Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix: Coverage for importing XML channels with no data #1931

Merged
merged 3 commits into from
Aug 10, 2022
Merged

fix: Coverage for importing XML channels with no data #1931

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
baff2bc
add test for runtime error addition
kratsg Aug 9, 2022
81351b8
add test to cover missing POI in spec
kratsg Aug 9, 2022
f150460
pass tests
kratsg Aug 10, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 7 additions & 6 deletions src/pyhf/readxml.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ def import_root_histogram(rootdir, filename, path, name, filecache=None):


def process_sample(
sample, rootdir, inputfile, histopath, channelname, track_progress=False
sample, rootdir, inputfile, histopath, channel_name, track_progress=False
):
if 'InputFile' in sample.attrib:
inputfile = sample.attrib.get('InputFile')
Expand Down Expand Up @@ -164,7 +164,7 @@ def process_sample(
raise RuntimeError('cannot determine stat error.')
modifiers.append(
{
'name': f'staterror_{channelname}',
'name': f'staterror_{channel_name}',
'type': 'staterror',
'data': staterr,
}
Expand Down Expand Up @@ -226,24 +226,25 @@ def process_channel(channelxml, rootdir, track_progress=False):
channel.findall('Sample'), unit='sample', disable=not (track_progress)
)

channel_name = channel.attrib['Name']

data = channel.findall('Data')
if data:
parsed_data = process_data(data[0], rootdir, inputfile, histopath)
else:
parsed_data = None
channelname = channel.attrib['Name']
raise RuntimeError(f"Channel {channel_name} is missing data. See issue #1911.")

results = []
channel_parameter_configs = []
for sample in samples:
samples.set_description(f" - sample {sample.attrib.get('Name')}")
result = process_sample(
sample, rootdir, inputfile, histopath, channelname, track_progress
sample, rootdir, inputfile, histopath, channel_name, track_progress
)
channel_parameter_configs.extend(result.pop('parameter_configs'))
results.append(result)

return channelname, parsed_data, results, channel_parameter_configs
return channel_name, parsed_data, results, channel_parameter_configs


def process_measurements(toplvl, other_parameter_configs=None):
Expand Down
11 changes: 11 additions & 0 deletions tests/test_import.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -474,3 +474,14 @@ def test_import_validation_exception(mocker, caplog):
'validation/xmlimport_input2',
validation_as_error=True,
)


def test_import_noChannelData(mocker, datadir):
_data = [0.0]
_err = [1.0]
mocker.patch('pyhf.readxml.import_root_histogram', return_value=(_data, _err))

basedir = datadir.joinpath("xmlimport_noChannelData")
with pytest.raises(RuntimeError) as excinfo:
pyhf.readxml.parse(basedir.joinpath("config/example.xml"), basedir)
assert 'Channel channel1 is missing data. See issue #1911' in str(excinfo.value)
160 changes: 160 additions & 0 deletions tests/test_import/xmlimport_noChannelData/config/HistFactorySchema.dtd
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,160 @@

<!-- The top level combination spec -->
<!-- OutputFilePrefix: Prefix to the output root file to be created (inspection histograms) -->
<!-- Mode: Type of the analysis -->
<!ELEMENT Combination (Function*,Input+,Measurement*)>
<!ATTLIST Combination
OutputFilePrefix CDATA #REQUIRED
Mode CDATA #IMPLIED
>

<!-- Input files detailing the channels. One channel per file -->
<!ELEMENT Function EMPTY>
<!ATTLIST Function
Name CDATA #REQUIRED
Expression CDATA #REQUIRED
Dependents CDATA #REQUIRED
>

<!-- Input files detailing the channels. One channel per file -->
<!ELEMENT Input (#PCDATA) >

<!-- Configuration for each measurement -->
<!-- Name: to be used as the heading in the table -->
<!-- Lumi: the luminosity of the measurement -->
<!-- LumiRelErr: the relative error known for the lumi -->
<!-- BinLow: the lowest bin number used for the measurement (inclusive) -->
<!-- BinHigh: the highest bin number used for the measurement (exclusive) -->
<!-- Mode: type of the measurement (a closed list of ...) -->
<!-- ExportOnly: if "True" skip fit, only export model -->
<!ELEMENT Measurement (POI,ParamSetting*,ConstraintTerm*) >
<!ATTLIST Measurement
Name CDATA #REQUIRED
Lumi CDATA #REQUIRED
LumiRelErr CDATA #REQUIRED
BinLow CDATA #IMPLIED
BinHigh CDATA #IMPLIED
Mode CDATA #IMPLIED
ExportOnly CDATA #IMPLIED
>

<!-- Specify what you are measuring. Corresponds to the name specified in the construction
of the model in the channel setup. Typically the NormFactor for xsec measurements -->
<!ELEMENT POI (#PCDATA) >

<!-- Specify what parameters are fixed, or have particular value -->
<!-- Val: set the value of the parameter -->
<!-- Const: set this parameter constant -->
<!ELEMENT ParamSetting (#PCDATA)>
<!ATTLIST ParamSetting
Val CDATA #IMPLIED
Const CDATA #IMPLIED
>

<!-- Specify an alternative shape to use for given constraint terms (Gaussian is used if this is not specified) -->
<!-- Type: can be Gamma or Uniform -->
<!-- RelativeUncertainty: relative uncertainty on the shape -->
<!ELEMENT ConstraintTerm (#PCDATA)>
<!ATTLIST ConstraintTerm
Type CDATA #REQUIRED
RelativeUncertainty CDATA #IMPLIED
>

<!-- Top element for channels. InputFile, HistoName and HistoPath
can be set at this level in which case they will become defaul to
all subsequent elements. Otherwise they can be set in individual
subelements -->
<!ELEMENT Channel (Data*,StatErrorConfig*,Sample+)>
<!-- InputFile: input file where the input histogram can be found (use abs path) -->
<!-- HistoPath: the path (within the root file) where the histogram can be found -->
<!-- HistoName: the name of the histogram to be used for this (and following in not overridden) item -->
<!ATTLIST Channel
Name CDATA #REQUIRED
InputFile CDATA #IMPLIED
HistoPath CDATA #IMPLIED
HistoName CDATA #IMPLIED
>

<!-- Data to be fit. If you don't provide it, Asimov data will be created -->
<!-- InputFile: any item set here will override the configuration for the subelements.
For this element there is no sublemenents so the setting will only have local effects -->
<!ELEMENT Data EMPTY>
<!ATTLIST Data
InputFile CDATA #IMPLIED
HistoPath CDATA #IMPLIED
HistoName CDATA #IMPLIED
>

<!ELEMENT StatErrorConfig EMPTY>
<!ATTLIST StatErrorConfig
RelErrorThreshold CDATA #IMPLIED
ConstraintType CDATA #IMPLIED
>


<!-- Sample elements are made up of systematic variations -->
<!ELEMENT Sample (StatError | HistoSys | OverallSys | ShapeSys | NormFactor | ShapeFactor)*>
<!ATTLIST Sample
Name CDATA #REQUIRED
InputFile CDATA #IMPLIED
HistoName CDATA #IMPLIED
HistoPath CDATA #IMPLIED
NormalizeByTheory CDATA #IMPLIED
>

<!-- Systematics for which the variation is provided by histograms -->
<!ELEMENT StatError EMPTY>
<!ATTLIST StatError
Activate CDATA #REQUIRED
HistoName CDATA #IMPLIED
InputFile CDATA #IMPLIED
HistoPath CDATA #IMPLIED
>

<!ELEMENT HistoSys EMPTY>
<!ATTLIST HistoSys
Name CDATA #REQUIRED
InputFile CDATA #IMPLIED
HistoFileHigh CDATA #IMPLIED
HistoPathHigh CDATA #IMPLIED
HistoNameHigh CDATA #IMPLIED
HistoFileLow CDATA #IMPLIED
HistoPathLow CDATA #IMPLIED
HistoNameLow CDATA #IMPLIED
>

<!-- Systematics for which the variation is provided by simple overall scaling -->
<!ELEMENT OverallSys EMPTY>
<!ATTLIST OverallSys
Name CDATA #REQUIRED
High CDATA #REQUIRED
Low CDATA #REQUIRED
>

<!-- Systematics for which the variation is provided by simple overall scaling -->
<!ELEMENT ShapeSys EMPTY>
<!ATTLIST ShapeSys
Name CDATA #REQUIRED
HistoName CDATA #REQUIRED
HistoPath CDATA #IMPLIED
InputFile CDATA #IMPLIED
ConstraintType CDATA #IMPLIED
>

<!-- Scaling factor, which may be the parameter of interest for cross section measurements-->
<!ELEMENT NormFactor EMPTY>
<!ATTLIST NormFactor
Name CDATA #REQUIRED
Val CDATA #REQUIRED
High CDATA #REQUIRED
Low CDATA #REQUIRED
Const CDATA #IMPLIED
>


<!-- Systematics for which the variation is provided by simple overall scaling -->
<!ELEMENT ShapeFactor EMPTY>
<!ATTLIST ShapeFactor
Name CDATA #REQUIRED
>

8 changes: 8 additions & 0 deletions tests/test_import/xmlimport_noChannelData/config/example.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
<!DOCTYPE Combination SYSTEM 'HistFactorySchema.dtd'>
<Combination OutputFilePrefix="./results/example" >
<Input>./config/example_channel.xml</Input>
<Measurement Name="GaussExample" Lumi="1." LumiRelErr="0.1" >
<POI>SigXsecOverSM</POI>
<ParamSetting Const="True">Lumi alpha_syst1</ParamSetting>
</Measurement>
</Combination>
16 changes: 16 additions & 0 deletions tests/test_import/xmlimport_noChannelData/config/example_channel.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
<!DOCTYPE Channel SYSTEM 'HistFactorySchema.dtd'>
<Channel Name="channel1" InputFile="./data/example.root" >
<!--<Data HistoName="data" HistoPath="" />-->
<Sample Name="signal" HistoPath="" HistoName="signal">
<OverallSys Name="syst1" High="1.05" Low="0.95"/>
<NormFactor Name="SigXsecOverSM" Val="1" Low="0." High="3." />
</Sample>
<Sample Name="background1" HistoPath="" NormalizeByTheory="True" HistoName="background1">
<StatError Activate="True" HistoName="background1_statUncert" />
<OverallSys Name="syst2" Low="0.95" High="1.05"/>
</Sample>
<Sample Name="background2" HistoPath="" NormalizeByTheory="True" HistoName="background2">
<StatError Activate="True" /> <!-- Use Default Histogram Errors as input to StatError -->
<OverallSys Name="syst3" Low="0.95" High="1.05"/>
</Sample>
</Channel>