Merge d638ff2 into e6c3507

.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '2.7', '3.6', '3.7', '3.8' ]
+        python-version: [ '3.6', '3.7', '3.8', '3.9' ]
 
     steps:
     - uses: actions/checkout@v2

hepdata_validator/__init__.py

@@ -116,6 +116,31 @@ def clear_messages(self):
         """
         self.messages = {}
 
+    def add_validation_error(self, file_path, ve):
+        """
+        Formats a validation error into a readable error message and adds it to
+        the messages dict
+        """
+        location = ''
+        if ve.path:
+            for part in ve.path:
+                if type(part) == int:
+                    location += '[{0}]'.format(part)
+                elif not location:
+                    location = part
+                else:
+                    location += '.' + part
+
+        message = ve.message
+        if location:
+            message += f" in '{location}'"
+        # Add expected schema section if it it's present and isn't the full schema
+        if isinstance(ve.schema, dict) and '$schema' not in ve.schema.keys():
+            message += f" (expected: {ve.schema})"
+
+        self.add_validation_message(ValidationMessage(file=file_path,
+                                                      message=message))
+
     def add_validation_message(self, message):
         """
         Adds a message to the messages dict.

hepdata_validator/data_file_validator.py

@@ -124,10 +124,7 @@ def validate(self, **kwargs):
                     check_length_values(data)
 
         except ValidationError as ve:
-            self.add_validation_message(ValidationMessage(
-                file=file_path,
-                message=ve.message + ' in ' + str(ve.instance),
-            ))
+            self.add_validation_error(file_path, ve)
 
         except UnsupportedDataSchemaException as ex:
             self.add_validation_message(ValidationMessage(
@@ -155,14 +152,14 @@ def __unicode__(self):
 def check_for_zero_uncertainty(data):
     """
     Check that uncertainties are not all zero.
-    
+
     :param data: data table in YAML format
     :return: raise ValidationError if uncertainties are all zero
     """
     for dependent_variable in data['dependent_variables']:
 
         if 'values' in dependent_variable:
-            for value in dependent_variable['values']:
+            for i, value in enumerate(dependent_variable['values']):
 
                 if 'errors' in value:
                     zero_uncertainties = []
@@ -183,7 +180,9 @@ def check_for_zero_uncertainty(data):
                             zero_uncertainties.append(False)
 
                     if len(zero_uncertainties) > 0 and all(zero_uncertainties):
-                        raise ValidationError('Uncertainties should not all be zero', instance=value)
+                        raise ValidationError("Uncertainties should not all be zero",
+                                              path=['dependent_variables', 'values', i, 'errors'],
+                                              instance=data['dependent_variables'])
 
 
 def convert_to_float(error):
@@ -207,13 +206,13 @@ def check_length_values(data):
     """
     Check that the length of the 'values' list is consistent for
     each of the independent_variables and dependent_variables.
-    
+
     :param data: data table in YAML format
     :return: raise ValidationError if inconsistent
     """
     indep_count = [len(indep['values']) for indep in data['independent_variables']]
     dep_count = [len(dep['values']) for dep in data['dependent_variables']]
     if len(set(indep_count + dep_count)) > 1:  # if more than one unique count
-        raise ValidationError("Inconsistent length of 'values' list: " + 
-                              "independent_variables%s, dependent_variables%s" % (str(indep_count), str(dep_count)),
-                              instance=data)
+        raise ValidationError("Inconsistent length of 'values' list: " +
+                              "independent_variables %s, dependent_variables %s" % (str(indep_count), str(dep_count)),
+                              instance=data)

hepdata_validator/submission_file_validator.py

@@ -43,7 +43,7 @@ def validate(self, **kwargs):
         try:
             submission_file_schema = None
             additional_file_section_schema = None
-            
+
             with open(self.default_schema_file, 'r') as submission_schema:
                 submission_file_schema = json.load(submission_schema)
 
@@ -74,9 +74,7 @@ def validate(self, **kwargs):
                             check_cmenergies(data_item)
 
                 except ValidationError as ve:
-                    self.add_validation_message(
-                            ValidationMessage(file=file_path,
-                                                message=ve.message + ' in ' + str(ve.instance)))
+                    self.add_validation_error(file_path, ve)
 
             if not self.has_errors(file_path):
                 return_value = True
@@ -111,7 +109,7 @@ def check_cmenergies(data_item):
     :param data_item: YAML document from submission.yaml
     :return: raise ValidationError if not numeric
     """
-    for keyword in data_item['keywords']:
+    for i, keyword in enumerate(data_item['keywords']):
         if keyword['name'] == 'cmenergies':
             cmenergies = keyword['values']
             for cmenergy in cmenergies:
@@ -120,5 +118,7 @@ def check_cmenergies(data_item):
                 except ValueError:
                     m = re.match(r'^\d+\.?\d?-\d+\.?\d?$', cmenergy)
                     if not m or len(cmenergies) > 1:
-                        raise ValidationError("Invalid value (in GeV) for cmenergies: %s" % cmenergy,
-                                              instance=data_item)
+                        raise ValidationError("Invalid value (in GeV) for cmenergies: '%s'" % cmenergy,
+                                              path=['keywords', i, 'name', 'cmenergies'],
+                                              instance=data_item['keywords'],
+                                              schema={ "type": "number or hyphen-separated range of numbers e.g. 1.7-4.7"})

testsuite/test_data/invalid_parser_submission.yaml

@@ -8,7 +8,7 @@ keywords: # used for searching, possibly multiple values for each keyword
   - { name: cmenergies, value: [7000]}
 data_file: data3.yaml
 additional_resources:
-  - location: "http:github.com/HEPData/hepdata"
+  - location: "https://github.com/HEPData/hepdata"
     description: "Full source code for creating this data"
-  - location: "http:github.com/HEPData/hepdata"
+  - location: "https://github.com/HEPData/hepdata"
     description: "Full source code for creating this data"

testsuite/test_data/invalid_submission.yaml

@@ -8,7 +8,7 @@ keywords: # used for searching, possibly multiple values for each keyword
   - { name: cmenergies, value: [7000]}
 data_file: 12321
 additional_resources:
-  - location: "http:github.com/HEPData/hepdata"
+  - location: "https://github.com/HEPData/hepdata"
+    description: "Full source code for creating this data"
+  - location: "https://github.com/HEPData/hepdata"
     description: "Full source code for creating this data"
-  - location: "http:github.com/HEPData/hepdata"
-    description: "Full source code for creating this data"

testsuite/test_data/invalid_submission_license.yaml

@@ -0,0 +1,69 @@
+---
+
+additional_resources:
+  - location: "https://github.com/HEPData/hepdata"
+    description: "Full source code for creating this data"
+  - location: "https://github.com/HEPData/hepdata"
+    description: "Full source code for creating this data"
+    license:
+      name: 'GPL 2'
+      url: 'somewhere over the rainbow...'
+      description: blah
+
+modifications: # what, by whom and when encoded or changed
+  - {action: 'Encoded', date: '27 FEB 2014', who: 'Graeme Watt'}
+  - {action: 'Modified', date: '30 APR 2014', who: 'Graeme Watt'}
+
+comment: | # Information that applies to all data tables.
+  CERN-LHC.  Measurements of the cross section  for ZZ production using the 4l and 2l2nu decay channels in proton-proton collisions at a centre-of-mass energy of 7 TeV with 4.6 fb^-1 of data collected in 2011.  The final states used are 4 electrons, 4 muons, 2 electrons and 2 muons, 2 electrons and missing transverse momentum, and 2 muons and missing transverse momentum (MET).
+
+  The cross section values reported in the tables should be multiplied by a factor of 1.0141 to take into account the updated value of the integrated luminosity for the ATLAS 2011 data taking period.  The uncertainty on the global normalisation ("Lumi") remains at 1.8%.  See Eur.Phys.J. C73 (2013) 2518 for more details.
+
+  The 4l channel fiducial region is defined as:
+  - 4e, 4mu or 2e2mu
+  - Ambiguities in pairing are resolved by choosing the combination that results in the smaller value of the sum |mll - mZ| for the two pairs, where mll is the mass of the dilepton system.
+  - ptLepton > 7 GeV (at least one with ptLepton > 20 (25) GeV for muons (electrons))
+  - |etaLepton| < 3.16
+  - At least one lepton pair is required to have invariant mass between 66 and 116 GeV. If the second pair also satisfies this, the event is ZZ, otherwise if the second pair satisfies mll > 20 GeV it is ZZ*.
+  - min(DeltaR(l,l)) > 0.2.
+
+  The 2l2nu channel fiducial region is defined as:
+  - 2e+MET or 2mu+MET
+  - ptLepton > 20 GeV
+  - |etaLepton| < 2.5
+  - mll must be between 76 and 106 GeV
+  - -MET*cos(phi_METZ)>75 GeV, where phi_METZ is the angle between the Z and the MET
+  - |MET - pTZ| / pTZ < 0.4, where pTZ is the transverse momentum of the dilepton system
+  - No events with a jet for which ptJet > 25 GeV and |etaJet| < 4.5
+  - No events with a third lepton for which ptLepton > 10 GeV
+  - min(DeltaR(l,l)) > 0.3
+
+
+---
+name: "Table 1"
+location: Page 17 of preprint
+description: The measured fiducial cross sections.  The first systematic uncertainty is the combined systematic uncertainty excluding luminosity, the second is the luminosity
+keywords: # used for searching, possibly multiple values for each keyword
+  - { name: reactions, values: [P P --> Z0 Z0 X]}
+  - { name: observables, values: [SIG]}
+  - { name: cmenergies, values: [7000]}
+data_file: data1.yaml
+data_license: {description: null, name: null, url: null}
+additional_resources:
+  - location: "https://github.com/HEPData/hepdata"
+    description: "Full source code for creating this data"
+  - location: "https://github.com/HEPData/hepdata"
+    description: "Full source code for creating this data"
+    license:
+      name: 'GPL 2'
+      url: 'some url'
+---
+# This is Table 2.
+name: "Table 2"
+location: Page 20 of preprint
+description: The measured total cross sections.  The first systematic uncertainty is the combined systematic uncertainty excluding luminosity, the second is the luminosity
+keywords: # used for searching, possibly multiple values for each keyword
+  - { name: reactions, values: [P P --> Z0 Z0 X]}
+  - { name: observables, values: [SIG]}
+  - { name: cmenergies, values: [7000]}
+data_file: data2.yaml

testsuite/test_data/invalid_syntax_submission.yaml

@@ -8,7 +8,7 @@ keywords: # used for searching, possibly multiple values for each keyword
   - { name: cmenergies, value: [7000]}
 data_file:'12321'
 additional_resources:
-  - location: "http:github.com/HEPData/hepdata"
+  - location: "https://github.com/HEPData/hepdata"
     description: "Full source code for creating this data"
-  - location: "http:github.com/HEPData/hepdata"
+  - location: "https://github.com/HEPData/hepdata"
     description: "Full source code for creating this data"

testsuite/test_data/valid_submission_license.yaml

@@ -1,9 +1,9 @@
 ---
 
 additional_resources:
-  - location: "http:github.com/HEPData/hepdata"
+  - location: "https://github.com/HEPData/hepdata"
     description: "Full source code for creating this data"
-  - location: "http:github.com/HEPData/hepdata"
+  - location: "https://github.com/HEPData/hepdata"
     description: "Full source code for creating this data"
     license:
       name: 'GPL 2'
@@ -52,9 +52,9 @@ data_license:
   name: 'GPL 2'
   url: 'some url'
 additional_resources:
-  - location: "http:github.com/HEPData/hepdata"
+  - location: "https://github.com/HEPData/hepdata"
     description: "Full source code for creating this data"
-  - location: "http:github.com/HEPData/hepdata"
+  - location: "https://github.com/HEPData/hepdata"
     description: "Full source code for creating this data"
     license:
       name: 'GPL 2'
@@ -68,4 +68,4 @@ keywords: # used for searching, possibly multiple values for each keyword
   - { name: reactions, values: [P P --> Z0 Z0 X]}
   - { name: observables, values: [SIG]}
   - { name: cmenergies, values: [7000]}
-data_file: data2.yaml
+data_file: data2.yaml