class Report(BrowserView):
implements(IViewView)
default_template = ViewPageTemplateFile("templates/productivity.pt")
template = ViewPageTemplateFile(
"templates/productivity_analysesperdepartment.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def __call__(self):
parms = []
titles = []
# Apply filters
self.contentFilter = {'portal_type': 'Analysis'}
val = self.selection_macros.parse_daterange(self.request,
'getDateRequested',
_('Date Requested'))
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_analysis_workflow',
'getAnalysisState',
_('Analysis State'))
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
# Query the catalog and store results in a dictionary
analyses = self.bika_analysis_catalog(self.contentFilter)
if not analyses:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
groupby = self.request.form.get('GroupingPeriod', '')
if (groupby != ''):
parms.append({"title": _("Grouping period"), "value": _(groupby)})
datalines = {}
footlines = {}
totalcount = len(analyses)
totalpublishedcount = 0
totalperformedcount = 0
for analysis in analyses:
analysis = analysis.getObject()
analysisservice = analysis.getService()
department = analysisservice.getDepartment()
department = department.Title() if department else ''
daterequested = analysis.created()
group = ''
if groupby == 'Day':
group = self.ulocalized_time(daterequested)
elif groupby == 'Week':
group = daterequested.strftime(
"%Y") + ", " + daterequested.strftime("%U")
elif groupby == 'Month':
group = daterequested.strftime(
"%B") + " " + daterequested.strftime("%Y")
elif groupby == 'Year':
group = daterequested.strftime("%Y")
else:
group = ''
dataline = {'Group': group, 'Requested': 0, 'Performed': 0,
'Published': 0, 'Departments': {}}
deptline = {'Department': department, 'Requested': 0, 'Performed': 0,
'Published': 0}
if (group in datalines):
dataline = datalines[group]
if (department in dataline['Departments']):
deptline = dataline['Departments'][department]
grouptotalcount = dataline['Requested'] + 1
groupperformedcount = dataline['Performed']
grouppublishedcount = dataline['Published']
depttotalcount = deptline['Requested'] + 1
deptperformedcount = deptline['Performed']
deptpubishedcount = deptline['Published']
workflow = getToolByName(self.context, 'portal_workflow')
arstate = workflow.getInfoFor(analysis.aq_parent, 'review_state', '')
if (arstate == 'published'):
deptpubishedcount += 1
grouppublishedcount += 1
totalpublishedcount += 1
if (analysis.getResult()):
deptperformedcount += 1
groupperformedcount += 1
totalperformedcount += 1
group_performedrequested_ratio = float(groupperformedcount) / float(
grouptotalcount)
group_publishedperformed_ratio = groupperformedcount > 0 and float(
grouppublishedcount) / float(groupperformedcount) or 0
anl_performedrequested_ratio = float(deptperformedcount) / float(
depttotalcount)
anl_publishedperformed_ratio = deptperformedcount > 0 and float(
deptpubishedcount) / float(deptperformedcount) or 0
dataline['Requested'] = grouptotalcount
dataline['Performed'] = groupperformedcount
dataline['Published'] = grouppublishedcount
dataline['PerformedRequestedRatio'] = group_performedrequested_ratio
dataline['PerformedRequestedRatioPercentage'] = ('{0:.0f}'.format(
group_performedrequested_ratio * 100)) + "%"
dataline['PublishedPerformedRatio'] = group_publishedperformed_ratio
dataline['PublishedPerformedRatioPercentage'] = ('{0:.0f}'.format(
group_publishedperformed_ratio * 100)) + "%"
deptline['Requested'] = depttotalcount
deptline['Performed'] = deptperformedcount
deptline['Published'] = deptpubishedcount
deptline['PerformedRequestedRatio'] = anl_performedrequested_ratio
deptline['PerformedRequestedRatioPercentage'] = ('{0:.0f}'.format(
anl_performedrequested_ratio * 100)) + "%"
deptline['PublishedPerformedRatio'] = anl_publishedperformed_ratio
deptline['PublishedPerformedRatioPercentage'] = ('{0:.0f}'.format(
anl_publishedperformed_ratio * 100)) + "%"
dataline['Departments'][department] = deptline
datalines[group] = dataline
# Footer total data
total_performedrequested_ratio = float(totalperformedcount) / float(
totalcount)
total_publishedperformed_ratio = totalperformedcount > 0 and float(
totalpublishedcount) / float(totalperformedcount) or 0
footline = {'Requested': totalcount,
'Performed': totalperformedcount,
'Published': totalpublishedcount,
'PerformedRequestedRatio': total_performedrequested_ratio,
'PerformedRequestedRatioPercentage': ('{0:.0f}'.format(
total_performedrequested_ratio * 100)) + "%",
'PublishedPerformedRatio': total_publishedperformed_ratio,
'PublishedPerformedRatioPercentage': ('{0:.0f}'.format(
total_publishedperformed_ratio * 100)) + "%"}
footlines['Total'] = footline
self.report_data = {'parameters': parms,
'datalines': datalines,
'footlines': footlines}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
'Group',
'Department',
'Requested',
'Performed',
'Published',
]
output = StringIO.StringIO()
dw = csv.DictWriter(output, extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for group_name, group in datalines.items():
for dept_name, dept in group['Departments'].items():
dw.writerow({
'Group': group_name,
'Department': dept_name,
'Requested': dept['Requested'],
'Performed': dept['Performed'],
'Published': dept['Published'],
})
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition",
"attachment;filename=\"analysesperdepartment_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {'report_title': _('Analyses summary per department'),
'report_data': self.template()}
class Report(BrowserView):
implements(IViewView)
template = ViewPageTemplateFile(
"templates/qualitycontrol_resultspersamplepoint.pt")
# if unsuccessful we return here:
default_template = ViewPageTemplateFile("templates/qualitycontrol.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def get_analysis_spec(self, analysis):
rr = dicts_to_dict(analysis.aq_parent.getResultsRange(), 'keyword')
return rr.get(analysis.getKeyword(), None)
def ResultOutOfRange(self, analysis):
""" Template wants to know, is this analysis out of range?
We scan IResultOutOfRange adapters, and return True if any IAnalysis
adapters trigger a result.
"""
adapters = getAdapters((analysis, ), IResultOutOfRange)
spec = self.get_analysis_spec(analysis)
for name, adapter in adapters:
if not spec:
return False
if adapter(specification=spec):
return True
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(),
}
class Report(BrowserView):
implements(IViewView)
default_template = ViewPageTemplateFile("templates/productivity.pt")
template = ViewPageTemplateFile("templates/productivity_dataentrydaybook.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def __call__(self):
parms = []
titles = []
# Apply filters
self.contentFilter = {'portal_type': 'AnalysisRequest'}
val = self.selection_macros.parse_daterange(self.request,
'getDateCreated',
_('Date Created'))
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
# Query the catalog and store results in a dictionary
ars = self.bika_catalog(self.contentFilter)
if not ars:
message = _("No Analysis Requests matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
datalines = {}
footlines = {}
totalcreatedcount = len(ars)
totalreceivedcount = 0
totalpublishedcount = 0
totalanlcount = 0
totalreceptionlag = 0
totalpublicationlag = 0
for ar in ars:
ar = ar.getObject()
datecreated = ar.created()
datereceived = ar.getDateReceived()
datepublished = ar.getDatePublished()
receptionlag = 0
publicationlag = 0
anlcount = len(ar.getAnalyses())
dataline = {
"AnalysisRequestID": ar.getRequestID(),
"DateCreated": self.ulocalized_time(datecreated),
"DateReceived": self.ulocalized_time(datereceived),
"DatePublished": self.ulocalized_time(datepublished),
"ReceptionLag": receptionlag,
"PublicationLag": publicationlag,
"TotalLag": receptionlag + publicationlag,
"BatchID": ar.getBatch().getId() if ar.getBatch() else '',
"SampleID": ar.getSample().Title(),
"SampleType": ar.getSampleTypeTitle(),
"NumAnalyses": anlcount,
"ClientID": ar.aq_parent.id,
"Creator": ar.Creator(),
"Remarks": ar.getRemarks()
}
datalines[ar.getRequestID()] = dataline
totalreceivedcount += ar.getDateReceived() and 1 or 0
totalpublishedcount += ar.getDatePublished() and 1 or 0
totalanlcount += anlcount
totalreceptionlag += receptionlag
totalpublicationlag += publicationlag
# Footer total data
totalreceivedcreated_ratio = float(totalreceivedcount) / float(
totalcreatedcount)
totalpublishedcreated_ratio = float(totalpublishedcount) / float(
totalcreatedcount)
totalpublishedreceived_ratio = totalreceivedcount and float(
totalpublishedcount) / float(totalreceivedcount) or 0
footline = {'Created': totalcreatedcount,
'Received': totalreceivedcount,
'Published': totalpublishedcount,
'ReceivedCreatedRatio': totalreceivedcreated_ratio,
'ReceivedCreatedRatioPercentage': ('{0:.0f}'.format(
totalreceivedcreated_ratio * 100)) + "%",
'PublishedCreatedRatio': totalpublishedcreated_ratio,
'PublishedCreatedRatioPercentage': ('{0:.0f}'.format(
totalpublishedcreated_ratio * 100)) + "%",
'PublishedReceivedRatio': totalpublishedreceived_ratio,
'PublishedReceivedRatioPercentage': ('{0:.0f}'.format(
totalpublishedreceived_ratio * 100)) + "%",
'AvgReceptionLag': (
'{0:.1f}'.format(totalreceptionlag / totalcreatedcount)),
'AvgPublicationLag': (
'{0:.1f}'.format(totalpublicationlag / totalcreatedcount)),
'AvgTotalLag': ('{0:.1f}'.format((
totalreceptionlag + totalpublicationlag) / totalcreatedcount)),
'NumAnalyses': totalanlcount
}
footlines['Total'] = footline
self.report_data = {'parameters': parms,
'datalines': datalines,
'footlines': footlines}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
"AnalysisRequestID",
"DateCreated",
"DateReceived",
"DatePublished",
"ReceptionLag",
"PublicationLag",
"TotalLag",
"BatchID",
"SampleID",
"SampleType",
"NumAnalyses",
"ClientID",
"Creator",
"Remarks",
]
output = StringIO.StringIO()
dw = csv.DictWriter(output, extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for ar_id, row in datalines.items():
dw.writerow({
"AnalysisRequestID": row["AnalysisRequestID"],
"DateCreated": row["DateCreated"],
"DateReceived": row["DateReceived"],
"DatePublished": row["DatePublished"],
"ReceptionLag": row["ReceptionLag"],
"PublicationLag": row["PublicationLag"],
"TotalLag": row["TotalLag"],
"BatchID": row["BatchID"],
"SampleID": row["SampleID"],
"SampleType": row["SampleType"],
"NumAnalyses": row["NumAnalyses"],
"ClientID": row["ClientID"],
"Creator": row["Creator"],
"Remarks": row["Remarks"],
})
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition",
"attachment;filename=\"dataentrydaybook_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {'report_title': _('Data entry day book'),
'report_data': self.template()}
class Report(BrowserView):
implements(IViewView)
default_template = ViewPageTemplateFile("templates/productivity.pt")
template = ViewPageTemplateFile(
"templates/productivity_analysesperformedpertotal.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def __call__(self):
parms = []
titles = []
# Apply filters
self.contentFilter = {'portal_type': 'Analysis'}
val = self.selection_macros.parse_daterange(self.request,
'getDateRequested',
_('Date Requested'))
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
# Query the catalog and store results in a dictionary
analyses = self.bika_analysis_catalog(self.contentFilter)
if not analyses:
message = _("No analyses matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
groupby = self.request.form.get('GroupingPeriod', '')
if (groupby != ''):
parms.append({"title": _("Grouping period"), "value": _(groupby)})
datalines = {}
footlines = {}
totalcount = len(analyses)
totalpublishedcount = 0
totalperformedcount = 0
for analysis in analyses:
analysis = analysis.getObject()
ankeyword = analysis.getKeyword()
antitle = analysis.getServiceTitle()
daterequested = analysis.created()
group = ''
if groupby == 'Day':
group = self.ulocalized_time(daterequested)
elif groupby == 'Week':
group = daterequested.strftime(
"%Y") + ", " + daterequested.strftime("%U")
elif groupby == 'Month':
group = daterequested.strftime(
"%B") + " " + daterequested.strftime("%Y")
elif groupby == 'Year':
group = daterequested.strftime("%Y")
else:
group = ''
dataline = {'Group': group, 'Requested': 0, 'Performed': 0,
'Published': 0, 'Analyses': {}}
anline = {'Analysis': antitle, 'Requested': 0, 'Performed': 0,
'Published': 0}
if (group in datalines):
dataline = datalines[group]
if (ankeyword in dataline['Analyses']):
anline = dataline['Analyses'][ankeyword]
grouptotalcount = dataline['Requested'] + 1
groupperformedcount = dataline['Performed']
grouppublishedcount = dataline['Published']
anltotalcount = anline['Requested'] + 1
anlperformedcount = anline['Performed']
anlpublishedcount = anline['Published']
workflow = getToolByName(self.context, 'portal_workflow')
arstate = workflow.getInfoFor(analysis.aq_parent, 'review_state', '')
if (arstate == 'published'):
anlpublishedcount += 1
grouppublishedcount += 1
totalpublishedcount += 1
if (analysis.getResult()):
anlperformedcount += 1
groupperformedcount += 1
totalperformedcount += 1
group_performedrequested_ratio = float(groupperformedcount) / float(
grouptotalcount)
group_publishedperformed_ratio = groupperformedcount > 0 and float(
grouppublishedcount) / float(groupperformedcount) or 0
anl_performedrequested_ratio = float(anlperformedcount) / float(
anltotalcount)
anl_publishedperformed_ratio = anlperformedcount > 0 and float(
anlpublishedcount) / float(anlperformedcount) or 0
dataline['Requested'] = grouptotalcount
dataline['Performed'] = groupperformedcount
dataline['Published'] = grouppublishedcount
dataline['PerformedRequestedRatio'] = group_performedrequested_ratio
dataline['PerformedRequestedRatioPercentage'] = ('{0:.0f}'.format(
group_performedrequested_ratio * 100)) + "%"
dataline['PublishedPerformedRatio'] = group_publishedperformed_ratio
dataline['PublishedPerformedRatioPercentage'] = ('{0:.0f}'.format(
group_publishedperformed_ratio * 100)) + "%"
anline['Requested'] = anltotalcount
anline['Performed'] = anlperformedcount
anline['Published'] = anlpublishedcount
anline['PerformedRequestedRatio'] = anl_performedrequested_ratio
anline['PerformedRequestedRatioPercentage'] = ('{0:.0f}'.format(
anl_performedrequested_ratio * 100)) + "%"
anline['PublishedPerformedRatio'] = anl_publishedperformed_ratio
anline['PublishedPerformedRatioPercentage'] = ('{0:.0f}'.format(
anl_publishedperformed_ratio * 100)) + "%"
dataline['Analyses'][ankeyword] = anline
datalines[group] = dataline
# Footer total data
total_performedrequested_ratio = float(totalperformedcount) / float(
totalcount)
total_publishedperformed_ratio = totalperformedcount > 0 and float(
totalpublishedcount) / float(totalperformedcount) or 0
footline = {'Requested': totalcount,
'Performed': totalperformedcount,
'Published': totalpublishedcount,
'PerformedRequestedRatio': total_performedrequested_ratio,
'PerformedRequestedRatioPercentage': ('{0:.0f}'.format(
total_performedrequested_ratio * 100)) + "%",
'PublishedPerformedRatio': total_publishedperformed_ratio,
'PublishedPerformedRatioPercentage': ('{0:.0f}'.format(
total_publishedperformed_ratio * 100)) + "%"}
footlines['Total'] = footline
self.report_data = {'parameters': parms,
'datalines': datalines,
'footlines': footlines}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
'Group',
'Analysis',
'Requested',
'Performed',
'Published',
]
output = StringIO.StringIO()
dw = csv.DictWriter(output, extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for group_name, group in datalines.items():
for service_name, service in group['Analyses'].items():
dw.writerow({
'Group': group_name,
'Analysis': service_name,
'Requested': service['Requested'],
'Performed': service['Performed'],
'Published': service['Published'],
})
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition",
"attachment;filename=\"analysesperformedpertotal_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {'report_title': _('Analyses performed as % of total'),
'report_data': self.template()}
class Report(BrowserView):
implements(IViewView)
template = ViewPageTemplateFile(
"templates/qualitycontrol_resultspersamplepoint.pt")
# if unsuccessful we return here:
default_template = ViewPageTemplateFile("templates/qualitycontrol.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def get_analysis_spec(self, analysis):
rr = dicts_to_dict(analysis.aq_parent.getResultsRange(), 'keyword')
return rr.get(analysis.getKeyword(), None)
def ResultOutOfRange(self, analysis):
""" Template wants to know, is this analysis out of range?
We scan IResultOutOfRange adapters, and return True if any IAnalysis
adapters trigger a result.
"""
adapters = getAdapters((analysis, ), IResultOutOfRange)
spec = self.get_analysis_spec(analysis)
for name, adapter in adapters:
if not spec:
return False
if adapter(specification=spec):
return True
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(),
}
class Report(BrowserView):
implements(IViewView)
default_template = ViewPageTemplateFile("templates/administration.pt")
template = ViewPageTemplateFile("templates/administration_usershistory.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def __call__(self):
parms = []
titles = []
rt = getToolByName(self.context, 'portal_repository')
mt = getToolByName(self.context, 'portal_membership')
# Apply filters
self.contentFilter = {
'portal_type':
('Analysis', 'AnalysisCategory', 'AnalysisProfile',
'AnalysisRequest', 'AnalysisService', 'AnalysisSpec',
'ARTemplate', 'Attachment', 'Batch', 'Calculation', 'Client',
'Contact', 'Container', 'ContainerType', 'Department',
'DuplicateAnalysis', 'Instrument', 'InstrumentCalibration',
'InstrumentCertification', 'InstrumentMaintenanceTask',
'InstrumentScheduledTask', 'InstrumentType',
'InstrumentValidation', 'Manufacturer'
'Method', 'Preservation', 'Pricelist', 'ReferenceAnalysis',
'ReferenceDefinition', 'ReferenceSample', 'Sample',
'SampleMatrix', 'SamplePoint', 'SampleType', 'Supplier',
'SupplierContact', 'Worksheet', 'WorksheetTemplate')
}
val = self.selection_macros.parse_daterange(self.request,
'getModificationDate',
_('Modification date'))
if val:
self.contentFilter['modified'] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
user = ''
userfullname = ''
titles.append(user)
if self.request.form.get('User', '') != '':
user = self.request.form['User']
userobj = mt.getMemberById(user)
userfullname = userobj.getProperty('fullname') \
if userobj else ''
parms.append({
'title': _('User'),
'value': ("%s (%s)" % (userfullname, user))
})
# Query the catalog and store results in a dictionary
entities = self.bika_setup_catalog(self.contentFilter)
if not entities:
message = _("No historical actions matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
datalines = []
tmpdatalines = {}
footlines = {}
for entity in entities:
entity = entity.getObject()
entitytype = _(entity.__class__.__name__)
# Workflow states retrieval
for workflowid, workflow in entity.workflow_history.iteritems():
for action in workflow:
actiontitle = _('Created')
if not action['action'] or (action['action'] and
action['action'] == 'create'):
if workflowid == 'bika_inactive_workflow':
continue
actiontitle = _('Created')
else:
actiontitle = _(action['action'])
if (user == '' or action['actor'] == user):
actorfullname = userfullname == '' and mt.getMemberById(
user) or userfullname
dataline = {
'EntityNameOrId':
entity.title_or_id(),
'EntityAbsoluteUrl':
entity.absolute_url(),
'EntityCreationDate':
entity.CreationDate(),
'EntityModificationDate':
entity.ModificationDate(),
'EntityType':
entitytype,
'Workflow':
_(workflowid),
'Action':
actiontitle,
'ActionDate':
action['time'],
'ActionDateStr':
self.ulocalized_time(action['time'], 1),
'ActionActor':
action['actor'],
'ActionActorFullName':
actorfullname,
'ActionComments':
action['comments']
}
tmpdatalines[action['time']] = dataline
# History versioning retrieval
history = rt.getHistoryMetadata(entity)
if history:
hislen = history.getLength(countPurged=False)
for index in range(hislen):
meta = history.retrieve(index)['metadata']['sys_metadata']
metatitle = _(meta['comment'])
if (user == '' or meta['principal'] == user):
actorfullname = userfullname == '' and \
mt.getMemberById(user) or userfullname
dataline = {
'EntityNameOrId': entity.title_or_id(),
'EntityAbsoluteUrl': entity.absolute_url(),
'EntityCreationDate': entity.CreationDate(),
'EntityModificationDate':
entity.ModificationDate(),
'EntityType': entitytype,
'Workflow': '',
'Action': metatitle,
'ActionDate': meta['timestamp'],
'ActionDateStr': meta['timestamp'],
'ActionActor': meta['principal'],
'ActionActorFullName': actorfullname,
'ActionComments': ''
}
tmpdatalines[meta['timestamp']] = dataline
if len(tmpdatalines) == 0:
message = _("No actions found for user ${user}",
mapping={"user": userfullname})
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
else:
# Sort datalines
tmpkeys = tmpdatalines.keys()
tmpkeys.sort(reverse=True)
for index in range(len(tmpkeys)):
datalines.append(tmpdatalines[tmpkeys[index]])
self.report_data = {
'parameters': parms,
'datalines': datalines,
'footlines': footlines
}
return {
'report_title': _('Users history'),
'report_data': self.template()
}
class Report(BrowserView):
implements(IViewView)
default_template = ViewPageTemplateFile("templates/administration.pt")
template = ViewPageTemplateFile("templates/administration_usershistory.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def __call__(self):
parms = []
titles = []
rt = getToolByName(self.context, 'portal_repository')
mt = getToolByName(self.context, 'portal_membership')
# Apply filters
self.contentFilter = {'portal_type': ('Analysis',
'AnalysisCategory',
'AnalysisProfile',
'AnalysisRequest',
'AnalysisService',
'AnalysisSpec',
'ARTemplate',
'Attachment',
'Batch',
'Calculation',
'Client',
'Contact',
'Container',
'ContainerType',
'Department',
'DuplicateAnalysis',
'Instrument',
'InstrumentCalibration',
'InstrumentCertification',
'InstrumentMaintenanceTask',
'InstrumentScheduledTask',
'InstrumentType',
'InstrumentValidation',
'Manufacturer'
'Method',
'Preservation',
'Pricelist',
'ReferenceAnalysis',
'ReferenceDefinition',
'ReferenceSample',
'Sample',
'SampleMatrix',
'SamplePoint',
'SampleType',
'Supplier',
'SupplierContact',
'Worksheet',
'WorksheetTemplate'
)}
val = self.selection_macros.parse_daterange(self.request,
'getModificationDate',
_('Modification date'))
if val:
self.contentFilter['modified'] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
user = ''
userfullname = ''
titles.append(user)
if self.request.form.get('User', '') != '':
user = self.request.form['User']
userobj = mt.getMemberById(user)
userfullname = userobj.getProperty('fullname') \
if userobj else ''
parms.append(
{'title': _('User'), 'value': ("%s (%s)" % (userfullname, user))})
# Query the catalog and store results in a dictionary
entities = self.bika_setup_catalog(self.contentFilter)
if not entities:
message = _("No historical actions matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
datalines = []
tmpdatalines = {}
footlines = {}
for entity in entities:
entity = entity.getObject()
entitytype = _(entity.__class__.__name__)
# Workflow states retrieval
for workflowid, workflow in entity.workflow_history.iteritems():
for action in workflow:
actiontitle = _('Created')
if not action['action'] or (
action['action'] and action['action'] == 'create'):
if workflowid == 'bika_inactive_workflow':
continue
actiontitle = _('Created')
else:
actiontitle = _(action['action'])
if (user == '' or action['actor'] == user):
actorfullname = userfullname == '' and mt.getMemberById(
user) or userfullname
dataline = {'EntityNameOrId': entity.title_or_id(),
'EntityAbsoluteUrl': entity.absolute_url(),
'EntityCreationDate': entity.CreationDate(),
'EntityModificationDate': entity.ModificationDate(),
'EntityType': entitytype,
'Workflow': _(workflowid),
'Action': actiontitle,
'ActionDate': action['time'],
'ActionDateStr': self.ulocalized_time(
action['time'], 1),
'ActionActor': action['actor'],
'ActionActorFullName': actorfullname,
'ActionComments': action['comments']
}
tmpdatalines[action['time']] = dataline
# History versioning retrieval
history = rt.getHistoryMetadata(entity)
if history:
hislen = history.getLength(countPurged=False)
for index in range(hislen):
meta = history.retrieve(index)['metadata']['sys_metadata']
metatitle = _(meta['comment'])
if (user == '' or meta['principal'] == user):
actorfullname = userfullname == '' and \
mt.getMemberById(user) or userfullname
dataline = {'EntityNameOrId': entity.title_or_id(),
'EntityAbsoluteUrl': entity.absolute_url(),
'EntityCreationDate': entity.CreationDate(),
'EntityModificationDate': entity.ModificationDate(),
'EntityType': entitytype,
'Workflow': '',
'Action': metatitle,
'ActionDate': meta['timestamp'],
'ActionDateStr': meta['timestamp'],
'ActionActor': meta['principal'],
'ActionActorFullName': actorfullname,
'ActionComments': ''
}
tmpdatalines[meta['timestamp']] = dataline
if len(tmpdatalines) == 0:
message = _(
"No actions found for user ${user}",
mapping={"user": userfullname})
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
else:
# Sort datalines
tmpkeys = tmpdatalines.keys()
tmpkeys.sort(reverse=True)
for index in range(len(tmpkeys)):
datalines.append(tmpdatalines[tmpkeys[index]])
self.report_data = {'parameters': parms,
'datalines': datalines,
'footlines': footlines}
return {'report_title': _('Users history'),
'report_data': self.template()}
class Report(BrowserView):
implements(IViewView)
default_template = ViewPageTemplateFile("templates/productivity.pt")
template = ViewPageTemplateFile(
"templates/productivity_samplereceivedvsreported.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def __call__(self):
parms = []
titles = []
self.contentFilter = {
'portal_type': 'Sample',
'review_state': ['sample_received', 'expired', 'disposed'],
'sort_on': 'getDateReceived'
}
val = self.selection_macros.parse_daterange(self.request,
'getDateReceived',
_('Date Received'))
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
# Query the catalog and store results in a dictionary
samples = self.bika_catalog(self.contentFilter)
if not samples:
message = _("No samples matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
datalines = {}
footlines = {}
total_received_count = 0
total_published_count = 0
for sample in samples:
sample = sample.getObject()
# For each sample, retrieve check is has results published
# and add it to datalines
published = False
analyses = sample.getAnalyses({})
for analysis in analyses:
analysis = analysis.getObject()
if not (analysis.getDateAnalysisPublished() is None):
published = True
break
datereceived = sample.getDateReceived()
monthyear = datereceived.strftime(
"%B") + " " + datereceived.strftime("%Y")
received = 1
publishedcnt = published and 1 or 0
if (monthyear in datalines):
received = datalines[monthyear]['ReceivedCount'] + 1
publishedcnt = published and datalines[monthyear][
'PublishedCount'] + 1 or \
datalines[monthyear]['PublishedCount']
ratio = publishedcnt / received
dataline = {
'MonthYear':
monthyear,
'ReceivedCount':
received,
'PublishedCount':
publishedcnt,
'UnpublishedCount':
received - publishedcnt,
'Ratio':
ratio,
'RatioPercentage':
'%02d' % (100 * (float(publishedcnt) / float(received))) + '%'
}
datalines[monthyear] = dataline
total_received_count += 1
total_published_count = published and total_published_count + 1 or total_published_count
# Footer total data
ratio = total_published_count / total_received_count
footline = {
'ReceivedCount':
total_received_count,
'PublishedCount':
total_published_count,
'UnpublishedCount':
total_received_count - total_published_count,
'Ratio':
ratio,
'RatioPercentage':
'%02d' %
(100 *
(float(total_published_count) / float(total_received_count))) +
'%'
}
footlines['Total'] = footline
self.report_data = {
'parameters': parms,
'datalines': datalines,
'footlines': footlines
}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
'MonthYear',
'ReceivedCount',
'PublishedCount',
'RatioPercentage',
]
output = StringIO.StringIO()
dw = csv.DictWriter(output,
extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for row in datalines.values():
dw.writerow(row)
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader(
"Content-Disposition",
"attachment;filename=\"receivedvspublished_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {
'report_title': _('Samples received vs. reported'),
'report_data': self.template()
}
class Report(BrowserView):
implements(IViewView)
default_template = ViewPageTemplateFile("templates/productivity.pt")
template = ViewPageTemplateFile(
"templates/productivity_samplereceivedvsreported.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def __call__(self):
parms = []
titles = []
self.contentFilter = {'portal_type': 'Sample',
'review_state': ['sample_received', 'expired',
'disposed'],
'sort_on': 'getDateReceived'}
val = self.selection_macros.parse_daterange(self.request,
'getDateReceived',
_('Date Received'))
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
# Query the catalog and store results in a dictionary
samples = self.bika_catalog(self.contentFilter)
if not samples:
message = _("No samples matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
datalines = {}
footlines = {}
total_received_count = 0
total_published_count = 0
for sample in samples:
sample = sample.getObject()
# For each sample, retrieve check is has results published
# and add it to datalines
published = False
analyses = sample.getAnalyses({})
for analysis in analyses:
analysis = analysis.getObject()
if not (analysis.getDateAnalysisPublished() is None):
published = True
break
datereceived = sample.getDateReceived()
monthyear = datereceived.strftime("%B") + " " + datereceived.strftime(
"%Y")
received = 1
publishedcnt = published and 1 or 0
if (monthyear in datalines):
received = datalines[monthyear]['ReceivedCount'] + 1
publishedcnt = published and datalines[monthyear][
'PublishedCount'] + 1 or \
datalines[monthyear]['PublishedCount']
ratio = publishedcnt / received
dataline = {'MonthYear': monthyear,
'ReceivedCount': received,
'PublishedCount': publishedcnt,
'UnpublishedCount': received - publishedcnt,
'Ratio': ratio,
'RatioPercentage': '%02d' % (
100 * (float(publishedcnt) / float(received))) + '%'}
datalines[monthyear] = dataline
total_received_count += 1
total_published_count = published and total_published_count + 1 or total_published_count
# Footer total data
ratio = total_published_count / total_received_count
footline = {'ReceivedCount': total_received_count,
'PublishedCount': total_published_count,
'UnpublishedCount': total_received_count - total_published_count,
'Ratio': ratio,
'RatioPercentage': '%02d' % (100 * (
float(total_published_count) / float(
total_received_count))) + '%'
}
footlines['Total'] = footline
self.report_data = {
'parameters': parms,
'datalines': datalines,
'footlines': footlines}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
'MonthYear',
'ReceivedCount',
'PublishedCount',
'RatioPercentage',
]
output = StringIO.StringIO()
dw = csv.DictWriter(output, extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for row in datalines.values():
dw.writerow(row)
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition",
"attachment;filename=\"receivedvspublished_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {'report_title': _('Samples received vs. reported'),
'report_data': self.template()}
class Report(BrowserView):
implements(IViewView)
default_template = ViewPageTemplateFile("templates/productivity.pt")
template = ViewPageTemplateFile(
"templates/productivity_dataentrydaybook.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def __call__(self):
parms = []
titles = []
# Apply filters
self.contentFilter = {'portal_type': 'AnalysisRequest'}
val = self.selection_macros.parse_daterange(self.request,
'getDateCreated',
_('Date Created'))
if val:
self.contentFilter[val['contentFilter']
[0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
# Query the catalog and store results in a dictionary
ars = self.bika_catalog(self.contentFilter)
if not ars:
message = _("No Analysis Requests matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
datalines = {}
footlines = {}
totalcreatedcount = len(ars)
totalreceivedcount = 0
totalpublishedcount = 0
totalanlcount = 0
totalreceptionlag = 0
totalpublicationlag = 0
for ar in ars:
ar = ar.getObject()
datecreated = ar.created()
datereceived = ar.getDateReceived()
datepublished = ar.getDatePublished()
receptionlag = 0
publicationlag = 0
anlcount = len(ar.getAnalyses())
dataline = {
"AnalysisRequestID": ar.getRequestID(),
"DateCreated": self.ulocalized_time(datecreated),
"DateReceived": self.ulocalized_time(datereceived),
"DatePublished": self.ulocalized_time(datepublished),
"ReceptionLag": receptionlag,
"PublicationLag": publicationlag,
"TotalLag": receptionlag + publicationlag,
"BatchID": ar.getBatch().getId() if ar.getBatch() else '',
"SampleID": ar.getSample().Title(),
"SampleType": ar.getSampleTypeTitle(),
"NumAnalyses": anlcount,
"ClientID": ar.aq_parent.id,
"Creator": ar.Creator(),
"Remarks": ar.getRemarks()
}
datalines[ar.getRequestID()] = dataline
totalreceivedcount += ar.getDateReceived() and 1 or 0
totalpublishedcount += ar.getDatePublished() and 1 or 0
totalanlcount += anlcount
totalreceptionlag += receptionlag
totalpublicationlag += publicationlag
# Footer total data
totalreceivedcreated_ratio = float(totalreceivedcount) / float(
totalcreatedcount)
totalpublishedcreated_ratio = float(totalpublishedcount) / float(
totalcreatedcount)
totalpublishedreceived_ratio = totalreceivedcount and float(
totalpublishedcount) / float(totalreceivedcount) or 0
footline = {
'Created':
totalcreatedcount,
'Received':
totalreceivedcount,
'Published':
totalpublishedcount,
'ReceivedCreatedRatio':
totalreceivedcreated_ratio,
'ReceivedCreatedRatioPercentage':
('{0:.0f}'.format(totalreceivedcreated_ratio * 100)) + "%",
'PublishedCreatedRatio':
totalpublishedcreated_ratio,
'PublishedCreatedRatioPercentage':
('{0:.0f}'.format(totalpublishedcreated_ratio * 100)) + "%",
'PublishedReceivedRatio':
totalpublishedreceived_ratio,
'PublishedReceivedRatioPercentage':
('{0:.0f}'.format(totalpublishedreceived_ratio * 100)) + "%",
'AvgReceptionLag':
('{0:.1f}'.format(totalreceptionlag / totalcreatedcount)),
'AvgPublicationLag':
('{0:.1f}'.format(totalpublicationlag / totalcreatedcount)),
'AvgTotalLag': ('{0:.1f}'.format(
(totalreceptionlag + totalpublicationlag) /
totalcreatedcount)),
'NumAnalyses':
totalanlcount
}
footlines['Total'] = footline
self.report_data = {
'parameters': parms,
'datalines': datalines,
'footlines': footlines
}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
"AnalysisRequestID",
"DateCreated",
"DateReceived",
"DatePublished",
"ReceptionLag",
"PublicationLag",
"TotalLag",
"BatchID",
"SampleID",
"SampleType",
"NumAnalyses",
"ClientID",
"Creator",
"Remarks",
]
output = StringIO.StringIO()
dw = csv.DictWriter(output,
extrasaction='ignore',
fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for ar_id, row in datalines.items():
dw.writerow({
"AnalysisRequestID": row["AnalysisRequestID"],
"DateCreated": row["DateCreated"],
"DateReceived": row["DateReceived"],
"DatePublished": row["DatePublished"],
"ReceptionLag": row["ReceptionLag"],
"PublicationLag": row["PublicationLag"],
"TotalLag": row["TotalLag"],
"BatchID": row["BatchID"],
"SampleID": row["SampleID"],
"SampleType": row["SampleType"],
"NumAnalyses": row["NumAnalyses"],
"ClientID": row["ClientID"],
"Creator": row["Creator"],
"Remarks": row["Remarks"],
})
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition",
"attachment;filename=\"dataentrydaybook_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {
'report_title': _('Data entry day book'),
'report_data': self.template()
}
class Report(BrowserView):
implements(IViewView)
default_template = ViewPageTemplateFile("templates/productivity.pt")
template = ViewPageTemplateFile(
"templates/productivity_dailysamplesreceived.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
def __call__(self):
parms = []
titles = []
self.contentFilter = {'portal_type': 'Sample',
'review_state': ['sample_received', 'expired',
'disposed'],
'sort_on': 'getDateReceived'}
val = self.selection_macros.parse_daterange(self.request,
'getDateReceived',
_('Date Received'))
if val:
self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1]
parms.append(val['parms'])
titles.append(val['titles'])
# Query the catalog and store results in a dictionary
samples = self.bika_catalog(self.contentFilter)
if not samples:
message = _("No samples matched your query")
self.context.plone_utils.addPortalMessage(message, "error")
return self.default_template()
datalines = []
analyses_count = 0
for sample in samples:
sample = sample.getObject()
# For each sample, retrieve the analyses and generate
# a data line for each one
analyses = sample.getAnalyses({})
for analysis in analyses:
analysis = analysis.getObject()
dataline = {'AnalysisKeyword': analysis.getKeyword(),
'AnalysisTitle': analysis.getServiceTitle(),
'SampleID': sample.getSampleID(),
'SampleType': sample.getSampleType().Title(),
'SampleDateReceived': self.ulocalized_time(
sample.getDateReceived(), long_format=1),
'SampleSamplingDate': self.ulocalized_time(
sample.getSamplingDate(), long_format=1)}
datalines.append(dataline)
analyses_count += 1
# Footer total data
footlines = []
footline = {'TotalCount': analyses_count}
footlines.append(footline)
self.report_data = {
'parameters': parms,
'datalines': datalines,
'footlines': footlines}
if self.request.get('output_format', '') == 'CSV':
import csv
import StringIO
import datetime
fieldnames = [
'SampleID',
'SampleType',
'SampleSamplingDate',
'SampleDateReceived',
'AnalysisTitle',
'AnalysisKeyword',
]
output = StringIO.StringIO()
dw = csv.DictWriter(output, fieldnames=fieldnames)
dw.writerow(dict((fn, fn) for fn in fieldnames))
for row in datalines:
dw.writerow(row)
report_data = output.getvalue()
output.close()
date = datetime.datetime.now().strftime("%Y%m%d%H%M")
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'text/csv')
setheader("Content-Disposition",
"attachment;filename=\"dailysamplesreceived_%s.csv\"" % date)
self.request.RESPONSE.write(report_data)
else:
return {'report_title': _('Daily samples received'),
'report_data': self.template()}
class Report(BrowserView):
implements(IViewView)
template = ViewPageTemplateFile(
"templates/qualitycontrol_referenceanalysisqc.pt")
# if unsuccessful we return here:
default_template = ViewPageTemplateFile("templates/qualitycontrol.pt")
def __init__(self, context, request, report=None):
super(Report, self).__init__(context, request)
self.report = report
self.selection_macros = SelectionMacrosView(self.context, self.request)
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 isSamplePointHidden(self):
return isAttributeHidden('AnalysisRequest', 'SamplePoint')