(
self.date_format_long),
'x_end': "%s" % max(result_dates).strftime(
self.date_format_long),
'date_format_long': self.date_format_long,
'date_format_short': self.date_format_short,
'time_format': self.time_format,
}
plot_png = plot(str(plotdata),
plotscript=str(_plotscript),
usefifo=False)
# Temporary PNG data file
fh, data_fn = tempfile.mkstemp(suffix='.png')
os.write(fh, plot_png)
plot_url = data_fn
self.request['to_remove'].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
'title': "%s: %s" % (
t(_("Analysis Service")),
service_title),
'parms': parms,
'columns': ['Request ID',
'Analyst',
'Result',
'Sampled',
'Captured'],
'data': analyses[service_title],
'plot_url': plot_url,
}
self.report_data['tables'].append(table)
translate = self.context.translate
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
self.report_data['footnotes'].append(
"%s %s" % (error_icon, t(msgid)))
if in_shoulder_range_count:
msgid = _("Analyses in error shoulder range")
self.report_data['footnotes'].append(
"%s %s" % (warning_icon, t(msgid)))
self.report_data['parms'].append(
{"title": _("Analyses out of range"),
"value": out_of_range_count})
self.report_data['parms'].append(
{"title": _("Analyses in error shoulder range"),
"value": in_shoulder_range_count})
title = t(header)
if titles:
title += " (%s)" % " ".join(titles)
return {
'report_title': title,
'report_data': self.template(),
}
def __call__(self):
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = (
"<img "
+ "src='"
+ self.portal_url
+ "/++resource++bika.lims.images/warning.png' "
+ "height='9' width='9'/>"
)
error_icon = (
"<img "
+ "src='"
+ self.portal_url
+ "/++resource++bika.lims.images/exclamation.png' "
+ "height='9' width='9'/>"
)
header = _("Results per sample point")
subheader = _("Analysis results for per sample point and analysis service")
self.contentFilter = {
"portal_type": "Analysis",
"review_state": ["verified", "published"],
"sort_on": "getDateSampled",
}
spec = self.request.form.get("spec", "lab")
spec_title = (spec == "lab") and _("Lab") or _("Client")
parms = []
titles = []
val = self.selection_macros.parse_client(self.request)
if val:
self.contentFilter[val["contentFilter"][0]] = val["contentFilter"][1]
parms.append(val["parms"])
titles.append(val["titles"])
val = self.selection_macros.parse_samplepoint(self.request)
sp_uid = val
if val:
self.contentFilter[val["contentFilter"][0]] = val["contentFilter"][1]
parms.append(val["parms"])
titles.append(val["titles"])
val = self.selection_macros.parse_sampletype(self.request)
st_uid = val
if val:
self.contentFilter[val["contentFilter"][0]] = val["contentFilter"][1]
parms.append(val["parms"])
titles.append(val["titles"])
val = self.selection_macros.parse_analysisservice(self.request)
if val:
self.contentFilter[val["contentFilter"][0]] = val["contentFilter"][1]
parms.append(val["parms"])
else:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
val = self.selection_macros.parse_daterange(self.request, "getDateSampled", "DateSampled")
if val:
self.contentFilter[val["contentFilter"][0]] = val["contentFilter"][1]
parms.append(val["parms"])
titles.append(val["titles"])
val = self.selection_macros.parse_state(
self.request, "bika_worksheetanalysis_workflow", "worksheetanalysis_review_state", "Worksheet state"
)
if val:
self.contentFilter[val["contentFilter"][0]] = val["contentFilter"][1]
parms.append(val["parms"])
# Query the catalog and store analysis data in a dict
analyses = {}
out_of_range_count = 0
in_shoulder_range_count = 0
analysis_count = 0
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
cached_specs = {} # keyed by parent_folder
def lookup_spec(analysis):
# If an analysis is OUT OF RANGE, the failed spec values are passed
# back from the result_in_range function. But if the analysis resuit
# is IN RANGE, we need to look it up.
service = analysis["service"]
keyword = service["Keyword"]
analysis = analysis["obj"]
if spec == "client":
parent = analysis.aq_parent.aq_parent
else:
parent = self.context.bika_setup.bika_analysisspecs
if not parent.UID() in cached_specs:
proxies = self.bika_setup_catalog(
portal_type="AnalysisSpec",
getSampleTypeUID=st_uid,
path={"query": "/".join(parent.getPhysicalPath()), "level": 0},
)
if proxies:
spec_obj = proxies[0].getObject()
this_spec = spec_obj.getResultsRangeDict()
else:
this_spec = {"min": None, "max": None}
cached_specs[parent.UID()] = this_spec
else:
this_spec = cached_specs[parent.UID()]
return this_spec
## Compile a list of dictionaries, with all relevant analysis data
for analysis in proxies:
analysis = analysis.getObject()
client = analysis.aq_parent.aq_parent
uid = analysis.UID()
service = analysis.getService()
keyword = service.getKeyword()
service_title = "%s (%s)" % (service.Title(), service.getKeyword())
result_in_range = analysis.result_in_range(specification=spec)
try:
precision = str(service.getPrecision())
except:
precision = "2"
if service_title not in analyses.keys():
analyses[service_title] = []
try:
result = float(analysis.getResult())
except:
# XXX Unfloatable analysis results should be indicated
continue
analyses[service_title].append(
{
"service": service,
"obj": analysis,
"Request ID": analysis.aq_parent.getId(),
"Analyst": analysis.getAnalyst(),
"Result": result,
"precision": precision,
"Sampled": analysis.getDateSampled(),
"Captured": analysis.getResultCaptureDate(),
"Uncertainty": analysis.getUncertainty(),
"result_in_range": result_in_range,
"Unit": service.getUnit(),
"Keyword": keyword,
"icons": "",
}
)
analysis_count += 1
keys = analyses.keys()
keys.sort()
parms += [
{"title": _("Total analyses"), "value": analysis_count},
{"title": _("Analysis specification"), "value": spec_title},
]
## This variable is output to the TAL
self.report_data = {"header": header, "subheader": subheader, "parms": parms, "tables": [], "footnotes": []}
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set key off
#set logscale
set timefmt "%(date_format_long)s"
set xdata time
set format x "%(date_format_short)s\\n%(time_format)s"
set xrange ["%(x_start)s":"%(x_end)s"]
set auto fix
set offsets graph 0, 0, 1, 1
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
f(x) = mean_y
fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y
stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1))
plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y with lines lc rgb '#ffffff' lw 3,\
"gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\
'' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\
'' using 1:4 with lines lc rgb '#000000' lw 1,\
'' using 1:5 with lines lc rgb '#000000' lw 1"""
## Compile plots and format data for display
for service_title in keys:
# used to calculate XY axis ranges
result_values = [int(o["Result"]) for o in analyses[service_title]]
result_dates = [o["Sampled"] for o in analyses[service_title]]
parms = []
plotdata = str()
range_min = ""
range_max = ""
for a in analyses[service_title]:
a["Sampled"] = a["Sampled"].strftime(self.date_format_long)
a["Captured"] = a["Captured"].strftime(self.date_format_long)
R = a["Result"]
U = a["Uncertainty"]
a["Result"] = str("%." + precision + "f") % a["Result"]
in_range = a["result_in_range"]
# in-range: lookup spec, if possible
if in_range[1] == None:
this_spec_results = lookup_spec(a)
if this_spec_results and a["Keyword"] in this_spec_results:
this_spec = this_spec_results[a["Keyword"]]
in_range[1] == this_spec
# If no specs are supplied, fake them
# and do not print specification values or errors
a["range_min"] = in_range[1] and in_range[1]["min"] or ""
a["range_max"] = in_range[1] and in_range[1]["max"] or ""
if a["range_min"] and a["range_max"]:
range_min = a["range_min"]
range_max = a["range_max"]
# result out of range
if str(in_range[0]) == "False":
out_of_range_count += 1
a["Result"] = "%s %s" % (a["Result"], error_icon)
# result almost out of range
if str(in_range[0]) == "1":
in_shoulder_range_count += 1
a["Result"] = "%s %s" % (a["Result"], warning_icon)
else:
a["range_min"] = min(result_values)
a["range_max"] = max(result_values)
plotdata += "%s\t%s\t%s\t%s\t%s\n" % (a["Sampled"], R, range_min, range_max, U and U or 0)
plotdata.encode("utf-8")
if range_min and range_max:
spec_str = "%s: %s, %s: %s" % (
self.context.translate(_("Range min")),
range_min,
self.context.translate(_("Range max")),
range_max,
)
parms.append({"title": _("Specification"), "value": spec_str})
unit = analyses[service_title][0]["Unit"]
if MinimumResults <= len(dict([(d, d) for d in result_dates])):
_plotscript = str(plotscript) % {
"title": "",
"xlabel": self.context.translate(_("Date Sampled")),
"ylabel": unit and unit or "",
"x_start": "%s" % min(result_dates).strftime(self.date_format_long),
"x_end": "%s" % max(result_dates).strftime(self.date_format_long),
"date_format_long": self.date_format_long,
"date_format_short": self.date_format_short,
"time_format": self.time_format,
}
plot_png = plot(str(plotdata), plotscript=str(_plotscript), usefifo=False)
# Temporary PNG data file
fh, data_fn = tempfile.mkstemp(suffix=".png")
os.write(fh, plot_png)
plot_url = data_fn
self.request["to_remove"].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
"title": "%s: %s" % (self.context.translate(_("Analysis Service")), service_title),
"parms": parms,
"columns": ["Request ID", "Analyst", "Result", "Sampled", "Captured"],
"data": analyses[service_title],
"plot_url": plot_url,
}
self.report_data["tables"].append(table)
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
translate = self.context.translate
self.report_data["footnotes"].append("%s %s" % (error_icon, translate(msgid)))
if in_shoulder_range_count:
msgid = _("Analyses in error shoulder range")
self.report_data["footnotes"].append("%s %s" % (warning_icon, self.context.translate(msgid)))
self.report_data["parms"].append({"title": _("Analyses out of range"), "value": out_of_range_count})
self.report_data["parms"].append(
{"title": _("Analyses in error shoulder range"), "value": in_shoulder_range_count}
)
title = self.context.translate(header)
if titles:
title += " (%s)" % " ".join(titles)
return {"report_title": title, "report_data": self.template()}
def __call__(self):
header = _("Reference analysis QC")
subheader = _("Reference analysis quality control graphs ")
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = "<img src='" + self.portal_url + "/++resource++bika.lims.images/warning.png' height='9' width='9'/>"
error_icon = "<img src='" + self.portal_url + "/++resource++bika.lims.images/exclamation.png' height='9' width='9'/>"
self.parms = []
titles = []
sample_uid = self.request.form.get('ReferenceSampleUID', '')
sample = self.reference_catalog.lookupObject(sample_uid)
if not sample:
message = _("No reference sample was selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.parms.append(
{'title': _("Reference Sample"), 'value': sample.Title()})
titles.append(sample.Title())
service_uid = self.request.form.get('ReferenceServiceUID', '')
service = self.reference_catalog.lookupObject(service_uid)
if not service:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.contentFilter = {'portal_type': 'ReferenceAnalysis',
'review_state': ['verified', 'published'],
'path': {
"query": "/".join(sample.getPhysicalPath()),
"level": 0}}
self.parms.append(
{'title': _("Analysis Service"), 'value': service.Title()})
titles.append(service.Title())
val = self.selection_macros.parse_daterange(self.request,
'getDateVerified',
'DateVerified')
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
self.parms.append(val['parms'])
titles.append(val['titles'])
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
# Compile a list with all relevant analysis data
analyses = []
out_of_range_count = 0
results = []
capture_dates = []
plotdata = ""
tabledata = []
for analysis in proxies:
analysis = analysis.getObject()
service = analysis.getService()
resultsrange = \
[x for x in sample.getReferenceResults() if x['uid'] == service_uid][
0]
try:
result = float(analysis.getResult())
results.append(result)
except:
result = analysis.getResult()
capture_dates.append(analysis.getResultCaptureDate())
if result < float(resultsrange['min']) or result > float(
resultsrange['max']):
out_of_range_count += 1
try:
precision = str(analysis.getPrecision())
except:
precision = "2"
try:
formatted_result = str("%." + precision + "f") % result
except:
formatted_result = result
tabledata.append({_("Analysis"): analysis.getId(),
_("Result"): formatted_result,
_("Analyst"): analysis.getAnalyst(),
_(
"Captured"): analysis.getResultCaptureDate().strftime(
self.date_format_long)})
plotdata += "%s\t%s\t%s\t%s\n" % (
analysis.getResultCaptureDate().strftime(self.date_format_long),
result,
resultsrange['min'],
resultsrange['max']
)
plotdata.encode('utf-8')
result_values = [int(r) for r in results]
result_dates = [c for c in capture_dates]
self.parms += [
{"title": _("Total analyses"), "value": len(proxies)},
]
# # This variable is output to the TAL
self.report_data = {
'header': header,
'subheader': subheader,
'parms': self.parms,
'tables': [],
'footnotes': [],
}
if MinimumResults <= len(proxies):
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set key off
#set logscale
set timefmt "%(timefmt)s"
set xdata time
set format x "%(xformat)s"
set xrange ["%(x_start)s":"%(x_end)s"]
set auto fix
set offsets graph 0, 0, 1, 1
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
f(x) = mean_y
fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y
stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1))
plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y with lines lc rgb '#ffffff' lw 3,\
"gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\
'' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\
'' using 1:4 with lines lc rgb '#000000' lw 1,\
'' using 1:5 with lines lc rgb '#000000' lw 1""" % \
{
'title': "",
'xlabel': "",
'ylabel': service.getUnit(),
'x_start': "%s" % min(result_dates).strftime(
self.date_format_short),
'x_end': "%s" % max(result_dates).strftime(
self.date_format_short),
'timefmt': r'%Y-%m-%d %H:%M',
'xformat': '%%Y-%%m-%%d\n%%H:%%M',
}
plot_png = plot(str(plotdata), plotscript=str(plotscript),
usefifo=False)
# Temporary PNG data file
fh, data_fn = tempfile.mkstemp(suffix='.png')
os.write(fh, plot_png)
plot_url = data_fn
self.request['to_remove'].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
'title': "%s: %s (%s)" % (
t(_("Analysis Service")),
service.Title(),
service.getKeyword()
),
'columns': [_('Analysis'),
_('Result'),
_('Analyst'),
_('Captured')],
'parms': [],
'data': tabledata,
'plot_url': plot_url,
}
self.report_data['tables'].append(table)
translate = self.context.translate
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
self.report_data['footnotes'].append(
"%s %s" % (error_icon, t(msgid)))
self.report_data['parms'].append(
{"title": _("Analyses out of range"),
"value": out_of_range_count})
title = t(header)
if titles:
title += " (%s)" % " ".join(titles)
return {
'report_title': title,
'report_data': self.template(),
}
def __call__(self):
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = "<img " +\
"src='"+self.portal_url+"/++resource++bika.lims.images/warning.png' " +\
"height='9' width='9'/>"
error_icon = "<img " +\
"src='"+self.portal_url+"/++resource++bika.lims.images/exclamation.png' " +\
"height='9' width='9'/>"
header = _("Results per sample point")
subheader = _(
"Analysis results for per sample point and analysis service")
self.contentFilter = {
'portal_type': 'Analysis',
'review_state': ['verified', 'published'],
'sort_on': "getDateSampled"
}
spec = self.request.form.get('spec', 'lab')
spec_title = (spec == 'lab') and _("Lab") or _("Client")
parms = []
titles = []
val = self.selection_macros.parse_client(self.request)
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_samplepoint(self.request)
sp_uid = val
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_sampletype(self.request)
st_uid = val
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_analysisservice(self.request)
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
else:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
val = self.selection_macros.parse_daterange(self.request,
'getDateSampled',
'DateSampled')
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
val = self.selection_macros.parse_state(
self.request, 'bika_worksheetanalysis_workflow',
'worksheetanalysis_review_state', 'Worksheet state')
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
# Query the catalog and store analysis data in a dict
analyses = {}
out_of_range_count = 0
in_shoulder_range_count = 0
analysis_count = 0
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
cached_specs = {} # keyed by parent_folder
def lookup_spec(analysis):
# If an analysis is OUT OF RANGE, the failed spec values are passed
# back from the result_in_range function. But if the analysis resuit
# is IN RANGE, we need to look it up.
service = analysis['service']
keyword = service['Keyword']
analysis = analysis['obj']
if spec == "client":
parent = analysis.aq_parent.aq_parent
else:
parent = self.context.bika_setup.bika_analysisspecs
if not parent.UID() in cached_specs:
proxies = self.bika_setup_catalog(
portal_type='AnalysisSpec',
getSampleTypeUID=st_uid,
path={
"query": "/".join(parent.getPhysicalPath()),
"level": 0
})
if proxies:
spec_obj = proxies[0].getObject()
this_spec = spec_obj.getResultsRangeDict()
else:
this_spec = {'min': None, 'max': None}
cached_specs[parent.UID()] = this_spec
else:
this_spec = cached_specs[parent.UID()]
return this_spec
## Compile a list of dictionaries, with all relevant analysis data
for analysis in proxies:
analysis = analysis.getObject()
client = analysis.aq_parent.aq_parent
uid = analysis.UID()
service = analysis.getService()
keyword = service.getKeyword()
service_title = "%s (%s)" % (service.Title(), service.getKeyword())
result_in_range = analysis.result_in_range(specification=spec)
try:
precision = str(service.getPrecision())
except:
precision = "2"
if service_title not in analyses.keys():
analyses[service_title] = []
try:
result = float(analysis.getResult())
except:
# XXX Unfloatable analysis results should be indicated
continue
analyses[service_title].append({
'service':
service,
'obj':
analysis,
'Request ID':
analysis.aq_parent.getId(),
'Analyst':
analysis.getAnalyst(),
'Result':
result,
'precision':
precision,
'Sampled':
analysis.getDateSampled(),
'Captured':
analysis.getResultCaptureDate(),
'Uncertainty':
analysis.getUncertainty(),
'result_in_range':
result_in_range,
'Unit':
service.getUnit(),
'Keyword':
keyword,
'icons':
'',
})
analysis_count += 1
keys = analyses.keys()
keys.sort()
parms += [
{
"title": _("Total analyses"),
"value": analysis_count
},
{
"title": _("Analysis specification"),
"value": spec_title
},
]
## This variable is output to the TAL
self.report_data = {
'header': header,
'subheader': subheader,
'parms': parms,
'tables': [],
'footnotes': [],
}
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set key off
#set logscale
set timefmt "%(date_format_long)s"
set xdata time
set format x "%(date_format_short)s\\n%(time_format)s"
set xrange ["%(x_start)s":"%(x_end)s"]
set auto fix
set offsets graph 0, 0, 1, 1
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
f(x) = mean_y
fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y
stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1))
plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\
mean_y with lines lc rgb '#ffffff' lw 3,\
"gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\
'' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\
'' using 1:4 with lines lc rgb '#000000' lw 1,\
'' using 1:5 with lines lc rgb '#000000' lw 1"""
## Compile plots and format data for display
for service_title in keys:
# used to calculate XY axis ranges
result_values = [int(o['Result']) for o in analyses[service_title]]
result_dates = [o['Sampled'] for o in analyses[service_title]]
parms = []
plotdata = str()
range_min = ''
range_max = ''
for a in analyses[service_title]:
a['Sampled'] = a['Sampled'].strftime(self.date_format_long)
a['Captured'] = a['Captured'].strftime(self.date_format_long)
R = a['Result']
U = a['Uncertainty']
a['Result'] = str("%." + precision + "f") % a['Result']
in_range = a['result_in_range']
# in-range: lookup spec, if possible
if in_range[1] == None:
this_spec_results = lookup_spec(a)
if this_spec_results and a['Keyword'] in this_spec_results:
this_spec = this_spec_results[a['Keyword']]
in_range[1] == this_spec
# If no specs are supplied, fake them
# and do not print specification values or errors
a['range_min'] = in_range[1] and in_range[1]['min'] or ''
a['range_max'] = in_range[1] and in_range[1]['max'] or ''
if a['range_min'] and a['range_max']:
range_min = a['range_min']
range_max = a['range_max']
# result out of range
if str(in_range[0]) == 'False':
out_of_range_count += 1
a['Result'] = "%s %s" % (a['Result'], error_icon)
# result almost out of range
if str(in_range[0]) == '1':
in_shoulder_range_count += 1
a['Result'] = "%s %s" % (a['Result'], warning_icon)
else:
a['range_min'] = min(result_values)
a['range_max'] = max(result_values)
plotdata += "%s\t%s\t%s\t%s\t%s\n" % (
a['Sampled'],
R,
range_min,
range_max,
U and U or 0,
)
plotdata.encode('utf-8')
if range_min and range_max:
spec_str = "%s: %s, %s: %s" % (
self.context.translate(_("Range min")),
range_min,
self.context.translate(_("Range max")),
range_max,
)
parms.append({
'title': _('Specification'),
'value': spec_str,
})
unit = analyses[service_title][0]['Unit']
if MinimumResults <= len(dict([(d, d) for d in result_dates])):
_plotscript = str(plotscript) % {
'title':
"",
'xlabel':
self.context.translate(_("Date Sampled")),
'ylabel':
unit and unit or '',
'x_start':
"%s" % min(result_dates).strftime(self.date_format_long),
'x_end':
"%s" % max(result_dates).strftime(self.date_format_long),
'date_format_long':
self.date_format_long,
'date_format_short':
self.date_format_short,
'time_format':
self.time_format,
}
plot_png = plot(str(plotdata),
plotscript=str(_plotscript),
usefifo=False)
# Temporary PNG data file
fh, data_fn = tempfile.mkstemp(suffix='.png')
os.write(fh, plot_png)
plot_url = data_fn
self.request['to_remove'].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
'title':
"%s: %s" %
(self.context.translate(_("Analysis Service")), service_title),
'parms':
parms,
'columns':
['Request ID', 'Analyst', 'Result', 'Sampled', 'Captured'],
'data':
analyses[service_title],
'plot_url':
plot_url,
}
self.report_data['tables'].append(table)
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
translate = self.context.translate
self.report_data['footnotes'].append(
"%s %s" % (error_icon, translate(msgid)))
if in_shoulder_range_count:
msgid = _("Analyses in error shoulder range")
self.report_data['footnotes'].append(
"%s %s" % (warning_icon, self.context.translate(msgid)))
self.report_data['parms'].append({
"title": _("Analyses out of range"),
"value": out_of_range_count
})
self.report_data['parms'].append({
"title":
_("Analyses in error shoulder range"),
"value":
in_shoulder_range_count
})
title = self.context.translate(header)
if titles:
title += " (%s)" % " ".join(titles)
return {
'report_title': title,
'report_data': self.template(),
}
def __call__(self):
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = "<img " +\
"src='"+self.portal_url+"/++resource++bika.lims.images/warning.png' " +\
"height='9' width='9'/>"
error_icon = "<img " +\
"src='"+self.portal_url+"/++resource++bika.lims.images/exclamation.png' " +\
"height='9' width='9'/>"
header = _("Reference analysis QC")
subheader = _("Reference analysis quality control graphs ")
self.contentFilter = {'portal_type': 'ReferenceAnalysis',
'review_state': ['verified', 'published'],
}
self.parms = []
titles = []
sample_uid = self.request.form.get('ReferenceSampleUID', '')
sample = self.reference_catalog.lookupObject(sample_uid)
if not sample:
message = _("No reference sample was selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.parms.append({'title':_("Reference Sample"),'value':sample.Title()})
titles.append(sample.Title())
service_uid = self.request.form.get('ReferenceServiceUID', '')
service = self.reference_catalog.lookupObject(service_uid)
if not service:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.contentFilter['path'] = {"query": "/".join(sample.getPhysicalPath()),
"level" : 0 }
keyword = service.getKeyword()
unit = service.getUnit()
service_title = "%s (%s)" % (service.Title(), service.getKeyword())
try:
precision = str(service.getPrecision())
except:
precision = "2"
self.parms.append({'title':_("Analysis Service"),'value':service.Title()})
titles.append(service.Title())
val = self.selection_macros.parse_daterange(self.request,
'getDateVerified',
'DateVerified')
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
self.parms.append(val['parms'])
titles.append(val['titles'])
# GET min/max for range checking
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
## Compile a list with all relevant analysis data
analyses = []
out_of_range_count = 0
in_shoulder_range_count = 0
plot_data = ""
formatted_results = []
results = []
tabledata = []
for analysis in proxies:
analysis = analysis.getObject()
analyses.append(analysis)
try:
result = float(analysis.getResult())
except ValueError:
pass
results.append(result)
captured = self.ulocalized_time(analysis.getResultCaptureDate(), long_format=1)
analyst = analysis.getAnalyst()
title = analysis.getId()
formatted_result = str("%." + precision + "f")%result
formatted_results.append(formatted_result)
tabledata.append({_("Analysis"): title,
_("Result"): formatted_result,
_("Analyst"): analyst,
_("Captured"): captured})
plotdata = "\n".join(formatted_results)
plotdata.encode('utf-8')
### CHECK RANGES
self.parms += [
{"title": _("Total analyses"), "value": len(analyses)},
]
## This variable is output to the TAL
self.report_data = {
'header': header,
'subheader': subheader,
'parms': self.parms,
'tables': [],
'footnotes': [],
}
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set yzeroaxis
#set logscale
set xrange [highest:lowest]
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
binwidth = %(highest)-%(lowest)/100
scale = (binwidth/(%(highest)-%(lowest)))
bin_number(x) = floor(x/binwidth)
rounded(x) = binwidth * ( binnumber(x) + 0.5 )
#f(x) = mean_x
#fit f(x) 'gpw_DATAFILE_gpw' u 1:2 via mean_x
#stddev_x = sqrt(FIT_WSSR / (FIT_NDF + 1))
#
#plot mean_y-stddev_y with lines y1=mean_y lt 1 lc rgb "#afafaf",\
# mean_y+stddev_y with lines y1=mean_y lt 1 lc rgb "#afafaf",\
# mean_y with lines lc rgb '#000000' lw 1,\
plot "gpw_DATAFILE_gpw" using (rounded($1)):(1) smooth frequency
"""
if MinimumResults <= len(analyses):
_plotscript = str(plotscript)%\
{'title': "",
'xlabel': "",
'ylabel': "",
'highest': max(results),
'lowest': min(results)}
plot_png = plot(str(plotdata),
plotscript=str(_plotscript),
usefifo=False)
print plotdata
print _plotscript
print "-------"
# Temporary PNG data file
fh,data_fn = tempfile.mkstemp(suffix='.png')
os.write(fh, plot_png)
plot_url = data_fn
self.request['to_remove'].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
'title': "%s: %s" % (
self.context.translate(_("Analysis Service")),
service_title),
'columns': [_('Analysis'),
_('Result'),
_('Analyst'),
_('Captured')],
'parms':[],
'data': tabledata,
'plot_url': plot_url,
}
self.report_data['tables'].append(table)
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
translate = self.context.translate
self.report_data['footnotes'].append(
"%s %s" % (error_icon, translate(msgid)))
if in_shoulder_range_count:
msgid = _("Analyses in error shoulder range")
self.report_data['footnotes'].append(
"%s %s" % (warning_icon, translate(msgid)))
self.report_data['parms'].append(
{"title": _("Analyses out of range"),
"value": out_of_range_count})
self.report_data['parms'].append(
{"title": _("Analyses in error shoulder range"),
"value": in_shoulder_range_count})
title = self.context.translate(header)
if titles:
title += " (%s)" % " ".join(titles)
return {
'report_title': title,
'report_data': self.template(),
}
def __call__(self):
MinimumResults = self.context.bika_setup.getMinimumResults()
warning_icon = "<img " +\
"src='"+self.portal_url+"/++resource++bika.lims.images/warning.png' " +\
"height='9' width='9'/>"
error_icon = "<img " +\
"src='"+self.portal_url+"/++resource++bika.lims.images/exclamation.png' " +\
"height='9' width='9'/>"
header = _("Reference analysis QC")
subheader = _("Reference analysis quality control graphs ")
self.contentFilter = {
'portal_type': 'ReferenceAnalysis',
'review_state': ['verified', 'published'],
}
self.parms = []
titles = []
sample_uid = self.request.form.get('ReferenceSampleUID', '')
sample = self.reference_catalog.lookupObject(sample_uid)
if not sample:
message = _("No reference sample was selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.parms.append({
'title': _("Reference Sample"),
'value': sample.Title()
})
titles.append(sample.Title())
service_uid = self.request.form.get('ReferenceServiceUID', '')
service = self.reference_catalog.lookupObject(service_uid)
if not service:
message = _("No analysis services were selected.")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
self.contentFilter['path'] = {
"query": "/".join(sample.getPhysicalPath()),
"level": 0
}
keyword = service.getKeyword()
unit = service.getUnit()
service_title = "%s (%s)" % (service.Title(), service.getKeyword())
try:
precision = str(service.getPrecision())
except:
precision = "2"
self.parms.append({
'title': _("Analysis Service"),
'value': service.Title()
})
titles.append(service.Title())
val = self.selection_macros.parse_daterange(self.request,
'getDateVerified',
'DateVerified')
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
self.parms.append(val['parms'])
titles.append(val['titles'])
# GET min/max for range checking
proxies = self.bika_analysis_catalog(self.contentFilter)
if not proxies:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, 'error')
return self.default_template()
## Compile a list with all relevant analysis data
analyses = []
out_of_range_count = 0
in_shoulder_range_count = 0
plot_data = ""
formatted_results = []
results = []
tabledata = []
for analysis in proxies:
analysis = analysis.getObject()
analyses.append(analysis)
try:
result = float(analysis.getResult())
except ValueError:
pass
results.append(result)
captured = self.ulocalized_time(analysis.getResultCaptureDate(),
long_format=1)
analyst = analysis.getAnalyst()
title = analysis.getId()
formatted_result = str("%." + precision + "f") % result
formatted_results.append(formatted_result)
tabledata.append({
_("Analysis"): title,
_("Result"): formatted_result,
_("Analyst"): analyst,
_("Captured"): captured
})
plotdata = "\n".join(formatted_results)
plotdata.encode('utf-8')
### CHECK RANGES
self.parms += [
{
"title": _("Total analyses"),
"value": len(analyses)
},
]
## This variable is output to the TAL
self.report_data = {
'header': header,
'subheader': subheader,
'parms': self.parms,
'tables': [],
'footnotes': [],
}
plotscript = """
set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8"
set title "%(title)s"
set xlabel "%(xlabel)s"
set ylabel "%(ylabel)s"
set yzeroaxis
#set logscale
set xrange [highest:lowest]
set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3
set ytics nomirror
binwidth = %(highest)-%(lowest)/100
scale = (binwidth/(%(highest)-%(lowest)))
bin_number(x) = floor(x/binwidth)
rounded(x) = binwidth * ( binnumber(x) + 0.5 )
#f(x) = mean_x
#fit f(x) 'gpw_DATAFILE_gpw' u 1:2 via mean_x
#stddev_x = sqrt(FIT_WSSR / (FIT_NDF + 1))
#
#plot mean_y-stddev_y with lines y1=mean_y lt 1 lc rgb "#afafaf",\
# mean_y+stddev_y with lines y1=mean_y lt 1 lc rgb "#afafaf",\
# mean_y with lines lc rgb '#000000' lw 1,\
plot "gpw_DATAFILE_gpw" using (rounded($1)):(1) smooth frequency
"""
if MinimumResults <= len(analyses):
_plotscript = str(plotscript)%\
{'title': "",
'xlabel': "",
'ylabel': "",
'highest': max(results),
'lowest': min(results)}
plot_png = plot(str(plotdata),
plotscript=str(_plotscript),
usefifo=False)
print plotdata
print _plotscript
print "-------"
# Temporary PNG data file
fh, data_fn = tempfile.mkstemp(suffix='.png')
os.write(fh, plot_png)
plot_url = data_fn
self.request['to_remove'].append(data_fn)
plot_url = data_fn
else:
plot_url = ""
table = {
'title':
"%s: %s" %
(self.context.translate(_("Analysis Service")), service_title),
'columns':
[_('Analysis'),
_('Result'),
_('Analyst'),
_('Captured')],
'parms': [],
'data':
tabledata,
'plot_url':
plot_url,
}
self.report_data['tables'].append(table)
## footnotes
if out_of_range_count:
msgid = _("Analyses out of range")
translate = self.context.translate
self.report_data['footnotes'].append(
"%s %s" % (error_icon, translate(msgid)))
if in_shoulder_range_count:
msgid = _("Analyses in error shoulder range")
self.report_data['footnotes'].append(
"%s %s" % (warning_icon, translate(msgid)))
self.report_data['parms'].append({
"title": _("Analyses out of range"),
"value": out_of_range_count
})
self.report_data['parms'].append({
"title":
_("Analyses in error shoulder range"),
"value":
in_shoulder_range_count
})
title = self.context.translate(header)
if titles:
title += " (%s)" % " ".join(titles)
return {
'report_title': title,
'report_data': self.template(),
}