Check that each value of cmenergies keyword is numeric (closes #18)

* Move _get_major_version to Validator for SubmissionFileValidator use.
* Add check that each value of cmenergies are numeric or a range.
* Add test for check that cmenergies values are numeric or a range.
* Modify valid_submission.yaml for example of cmenergies as a range.
* Correct duplicate test_valid_submission_yaml_v1 function name.
* Add Python 3.7 and 3.8 to versions checked in Travis CI.
* Explain in README.rst how to pass 'data' for SubmissionFileValidator.

.travis.yml

@@ -27,6 +27,8 @@ language: python
 python:
   - "2.7"
   - "3.6"
+  - "3.7"
+  - "3.8"
 
 cache:
   - pip

README.rst

@@ -116,6 +116,20 @@ for the error message lookup map.
 
     data_file_validator.print_errors('data.yaml')
 
+For the analogous case of the ``SubmissionFileValidator``:
+
+.. code:: python
+
+    from hepdata_validator.submission_file_validator import SubmissionFileValidator
+    import yaml
+    submission_file_path = 'submission.yaml'
+
+    # convert a generator returned by yaml.safe_load_all into a list
+    docs = list(yaml.safe_load_all(open(submission_file_path, 'r')))
+
+    submission_file_validator = SubmissionFileValidator()
+    is_valid_submission_file = submission_file_validator.validate(file_path=submission_file_path, data=docs)
+    submission_file_validator.print_errors(submission_file_path)
 
 An example `offline validation script <https://github.com/HEPData/hepdata-submission/blob/master/scripts/check.py>`_
 uses the ``hepdata_validator`` package to validate the ``submission.yaml`` file and all YAML data files of a

hepdata_validator/__init__.py

@@ -52,6 +52,14 @@ def __init__(self, *args, **kwargs):
         if self.schema_version not in VALID_SCHEMA_VERSIONS:
             raise ValueError('Invalid schema version ' + self.schema_version)
 
+    def _get_major_version(self):
+        """
+        Parses the major version of the validator.
+
+        :return: integer corresponding to the validator major version
+        """
+        return int(self.schema_version.split('.')[0])
+
     def _get_schema_filepath(self, schema_filename):
         full_filepath = os.path.join(self.base_path,
                                      self.schema_folder,

hepdata_validator/data_file_validator.py

@@ -50,14 +50,6 @@ def __init__(self, *args, **kwargs):
         super(DataFileValidator, self).__init__(*args, **kwargs)
         self.default_schema_file = self._get_schema_filepath(self.schema_name)
 
-    def _get_major_version(self):
-        """
-        Parses the major version of the validator.
-
-        :return: integer corresponding to the validator major version
-        """
-        return int(self.schema_version.split('.')[0])
-
     def load_custom_schema(self, type, schema_file_path=None):
         """
         Loads a custom schema, or will use a stored version for the given type if available.

hepdata_validator/submission_file_validator.py

@@ -1,6 +1,7 @@
 import json
 from jsonschema import validate, ValidationError
 import os
+import re
 import yaml
 from yaml.scanner import ScannerError
 
@@ -69,6 +70,8 @@ def validate(self, **kwargs):
                         validate(data_item, additional_file_section_schema)
                     else:
                         validate(data_item, submission_file_schema)
+                        if self._get_major_version() > 0:
+                            check_cmenergies(data_item)
 
                 except ValidationError as ve:
                     self.add_validation_message(
@@ -99,3 +102,23 @@ def validate(self, **kwargs):
                 data_file_handle.close()
 
         return return_value
+
+
+def check_cmenergies(data_item):
+    """
+    Check that 'cmenergies' values are numeric unless a range like 1.7-4.7.
+
+    :param data_item: YAML document from submission.yaml
+    :return: raise ValidationError if not numeric
+    """
+    for keyword in data_item['keywords']:
+        if keyword['name'] == 'cmenergies':
+            cmenergies = keyword['values']
+            for cmenergy in cmenergies:
+                try:
+                    cmenergy = float(cmenergy)
+                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)

testsuite/test_data/invalid_cmenergies.yaml

@@ -0,0 +1,10 @@
+---
+# 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 GeV]}
+data_file: data2.yaml

testsuite/test_data/valid_submission.yaml

@@ -56,5 +56,5 @@ description: The measured total cross sections.  The first systematic uncertaint
 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]}
+  - { name: cmenergies, values: [7000.0-8000.0]}
 data_file: data2.yaml

testsuite/test_submission_validator.py

@@ -218,7 +218,7 @@ def test_invalid_schema_file():
         VALID_SCHEMA_VERSIONS.pop()
 
 
-def test_valid_submission_yaml_v1(validator_v1, data_path):
+def test_data_schema_submission_yaml_v1(validator_v1, data_path):
     """
     Tests the SubmissionFileValidator V1 against a valid YAML with a data_schema key
     """
@@ -230,4 +230,19 @@ def test_valid_submission_yaml_v1(validator_v1, data_path):
         is_valid = validator_v1.validate(file_path=file, data=yaml_obj)
         validator_v1.print_errors(file)
 
-        assert is_valid is True
+        assert is_valid is True
+
+
+def test_invalid_cmenergies_submission_yaml_v1(validator_v1, data_path):
+    """
+    Tests the SubmissionFileValidator V1 against an invalid cmenergies value
+    """
+
+    file = os.path.join(data_path, 'invalid_cmenergies.yaml')
+
+    with open(file, 'r') as submission:
+        yaml_obj = yaml.load_all(submission, Loader=Loader)
+        is_valid = validator_v1.validate(file_path=file, data=yaml_obj)
+        validator_v1.print_errors(file)
+
+        assert is_valid is False