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mdsol/rwslib | rwslib/builders/metadata.py | GlobalVariables.build | def build(self, builder):
"""Build XML by appending to builder"""
builder.start("GlobalVariables", {})
make_element(builder, "StudyName", self.name)
make_element(builder, "StudyDescription", self.description)
make_element(builder, "ProtocolName", self.protocol_name)
builder.end("GlobalVariables") | python | def build(self, builder):
"""Build XML by appending to builder"""
builder.start("GlobalVariables", {})
make_element(builder, "StudyName", self.name)
make_element(builder, "StudyDescription", self.description)
make_element(builder, "ProtocolName", self.protocol_name)
builder.end("GlobalVariables") | [
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mdsol/rwslib | rwslib/builders/metadata.py | BasicDefinitions.build | def build(self, builder):
"""Build XML by appending to builder"""
builder.start("BasicDefinitions", {})
for child in self.measurement_units:
child.build(builder)
builder.end("BasicDefinitions") | python | def build(self, builder):
"""Build XML by appending to builder"""
builder.start("BasicDefinitions", {})
for child in self.measurement_units:
child.build(builder)
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mdsol/rwslib | rwslib/builders/metadata.py | MeasurementUnit.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(OID=self.oid, Name=self.name)
if self.unit_dictionary_name:
params["mdsol:UnitDictionaryName"] = self.unit_dictionary_name
for suffix in ["A", "B", "C", "K"]:
val = getattr(self, "constant_{0}".format(suffix.lower()))
params["mdsol:Constant{0}".format(suffix)] = str(val)
if self.standard_unit:
params["mdsol:StandardUnit"] = "Yes"
builder.start("MeasurementUnit", params)
for child in self.symbols:
child.build(builder)
builder.end("MeasurementUnit") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(OID=self.oid, Name=self.name)
if self.unit_dictionary_name:
params["mdsol:UnitDictionaryName"] = self.unit_dictionary_name
for suffix in ["A", "B", "C", "K"]:
val = getattr(self, "constant_{0}".format(suffix.lower()))
params["mdsol:Constant{0}".format(suffix)] = str(val)
if self.standard_unit:
params["mdsol:StandardUnit"] = "Yes"
builder.start("MeasurementUnit", params)
for child in self.symbols:
child.build(builder)
builder.end("MeasurementUnit") | [
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mdsol/rwslib | rwslib/builders/metadata.py | Symbol.build | def build(self, builder):
"""Build XML by appending to builder"""
builder.start("Symbol", {})
for child in self.translations:
child.build(builder)
builder.end("Symbol") | python | def build(self, builder):
"""Build XML by appending to builder"""
builder.start("Symbol", {})
for child in self.translations:
child.build(builder)
builder.end("Symbol") | [
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mdsol/rwslib | rwslib/builders/metadata.py | TranslatedText.build | def build(self, builder):
"""Build XML by appending to builder"""
params = {}
if self.lang is not None:
params["xml:lang"] = self.lang
builder.start("TranslatedText", params)
builder.data(self.text)
builder.end("TranslatedText") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = {}
if self.lang is not None:
params["xml:lang"] = self.lang
builder.start("TranslatedText", params)
builder.data(self.text)
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mdsol/rwslib | rwslib/builders/metadata.py | MetaDataVersion.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(OID=self.oid, Name=self.name)
if self.description is not None:
params["Description"] = self.description
if self.signature_prompt is not None:
params["mdsol:SignaturePrompt"] = self.signature_prompt
if self.primary_formoid is not None:
params["mdsol:PrimaryFormOID"] = self.primary_formoid
if self.default_matrix_oid is not None:
params["mdsol:DefaultMatrixOID"] = self.default_matrix_oid
params["mdsol:DeleteExisting"] = bool_to_yes_no(self.delete_existing)
builder.start("MetaDataVersion", params)
if self.protocol:
self.protocol.build(builder)
for event in self.study_event_defs:
event.build(builder)
for formdef in self.form_defs:
formdef.build(builder)
for itemgroupdef in self.item_group_defs:
itemgroupdef.build(builder)
for itemdef in self.item_defs:
itemdef.build(builder)
for codelist in self.codelists:
codelist.build(builder)
# Extensions must always come after core elements
if self.confirmation_message:
self.confirmation_message.build(builder)
for labeldef in self.label_defs:
labeldef.build(builder)
for edit_check in self.edit_checks:
edit_check.build(builder)
for derivation in self.derivations:
derivation.build(builder)
for custom_function in self.custom_functions:
custom_function.build(builder)
builder.end("MetaDataVersion") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(OID=self.oid, Name=self.name)
if self.description is not None:
params["Description"] = self.description
if self.signature_prompt is not None:
params["mdsol:SignaturePrompt"] = self.signature_prompt
if self.primary_formoid is not None:
params["mdsol:PrimaryFormOID"] = self.primary_formoid
if self.default_matrix_oid is not None:
params["mdsol:DefaultMatrixOID"] = self.default_matrix_oid
params["mdsol:DeleteExisting"] = bool_to_yes_no(self.delete_existing)
builder.start("MetaDataVersion", params)
if self.protocol:
self.protocol.build(builder)
for event in self.study_event_defs:
event.build(builder)
for formdef in self.form_defs:
formdef.build(builder)
for itemgroupdef in self.item_group_defs:
itemgroupdef.build(builder)
for itemdef in self.item_defs:
itemdef.build(builder)
for codelist in self.codelists:
codelist.build(builder)
# Extensions must always come after core elements
if self.confirmation_message:
self.confirmation_message.build(builder)
for labeldef in self.label_defs:
labeldef.build(builder)
for edit_check in self.edit_checks:
edit_check.build(builder)
for derivation in self.derivations:
derivation.build(builder)
for custom_function in self.custom_functions:
custom_function.build(builder)
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mdsol/rwslib | rwslib/builders/metadata.py | Protocol.build | def build(self, builder):
"""Build XML by appending to builder"""
builder.start("Protocol", {})
for child in self.study_event_refs:
child.build(builder)
for alias in self.aliases:
alias.build(builder)
builder.end("Protocol") | python | def build(self, builder):
"""Build XML by appending to builder"""
builder.start("Protocol", {})
for child in self.study_event_refs:
child.build(builder)
for alias in self.aliases:
alias.build(builder)
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mdsol/rwslib | rwslib/builders/metadata.py | StudyEventRef.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(StudyEventOID=self.oid, Mandatory=bool_to_yes_no(self.mandatory))
if self._order_number is not None:
params["OrderNumber"] = self._order_number
builder.start("StudyEventRef", params)
builder.end("StudyEventRef") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(StudyEventOID=self.oid, Mandatory=bool_to_yes_no(self.mandatory))
if self._order_number is not None:
params["OrderNumber"] = self._order_number
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mdsol/rwslib | rwslib/builders/metadata.py | StudyEventDef.build | def build(self, builder):
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params = dict(
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params["mdsol:StartWinDays"] = str(self.start_win_days)
if self.target_days is not None:
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if self.overdue_days is not None:
params["mdsol:OverDueDays"] = str(self.overdue_days)
if self.close_days is not None:
params["mdsol:CloseDays"] = str(self.close_days)
builder.start("StudyEventDef", params)
for formref in self.formrefs:
formref.build(builder)
for alias in self.aliases:
alias.build(builder)
builder.end("StudyEventDef") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(
OID=self.oid,
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Type=self.event_type,
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params["mdsol:StartWinDays"] = str(self.start_win_days)
if self.target_days is not None:
params["mdsol:TargetDays"] = str(self.target_days)
if self.end_win_days is not None:
params["mdsol:EndWinDays"] = str(self.end_win_days)
if self.overdue_days is not None:
params["mdsol:OverDueDays"] = str(self.overdue_days)
if self.close_days is not None:
params["mdsol:CloseDays"] = str(self.close_days)
builder.start("StudyEventDef", params)
for formref in self.formrefs:
formref.build(builder)
for alias in self.aliases:
alias.build(builder)
builder.end("StudyEventDef") | [
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mdsol/rwslib | rwslib/builders/metadata.py | FormDef.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(
OID=self.oid, Name=self.name, Repeating=bool_to_yes_no(self.repeating)
)
if self.order_number is not None:
params["mdsol:OrderNumber"] = str(self.order_number)
if self.active is not None:
params["mdsol:Active"] = bool_to_yes_no(self.active)
params["mdsol:Template"] = bool_to_yes_no(self.template)
params["mdsol:SignatureRequired"] = bool_to_yes_no(self.signature_required)
params["mdsol:LogDirection"] = self.log_direction
params["mdsol:DoubleDataEntry"] = self.double_data_entry
params["mdsol:ConfirmationStyle"] = self.confirmation_style
if self.link_study_event_oid:
params["mdsol:LinkStudyEventOID"] = self.link_study_event_oid
if self.link_form_oid:
params["mdsol:LinkFormOID"] = self.link_form_oid
builder.start("FormDef", params)
for itemgroup_ref in self.itemgroup_refs:
itemgroup_ref.build(builder)
for helptext in self.helptexts:
helptext.build(builder)
for view_restriction in self.view_restrictions:
view_restriction.build(builder)
for entry_restriction in self.entry_restrictions:
entry_restriction.build(builder)
for alias in self.aliases:
alias.build(builder)
builder.end("FormDef") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(
OID=self.oid, Name=self.name, Repeating=bool_to_yes_no(self.repeating)
)
if self.order_number is not None:
params["mdsol:OrderNumber"] = str(self.order_number)
if self.active is not None:
params["mdsol:Active"] = bool_to_yes_no(self.active)
params["mdsol:Template"] = bool_to_yes_no(self.template)
params["mdsol:SignatureRequired"] = bool_to_yes_no(self.signature_required)
params["mdsol:LogDirection"] = self.log_direction
params["mdsol:DoubleDataEntry"] = self.double_data_entry
params["mdsol:ConfirmationStyle"] = self.confirmation_style
if self.link_study_event_oid:
params["mdsol:LinkStudyEventOID"] = self.link_study_event_oid
if self.link_form_oid:
params["mdsol:LinkFormOID"] = self.link_form_oid
builder.start("FormDef", params)
for itemgroup_ref in self.itemgroup_refs:
itemgroup_ref.build(builder)
for helptext in self.helptexts:
helptext.build(builder)
for view_restriction in self.view_restrictions:
view_restriction.build(builder)
for entry_restriction in self.entry_restrictions:
entry_restriction.build(builder)
for alias in self.aliases:
alias.build(builder)
builder.end("FormDef") | [
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mdsol/rwslib | rwslib/builders/metadata.py | ItemGroupDef.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(
OID=self.oid,
Name=self.name,
Repeating=bool_to_yes_no(self.repeating),
IsReferenceData=bool_to_yes_no(self.is_reference_data),
)
if self.sas_dataset_name is not None:
params["SASDatasetName"] = self.sas_dataset_name
if self.domain is not None:
params["Domain"] = self.domain
if self.origin is not None:
params["Origin"] = self.origin
if self.role is not None:
params["Role"] = self.role
if self.purpose is not None:
params["Purpose"] = self.purpose
if self.comment is not None:
params["Comment"] = self.comment
builder.start("ItemGroupDef", params)
for itemref in self.item_refs:
itemref.build(builder)
# Extensions always listed AFTER core elements
for labelref in self.label_refs:
labelref.build(builder)
for alias in self.aliases:
alias.build(builder)
builder.end("ItemGroupDef") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(
OID=self.oid,
Name=self.name,
Repeating=bool_to_yes_no(self.repeating),
IsReferenceData=bool_to_yes_no(self.is_reference_data),
)
if self.sas_dataset_name is not None:
params["SASDatasetName"] = self.sas_dataset_name
if self.domain is not None:
params["Domain"] = self.domain
if self.origin is not None:
params["Origin"] = self.origin
if self.role is not None:
params["Role"] = self.role
if self.purpose is not None:
params["Purpose"] = self.purpose
if self.comment is not None:
params["Comment"] = self.comment
builder.start("ItemGroupDef", params)
for itemref in self.item_refs:
itemref.build(builder)
# Extensions always listed AFTER core elements
for labelref in self.label_refs:
labelref.build(builder)
for alias in self.aliases:
alias.build(builder)
builder.end("ItemGroupDef") | [
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mdsol/rwslib | rwslib/builders/metadata.py | ItemRef.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(ItemOID=self.oid, Mandatory=bool_to_yes_no(self.mandatory))
if self.order_number is not None:
params["OrderNumber"] = str(self.order_number)
if self.key_sequence is not None:
params["KeySequence"] = str(self.key_sequence)
if self.imputation_method_oid is not None:
params["ImputationMethodOID"] = self.imputation_method_oid
if self.role is not None:
params["Role"] = self.role
if self.role_codelist_oid is not None:
params["RoleCodeListOID"] = self.role_codelist_oid
builder.start("ItemRef", params)
for attribute in self.attributes:
attribute.build(builder)
builder.end("ItemRef") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(ItemOID=self.oid, Mandatory=bool_to_yes_no(self.mandatory))
if self.order_number is not None:
params["OrderNumber"] = str(self.order_number)
if self.key_sequence is not None:
params["KeySequence"] = str(self.key_sequence)
if self.imputation_method_oid is not None:
params["ImputationMethodOID"] = self.imputation_method_oid
if self.role is not None:
params["Role"] = self.role
if self.role_codelist_oid is not None:
params["RoleCodeListOID"] = self.role_codelist_oid
builder.start("ItemRef", params)
for attribute in self.attributes:
attribute.build(builder)
builder.end("ItemRef") | [
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mdsol/rwslib | rwslib/builders/metadata.py | ItemDef.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(
OID=self.oid,
Name=self.name,
DataType=self.datatype.value,
Length=str(self.length),
)
if self.date_time_format is not None:
params["mdsol:DateTimeFormat"] = self.date_time_format
params["mdsol:Active"] = bool_to_yes_no(self.active)
if self.significant_digits is not None:
params["SignificantDigits"] = str(self.significant_digits)
if self.sas_field_name is not None:
params["SASFieldName"] = self.sas_field_name
if self.sds_var_name is not None:
params["SDSVarName"] = self.sds_var_name
if self.origin is not None:
params["Origin"] = self.origin
if self.comment is not None:
params["Comment"] = self.comment
if self.control_type is not None:
params["mdsol:ControlType"] = self.control_type.value
if self.acceptable_file_extensions is not None:
params["mdsol:AcceptableFileExtensions"] = self.acceptable_file_extensions
if self.default_value is not None:
params["mdsol:DefaultValue"] = str(self.default_value)
params["mdsol:SourceDocument"] = bool_to_yes_no(self.source_document_verify)
params["mdsol:IndentLevel"] = str(self.indent_level)
if self.sas_format is not None:
params["mdsol:SASFormat"] = self.sas_format
if self.sas_label is not None:
params["mdsol:SASLabel"] = self.sas_label
params["mdsol:QueryFutureDate"] = bool_to_yes_no(self.query_future_date)
params["mdsol:Visible"] = bool_to_yes_no(self.visible)
params["mdsol:TranslationRequired"] = bool_to_yes_no(self.translation_required)
params["mdsol:QueryNonConformance"] = bool_to_yes_no(self.query_non_conformance)
params["mdsol:OtherVisits"] = bool_to_yes_no(self.other_visits)
params["mdsol:CanSetItemGroupDate"] = bool_to_yes_no(
self.can_set_item_group_date
)
params["mdsol:CanSetFormDate"] = bool_to_yes_no(self.can_set_form_date)
params["mdsol:CanSetStudyEventDate"] = bool_to_yes_no(
self.can_set_study_event_date
)
params["mdsol:CanSetSubjectDate"] = bool_to_yes_no(self.can_set_subject_date)
params["mdsol:VisualVerify"] = bool_to_yes_no(self.visual_verify)
params["mdsol:DoesNotBreakSignature"] = bool_to_yes_no(
self.does_not_break_signature
)
if self.field_number is not None:
params["mdsol:FieldNumber"] = self.field_number
if self.variable_oid is not None:
params["mdsol:VariableOID"] = self.variable_oid
builder.start("ItemDef", params)
if self.question is not None:
self.question.build(builder)
if self.codelistref is not None:
self.codelistref.build(builder)
for mur in self.measurement_unit_refs:
mur.build(builder)
for range_check in self.range_checks:
range_check.build(builder)
if self.header_text is not None:
self.header_text.build(builder)
for view_restriction in self.view_restrictions:
view_restriction.build(builder)
for entry_restriction in self.entry_restrictions:
entry_restriction.build(builder)
for help_text in self.help_texts:
help_text.build(builder)
for review_group in self.review_groups:
review_group.build(builder)
for alias in self.aliases:
alias.build(builder)
builder.end("ItemDef") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(
OID=self.oid,
Name=self.name,
DataType=self.datatype.value,
Length=str(self.length),
)
if self.date_time_format is not None:
params["mdsol:DateTimeFormat"] = self.date_time_format
params["mdsol:Active"] = bool_to_yes_no(self.active)
if self.significant_digits is not None:
params["SignificantDigits"] = str(self.significant_digits)
if self.sas_field_name is not None:
params["SASFieldName"] = self.sas_field_name
if self.sds_var_name is not None:
params["SDSVarName"] = self.sds_var_name
if self.origin is not None:
params["Origin"] = self.origin
if self.comment is not None:
params["Comment"] = self.comment
if self.control_type is not None:
params["mdsol:ControlType"] = self.control_type.value
if self.acceptable_file_extensions is not None:
params["mdsol:AcceptableFileExtensions"] = self.acceptable_file_extensions
if self.default_value is not None:
params["mdsol:DefaultValue"] = str(self.default_value)
params["mdsol:SourceDocument"] = bool_to_yes_no(self.source_document_verify)
params["mdsol:IndentLevel"] = str(self.indent_level)
if self.sas_format is not None:
params["mdsol:SASFormat"] = self.sas_format
if self.sas_label is not None:
params["mdsol:SASLabel"] = self.sas_label
params["mdsol:QueryFutureDate"] = bool_to_yes_no(self.query_future_date)
params["mdsol:Visible"] = bool_to_yes_no(self.visible)
params["mdsol:TranslationRequired"] = bool_to_yes_no(self.translation_required)
params["mdsol:QueryNonConformance"] = bool_to_yes_no(self.query_non_conformance)
params["mdsol:OtherVisits"] = bool_to_yes_no(self.other_visits)
params["mdsol:CanSetItemGroupDate"] = bool_to_yes_no(
self.can_set_item_group_date
)
params["mdsol:CanSetFormDate"] = bool_to_yes_no(self.can_set_form_date)
params["mdsol:CanSetStudyEventDate"] = bool_to_yes_no(
self.can_set_study_event_date
)
params["mdsol:CanSetSubjectDate"] = bool_to_yes_no(self.can_set_subject_date)
params["mdsol:VisualVerify"] = bool_to_yes_no(self.visual_verify)
params["mdsol:DoesNotBreakSignature"] = bool_to_yes_no(
self.does_not_break_signature
)
if self.field_number is not None:
params["mdsol:FieldNumber"] = self.field_number
if self.variable_oid is not None:
params["mdsol:VariableOID"] = self.variable_oid
builder.start("ItemDef", params)
if self.question is not None:
self.question.build(builder)
if self.codelistref is not None:
self.codelistref.build(builder)
for mur in self.measurement_unit_refs:
mur.build(builder)
for range_check in self.range_checks:
range_check.build(builder)
if self.header_text is not None:
self.header_text.build(builder)
for view_restriction in self.view_restrictions:
view_restriction.build(builder)
for entry_restriction in self.entry_restrictions:
entry_restriction.build(builder)
for help_text in self.help_texts:
help_text.build(builder)
for review_group in self.review_groups:
review_group.build(builder)
for alias in self.aliases:
alias.build(builder)
builder.end("ItemDef") | [
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params = dict(OID=self.oid, Name=self.name, DataType=self.datatype.value)
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mdsol/rwslib | rwslib/builders/metadata.py | CodeListItem.build | def build(self, builder):
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params["mdsol:OrderNumber"] = str(self.order_number)
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"""Build XML by appending to builder"""
params = dict(
Namespace=self.namespace,
Name=self.name,
Value=self.value,
TransactionType=self.transaction_type,
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builder.start("mdsol:Attribute", params)
builder.end("mdsol:Attribute") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(
Namespace=self.namespace,
Name=self.name,
Value=self.value,
TransactionType=self.transaction_type,
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params["AllVariablesInFolders"] = bool_to_true_false(
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if self.all_variables_in_fields is not None:
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if self.logical_record_position is not None:
params["LogicalRecordPosition"] = self.logical_record_position.value
builder.start("mdsol:DerivationDef", params)
for step in self.derivation_steps:
step.build(builder)
builder.end("mdsol:DerivationDef") | python | def build(self, builder):
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params = dict(
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params["VariableOID"] = self.variable_oid
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params["FieldOID"] = self.field_oid
if self.form_oid is not None:
params["FormOID"] = self.form_oid
if self.folder_oid is not None:
params["FolderOID"] = self.folder_oid
if self.record_position is not None:
params["RecordPosition"] = str(self.record_position)
if self.form_repeat_number is not None:
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if self.folder_repeat_number is not None:
params["FolderRepeatNumber"] = str(self.folder_repeat_number)
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if self.data_format is not None:
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builder.end("mdsol:CheckStep") | python | def build(self, builder):
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params = dict()
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raise AttributeError("Invalid check action %s" % value)
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"""Build XML by appending to builder"""
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mdsol/rwslib | rwslib/builders/metadata.py | MdsolLabelDef.build | def build(self, builder):
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mdsol/rwslib | rwslib/builders/metadata.py | MdsolReviewGroup.build | def build(self, builder):
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mdsol/rwslib | rwslib/builders/clinicaldata.py | ClinicalData.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(MetaDataVersionOID=str(self.metadata_version_oid),
StudyOID="%s (%s)" % (self.projectname, self.environment,),
)
# mixins
self.mixin_params(params)
builder.start("ClinicalData", params)
# Ask children
if self.subject_data:
for subject in self.subject_data:
subject.build(builder)
# Add the Annotations
if self.annotations is not None:
self.annotations.build(builder)
builder.end("ClinicalData") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(MetaDataVersionOID=str(self.metadata_version_oid),
StudyOID="%s (%s)" % (self.projectname, self.environment,),
)
# mixins
self.mixin_params(params)
builder.start("ClinicalData", params)
# Ask children
if self.subject_data:
for subject in self.subject_data:
subject.build(builder)
# Add the Annotations
if self.annotations is not None:
self.annotations.build(builder)
builder.end("ClinicalData") | [
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mdsol/rwslib | rwslib/builders/clinicaldata.py | SubjectData.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(SubjectKey=self.subject_key)
params['mdsol:SubjectKeyType'] = self.subject_key_type
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
# mixins
self.mixin()
self.mixin_params(params)
builder.start("SubjectData", params)
# Ask children
if self.audit_record is not None:
self.audit_record.build(builder)
if self.siteref:
self.siteref.build(builder)
else:
builder.start("SiteRef", {'LocationOID': self.sitelocationoid})
builder.end("SiteRef")
for event in self.study_events:
event.build(builder)
if self.signature is not None:
self.signature.build(builder)
for annotation in self.annotations:
annotation.build(builder)
builder.end("SubjectData") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(SubjectKey=self.subject_key)
params['mdsol:SubjectKeyType'] = self.subject_key_type
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
# mixins
self.mixin()
self.mixin_params(params)
builder.start("SubjectData", params)
# Ask children
if self.audit_record is not None:
self.audit_record.build(builder)
if self.siteref:
self.siteref.build(builder)
else:
builder.start("SiteRef", {'LocationOID': self.sitelocationoid})
builder.end("SiteRef")
for event in self.study_events:
event.build(builder)
if self.signature is not None:
self.signature.build(builder)
for annotation in self.annotations:
annotation.build(builder)
builder.end("SubjectData") | [
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mdsol/rwslib | rwslib/builders/clinicaldata.py | StudyEventData.build | def build(self, builder):
"""Build XML by appending to builder
:Example:
<StudyEventData StudyEventOID="SCREENING" StudyEventRepeatKey="1" TransactionType="Update">
"""
params = dict(StudyEventOID=self.study_event_oid)
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
if self.study_event_repeat_key is not None:
params["StudyEventRepeatKey"] = str(self.study_event_repeat_key)
# mixins
self.mixin()
self.mixin_params(params)
builder.start("StudyEventData", params)
# Ask children
for form in self.forms:
form.build(builder)
if self.signature is not None:
self.signature.build(builder)
for annotation in self.annotations:
annotation.build(builder)
builder.end("StudyEventData") | python | def build(self, builder):
"""Build XML by appending to builder
:Example:
<StudyEventData StudyEventOID="SCREENING" StudyEventRepeatKey="1" TransactionType="Update">
"""
params = dict(StudyEventOID=self.study_event_oid)
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
if self.study_event_repeat_key is not None:
params["StudyEventRepeatKey"] = str(self.study_event_repeat_key)
# mixins
self.mixin()
self.mixin_params(params)
builder.start("StudyEventData", params)
# Ask children
for form in self.forms:
form.build(builder)
if self.signature is not None:
self.signature.build(builder)
for annotation in self.annotations:
annotation.build(builder)
builder.end("StudyEventData") | [
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mdsol/rwslib | rwslib/builders/clinicaldata.py | FormData.build | def build(self, builder):
"""Build XML by appending to builder
:Example:
<FormData FormOID="MH" TransactionType="Update">
"""
params = dict(FormOID=self.formoid)
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
if self.form_repeat_key is not None:
params["FormRepeatKey"] = str(self.form_repeat_key)
# mixins
self.mixin()
self.mixin_params(params)
builder.start("FormData", params)
# Ask children
for itemgroup in self.itemgroups:
itemgroup.build(builder, self.formoid)
if self.signature is not None:
self.signature.build(builder)
for annotation in self.annotations:
annotation.build(builder)
builder.end("FormData") | python | def build(self, builder):
"""Build XML by appending to builder
:Example:
<FormData FormOID="MH" TransactionType="Update">
"""
params = dict(FormOID=self.formoid)
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
if self.form_repeat_key is not None:
params["FormRepeatKey"] = str(self.form_repeat_key)
# mixins
self.mixin()
self.mixin_params(params)
builder.start("FormData", params)
# Ask children
for itemgroup in self.itemgroups:
itemgroup.build(builder, self.formoid)
if self.signature is not None:
self.signature.build(builder)
for annotation in self.annotations:
annotation.build(builder)
builder.end("FormData") | [
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mdsol/rwslib | rwslib/builders/clinicaldata.py | ItemGroupData.build | def build(self, builder, formname=None):
"""Build XML by appending to builder"""
params = dict(ItemGroupOID=formname if formname else self.itemgroupoid)
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
if self.item_group_repeat_key is not None:
params["ItemGroupRepeatKey"] = str(
self.item_group_repeat_key) # may be @context for transaction type upsert or context
params["mdsol:Submission"] = "WholeItemGroup" if self.whole_item_group else "SpecifiedItemsOnly"
# mixins
self.mixin()
self.mixin_params(params)
builder.start("ItemGroupData", params)
# Ask children
for item in self.items.values():
item.build(builder)
# Add annotations
for annotation in self.annotations:
annotation.build(builder)
# Add the signature if it exists
if self.signature is not None:
self.signature.build(builder)
builder.end("ItemGroupData") | python | def build(self, builder, formname=None):
"""Build XML by appending to builder"""
params = dict(ItemGroupOID=formname if formname else self.itemgroupoid)
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
if self.item_group_repeat_key is not None:
params["ItemGroupRepeatKey"] = str(
self.item_group_repeat_key) # may be @context for transaction type upsert or context
params["mdsol:Submission"] = "WholeItemGroup" if self.whole_item_group else "SpecifiedItemsOnly"
# mixins
self.mixin()
self.mixin_params(params)
builder.start("ItemGroupData", params)
# Ask children
for item in self.items.values():
item.build(builder)
# Add annotations
for annotation in self.annotations:
annotation.build(builder)
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if self.signature is not None:
self.signature.build(builder)
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mdsol/rwslib | rwslib/builders/clinicaldata.py | ItemData.build | def build(self, builder):
"""
Build XML by appending to builder
"""
params = dict(ItemOID=self.itemoid)
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
if self.value in [None, '']:
params['IsNull'] = 'Yes'
else:
params['Value'] = str(self.value)
if self.specify_value is not None:
params['mdsol:SpecifyValue'] = self.specify_value
if self.lock is not None:
params['mdsol:Lock'] = bool_to_yes_no(self.lock)
if self.freeze is not None:
params['mdsol:Freeze'] = bool_to_yes_no(self.freeze)
if self.verify is not None:
params['mdsol:Verify'] = bool_to_yes_no(self.verify)
# mixins
self.mixin()
self.mixin_params(params)
builder.start("ItemData", params)
if self.audit_record is not None:
self.audit_record.build(builder)
# Measurement unit ref must be after audit record or RWS complains
if self.measurement_unit_ref is not None:
self.measurement_unit_ref.build(builder)
for query in self.queries: # type: MdsolQuery
query.build(builder)
for deviation in self.deviations: # type: MdsolProtocolDeviation
deviation.build(builder)
for annotation in self.annotations: # type: Annotation
annotation.build(builder)
builder.end("ItemData") | python | def build(self, builder):
"""
Build XML by appending to builder
"""
params = dict(ItemOID=self.itemoid)
if self.transaction_type is not None:
params["TransactionType"] = self.transaction_type
if self.value in [None, '']:
params['IsNull'] = 'Yes'
else:
params['Value'] = str(self.value)
if self.specify_value is not None:
params['mdsol:SpecifyValue'] = self.specify_value
if self.lock is not None:
params['mdsol:Lock'] = bool_to_yes_no(self.lock)
if self.freeze is not None:
params['mdsol:Freeze'] = bool_to_yes_no(self.freeze)
if self.verify is not None:
params['mdsol:Verify'] = bool_to_yes_no(self.verify)
# mixins
self.mixin()
self.mixin_params(params)
builder.start("ItemData", params)
if self.audit_record is not None:
self.audit_record.build(builder)
# Measurement unit ref must be after audit record or RWS complains
if self.measurement_unit_ref is not None:
self.measurement_unit_ref.build(builder)
for query in self.queries: # type: MdsolQuery
query.build(builder)
for deviation in self.deviations: # type: MdsolProtocolDeviation
deviation.build(builder)
for annotation in self.annotations: # type: Annotation
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mdsol/rwslib | rwslib/builders/clinicaldata.py | Signature.build | def build(self, builder):
"""
Build XML by appending to builder
"""
params = {}
if self.signature_id is not None:
# If a Signature element is contained within a Signatures element, the ID attribute is required.
params['ID'] = self.signature_id
builder.start("Signature", params)
if self.user_ref is None:
raise ValueError("User Reference not set.")
self.user_ref.build(builder)
if self.location_ref is None:
raise ValueError("Location Reference not set.")
self.location_ref.build(builder)
if self.signature_ref is None:
raise ValueError("Signature Reference not set.")
self.signature_ref.build(builder)
if self.date_time_stamp is None:
raise ValueError("DateTime not set.")
self.date_time_stamp.build(builder)
builder.end("Signature") | python | def build(self, builder):
"""
Build XML by appending to builder
"""
params = {}
if self.signature_id is not None:
# If a Signature element is contained within a Signatures element, the ID attribute is required.
params['ID'] = self.signature_id
builder.start("Signature", params)
if self.user_ref is None:
raise ValueError("User Reference not set.")
self.user_ref.build(builder)
if self.location_ref is None:
raise ValueError("Location Reference not set.")
self.location_ref.build(builder)
if self.signature_ref is None:
raise ValueError("Signature Reference not set.")
self.signature_ref.build(builder)
if self.date_time_stamp is None:
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self.date_time_stamp.build(builder)
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mdsol/rwslib | rwslib/builders/clinicaldata.py | Annotation.annotation_id | def annotation_id(self, value):
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mdsol/rwslib | rwslib/builders/clinicaldata.py | Annotation.seqnum | def seqnum(self, value):
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"""
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"""
Set SeqNum for Annotation
:param value: SeqNum value
:type value: int
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Build XML by appending to builder
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raise ValueError("SeqNum is not set.") # pragma: no cover
params["SeqNum"] = str(self.seqnum)
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params["ID"] = self.annotation_id
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"""
Build XML by appending to builder
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mdsol/rwslib | rwslib/builders/clinicaldata.py | Comment.text | def text(self, value):
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mdsol/rwslib | rwslib/builders/clinicaldata.py | Comment.sponsor_or_site | def sponsor_or_site(self, value):
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mdsol/rwslib | rwslib/builders/clinicaldata.py | SiteRef.build | def build(self, builder):
"""
Build XML by appending to builder
"""
params = dict(LocationOID=self.oid)
# mixins
self.mixin()
self.mixin_params(params)
builder.start("SiteRef", params)
builder.end("SiteRef") | python | def build(self, builder):
"""
Build XML by appending to builder
"""
params = dict(LocationOID=self.oid)
# mixins
self.mixin()
self.mixin_params(params)
builder.start("SiteRef", params)
builder.end("SiteRef") | [
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"""
Build XML by appending to builder
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"""
Build XML by appending to builder
"""
builder.start("SignatureRef", dict(SignatureOID=self.oid))
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mdsol/rwslib | rwslib/builders/clinicaldata.py | ReasonForChange.build | def build(self, builder):
"""
Build XML by appending to builder
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builder.end("ReasonForChange") | python | def build(self, builder):
"""
Build XML by appending to builder
"""
builder.start("ReasonForChange", {})
builder.data(self.reason)
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"""
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builder.end("DateTimeStamp") | python | def build(self, builder):
"""
Build XML by appending to builder
"""
builder.start("DateTimeStamp", {})
if isinstance(self.date_time, datetime):
builder.data(dt_to_iso8601(self.date_time))
else:
builder.data(self.date_time)
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"""
Build XML by appending to builder
"""
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builder.end("SourceID") | python | def build(self, builder):
"""
Build XML by appending to builder
"""
builder.start("SourceID", {})
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mdsol/rwslib | rwslib/builders/clinicaldata.py | AuditRecord.build | def build(self, builder):
"""Build XML by appending to builder"""
params = {}
if self.edit_point is not None:
params["EditPoint"] = self.edit_point
if self.used_imputation_method is not None:
params['UsedImputationMethod'] = bool_to_yes_no(self.used_imputation_method)
if self.audit_id is not None:
params['ID'] = str(self.audit_id)
if self.include_file_oid is not None:
params['mdsol:IncludeFileOID'] = bool_to_yes_no(self.include_file_oid)
builder.start("AuditRecord", params)
if self.user_ref is None:
raise ValueError("User Reference not set.")
self.user_ref.build(builder)
if self.location_ref is None:
raise ValueError("Location Reference not set.")
self.location_ref.build(builder)
if self.date_time_stamp is None:
raise ValueError("DateTime not set.")
self.date_time_stamp.build(builder)
# Optional
if self.source_id:
self.source_id.build(builder)
# Optional
if self.reason_for_change is not None:
self.reason_for_change.build(builder)
builder.end("AuditRecord") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = {}
if self.edit_point is not None:
params["EditPoint"] = self.edit_point
if self.used_imputation_method is not None:
params['UsedImputationMethod'] = bool_to_yes_no(self.used_imputation_method)
if self.audit_id is not None:
params['ID'] = str(self.audit_id)
if self.include_file_oid is not None:
params['mdsol:IncludeFileOID'] = bool_to_yes_no(self.include_file_oid)
builder.start("AuditRecord", params)
if self.user_ref is None:
raise ValueError("User Reference not set.")
self.user_ref.build(builder)
if self.location_ref is None:
raise ValueError("Location Reference not set.")
self.location_ref.build(builder)
if self.date_time_stamp is None:
raise ValueError("DateTime not set.")
self.date_time_stamp.build(builder)
# Optional
if self.source_id:
self.source_id.build(builder)
# Optional
if self.reason_for_change is not None:
self.reason_for_change.build(builder)
builder.end("AuditRecord") | [
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mdsol/rwslib | rwslib/builders/clinicaldata.py | MdsolProtocolDeviation.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(Value=self.value,
Status=self.status.value,
ProtocolDeviationRepeatKey=self.repeat_key
)
if self.code:
params['Code'] = self.code
if self.pdclass:
params['Class'] = self.pdclass
if self.transaction_type:
params['TransactionType'] = self.transaction_type
builder.start('mdsol:ProtocolDeviation', params)
builder.end('mdsol:ProtocolDeviation') | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(Value=self.value,
Status=self.status.value,
ProtocolDeviationRepeatKey=self.repeat_key
)
if self.code:
params['Code'] = self.code
if self.pdclass:
params['Class'] = self.pdclass
if self.transaction_type:
params['TransactionType'] = self.transaction_type
builder.start('mdsol:ProtocolDeviation', params)
builder.end('mdsol:ProtocolDeviation') | [
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mdsol/rwslib | rwslib/builders/clinicaldata.py | MdsolQuery.status | def status(self, value):
"""Set Query Status"""
if value is not None:
if not isinstance(value, QueryStatusType):
raise AttributeError("%s action type is invalid in mdsol:Query." % (value,))
self._status = value | python | def status(self, value):
"""Set Query Status"""
if value is not None:
if not isinstance(value, QueryStatusType):
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mdsol/rwslib | rwslib/builders/clinicaldata.py | MdsolQuery.build | def build(self, builder):
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Build XML by appending to builder
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if self.response is not None:
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"""
Build XML by appending to builder
"""
params = {}
if self.value is not None:
params['Value'] = str(self.value)
if self.query_repeat_key is not None:
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if self.recipient is not None:
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params['RequiresResponse'] = bool_to_yes_no(self.requires_response)
# When closing a query
if self.response is not None:
params['Response'] = str(self.response)
builder.start("mdsol:Query", params)
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mdsol/rwslib | rwslib/builders/core.py | ODM.getroot | def getroot(self):
"""Build XML object, return the root"""
builder = ET.TreeBuilder()
self.build(builder)
return builder.close() | python | def getroot(self):
"""Build XML object, return the root"""
builder = ET.TreeBuilder()
self.build(builder)
return builder.close() | [
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mdsol/rwslib | rwslib/builders/core.py | ODM.build | def build(self, builder):
"""Build XML object, return the root, this is a copy for consistency and testing"""
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params['SourceSystem'] = self.source_system
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params['SourceSystemVersion'] = self.source_system_version
params['xmlns:mdsol'] = "http://www.mdsol.com/ns/odm/metadata"
if self.description:
params['Description'] = self.description
builder.start("ODM", params)
# Ask the children
if self.study is not None:
self.study.build(builder)
if self.clinical_data:
for clinical_data in self.clinical_data:
clinical_data.build(builder)
if self.admindata is not None:
self.admindata.build(builder)
builder.end("ODM")
return builder.close() | python | def build(self, builder):
"""Build XML object, return the root, this is a copy for consistency and testing"""
params = dict(ODMVersion="1.3",
FileType=self.filetype,
CreationDateTime=self.creationdatetime,
Originator=self.originator,
FileOID=self.fileoid,
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params['Granularity'] = self.granularity_type.value
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params['SourceSystem'] = self.source_system
if self.source_system_version:
params['SourceSystemVersion'] = self.source_system_version
params['xmlns:mdsol'] = "http://www.mdsol.com/ns/odm/metadata"
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params['Description'] = self.description
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clinical_data.build(builder)
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mdsol/rwslib | rwslib/rws_requests/odm_adapter.py | UsersRequest._querystring | def _querystring(self):
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kw = {"studyoid": self.studyoid}
if self.location_oid is not None:
kw["locationoid"] = self.location_oid
return kw | python | def _querystring(self):
"""Additional keyword arguments"""
kw = {"studyoid": self.studyoid}
if self.location_oid is not None:
kw["locationoid"] = self.location_oid
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mdsol/rwslib | rwslib/builders/modm.py | MODMAttribute.value | def value(self):
"""
Normalise the Attribute value and return
.. note: `datetime` objects are normalised to ISO datestring, `bool` objects are normalised to Yes or No
:rtype: str
:return: The normalised value
"""
if isinstance(self.raw_value, (datetime.datetime, datetime.date)):
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return 'Yes' if self.raw_value else 'No'
return self.raw_value | python | def value(self):
"""
Normalise the Attribute value and return
.. note: `datetime` objects are normalised to ISO datestring, `bool` objects are normalised to Yes or No
:rtype: str
:return: The normalised value
"""
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mdsol/rwslib | rwslib/builders/modm.py | MODMMixin.add_attribute | def add_attribute(self, attribute, value):
"""
Add an attribute to the current instance
:param str attribute: Attribute name
:type value: Union[datetime,bool,str]
:param value: Attribute value
"""
class_name = self.__class__.__name__
if class_name.startswith('ItemData'):
# ItemData* Elements
class_name = 'ItemData'
if attribute not in MODMExtensionRegistry[class_name].value:
raise ValueError("Can't add {} to {}".format(attribute, self.__class__.__name__))
self.attributes.append(MODMAttribute(attribute, value)) | python | def add_attribute(self, attribute, value):
"""
Add an attribute to the current instance
:param str attribute: Attribute name
:type value: Union[datetime,bool,str]
:param value: Attribute value
"""
class_name = self.__class__.__name__
if class_name.startswith('ItemData'):
# ItemData* Elements
class_name = 'ItemData'
if attribute not in MODMExtensionRegistry[class_name].value:
raise ValueError("Can't add {} to {}".format(attribute, self.__class__.__name__))
self.attributes.append(MODMAttribute(attribute, value)) | [
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mdsol/rwslib | rwslib/builders/modm.py | MODMMixin.mixin_params | def mixin_params(self, params):
"""
Merge in the MdsolAttribute for the passed parameter
:param dict params: dictionary of object parameters
"""
if not isinstance(params, (dict,)):
raise AttributeError("Cannot mixin to object of type {}".format(type(params)))
for attribute in self.attributes:
params.update({attribute.tag: attribute.value}) | python | def mixin_params(self, params):
"""
Merge in the MdsolAttribute for the passed parameter
:param dict params: dictionary of object parameters
"""
if not isinstance(params, (dict,)):
raise AttributeError("Cannot mixin to object of type {}".format(type(params)))
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params.update({attribute.tag: attribute.value}) | [
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mdsol/rwslib | rwslib/builders/modm.py | LastUpdateMixin.last_update_time | def last_update_time(self, value):
"""
Setter for the last_update_time attribute
:param datetime.datetime value: value to set for the element
"""
if isinstance(value, (datetime.datetime,)):
self._last_update_time = value
else:
raise ValueError("Expect last_update_time to be a datetime") | python | def last_update_time(self, value):
"""
Setter for the last_update_time attribute
:param datetime.datetime value: value to set for the element
"""
if isinstance(value, (datetime.datetime,)):
self._last_update_time = value
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mdsol/rwslib | rwslib/builders/modm.py | LastUpdateMixin.set_update_time | def set_update_time(self, update_time=None):
"""
Set the Update Time from the local clock (in UTC)
"""
if update_time and isinstance(update_time, (datetime.datetime,)):
self.last_update_time = update_time
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"""
Set the Update Time from the local clock (in UTC)
"""
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self.last_update_time = datetime.datetime.utcnow() | [
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mdsol/rwslib | rwslib/builders/modm.py | LastUpdateMixin.mixin_params | def mixin_params(self, params):
"""
Add the mdsol:LastUpdateTime attribute
:return:
"""
super(LastUpdateMixin, self).mixin_params(params)
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"""
Add the mdsol:LastUpdateTime attribute
:return:
"""
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mdsol/rwslib | rwslib/builders/modm.py | MilestoneMixin.add_milestone | def add_milestone(self,
milestone,
codelistoid="MILESTONES"):
"""
Add a milestone
:param codelistoid: specify the CodeListOID (defaults to MILESTONES)
:param str milestone: Milestone to add
"""
if milestone not in self.milestones.get(codelistoid, []):
self._milestones.setdefault(codelistoid, []).append(milestone) | python | def add_milestone(self,
milestone,
codelistoid="MILESTONES"):
"""
Add a milestone
:param codelistoid: specify the CodeListOID (defaults to MILESTONES)
:param str milestone: Milestone to add
"""
if milestone not in self.milestones.get(codelistoid, []):
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mdsol/rwslib | rwslib/builders/modm.py | MilestoneMixin.mixin | def mixin(self):
"""
Add the annotations to the ODM Element (if defined)
:return:
"""
if self.milestones:
from rwslib.builders.clinicaldata import Annotation, Flag, FlagValue
annotation = Annotation()
for codelist, milestones in self.milestones.items():
for milestone in milestones:
annotation << Flag() << FlagValue(milestone, codelist_oid=codelist)
self.annotations.append(annotation) | python | def mixin(self):
"""
Add the annotations to the ODM Element (if defined)
:return:
"""
if self.milestones:
from rwslib.builders.clinicaldata import Annotation, Flag, FlagValue
annotation = Annotation()
for codelist, milestones in self.milestones.items():
for milestone in milestones:
annotation << Flag() << FlagValue(milestone, codelist_oid=codelist)
self.annotations.append(annotation) | [
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mdsol/rwslib | rwslib/rwsobjects.py | getEnvironmentFromNameAndProtocol | def getEnvironmentFromNameAndProtocol(studyname, protocolname):
"""
Extract environment name using studyname and protocolname to guide
:param str studyname: Name of the study (including Env)
:param str protocolname: Name of the study
"""
# StudyName = "TEST (1) (DEV)"
# ProtocolName = "TEST (1)"
# Raw Env = "(DEV)"
raw_env = studyname[len(protocolname) :].strip()
if "(" in raw_env:
l_brace_pos = raw_env.rfind("(")
r_brace_pos = raw_env.rfind(")")
return raw_env[l_brace_pos + 1 : r_brace_pos]
else:
return raw_env | python | def getEnvironmentFromNameAndProtocol(studyname, protocolname):
"""
Extract environment name using studyname and protocolname to guide
:param str studyname: Name of the study (including Env)
:param str protocolname: Name of the study
"""
# StudyName = "TEST (1) (DEV)"
# ProtocolName = "TEST (1)"
# Raw Env = "(DEV)"
raw_env = studyname[len(protocolname) :].strip()
if "(" in raw_env:
l_brace_pos = raw_env.rfind("(")
r_brace_pos = raw_env.rfind(")")
return raw_env[l_brace_pos + 1 : r_brace_pos]
else:
return raw_env | [
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mdsol/rwslib | rwslib/rwsobjects.py | parseXMLString | def parseXMLString(xml):
"""
Parse XML string, return root
:param str: Passed in XML
"""
# Remove BOM if it exists (different requests seem to have different BOMs)
unichr_captured = ""
if not xml.strip():
return u""
while xml[0] != u"<":
unichr_captured += xml[0]
xml = xml[1:]
parser = etree.XMLParser(ns_clean=True, collect_ids=False, huge_tree=True)
try:
return etree.fromstring(xml.encode("utf-8"), parser=parser)
except etree.XMLSyntaxError:
raise Exception(xml) | python | def parseXMLString(xml):
"""
Parse XML string, return root
:param str: Passed in XML
"""
# Remove BOM if it exists (different requests seem to have different BOMs)
unichr_captured = ""
if not xml.strip():
return u""
while xml[0] != u"<":
unichr_captured += xml[0]
xml = xml[1:]
parser = etree.XMLParser(ns_clean=True, collect_ids=False, huge_tree=True)
try:
return etree.fromstring(xml.encode("utf-8"), parser=parser)
except etree.XMLSyntaxError:
raise Exception(xml) | [
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mdsol/rwslib | rwslib/rwsobjects.py | RWSStudyListItem.fromElement | def fromElement(cls, elem):
"""
Read properties from an XML Element to build a StudyList Item
:param lxml.etree.Element elem: The source Study XML Element
.. code-block:: xml
<Study OID="Fixitol(Dev)" mdsol:ProjectType="GlobalLibraryVolume">
<GlobalVariables>
<StudyName>Fixitol (Dev)</StudyName>
<StudyDescription/>
<ProtocolName>Fixitol</ProtocolName>
</GlobalVariables>
</Study>
"""
e_global_variables = elem.find(ODM_NS + "GlobalVariables")
studyname = e_global_variables.find(ODM_NS + "StudyName").text
protocolname = e_global_variables.find(ODM_NS + "ProtocolName").text
self = cls(
oid=elem.get("OID"),
projecttype=elem.get(MEDI_NS + "ProjectType", "Project"),
studyname=studyname,
protocolname=protocolname,
environment=getEnvironmentFromNameAndProtocol(studyname, protocolname),
)
return self | python | def fromElement(cls, elem):
"""
Read properties from an XML Element to build a StudyList Item
:param lxml.etree.Element elem: The source Study XML Element
.. code-block:: xml
<Study OID="Fixitol(Dev)" mdsol:ProjectType="GlobalLibraryVolume">
<GlobalVariables>
<StudyName>Fixitol (Dev)</StudyName>
<StudyDescription/>
<ProtocolName>Fixitol</ProtocolName>
</GlobalVariables>
</Study>
"""
e_global_variables = elem.find(ODM_NS + "GlobalVariables")
studyname = e_global_variables.find(ODM_NS + "StudyName").text
protocolname = e_global_variables.find(ODM_NS + "ProtocolName").text
self = cls(
oid=elem.get("OID"),
projecttype=elem.get(MEDI_NS + "ProjectType", "Project"),
studyname=studyname,
protocolname=protocolname,
environment=getEnvironmentFromNameAndProtocol(studyname, protocolname),
)
return self | [
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mdsol/rwslib | rwslib/rwsobjects.py | MetaDataVersion.fromElement | def fromElement(cls, elem):
"""
Read properties from a MetaDataVersion element
:param lxml.etree._Element elem: Source etree Element
"""
self = cls()
self.oid = elem.get("OID")
self.name = elem.get("Name")
return self | python | def fromElement(cls, elem):
"""
Read properties from a MetaDataVersion element
:param lxml.etree._Element elem: Source etree Element
"""
self = cls()
self.oid = elem.get("OID")
self.name = elem.get("Name")
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mdsol/rwslib | rwslib/rwsobjects.py | RWSSubjectListItem.subject_name | def subject_name(self):
"""
Get the subject name consistently
:rtype str
:return: The Subject ID for the subject
.. note::
* If the `SubjectKeyType` is `SubjectUUID` then the subject name lives in the `mdsol:SubjectName` attribute
* If the `SubjectKeyType` is `SubjectName` then the subject name lives in the `SubjectKey` attribute
"""
if self.subjectkeytype and self.subjectkeytype == "SubjectUUID".lower():
# if the SubjectKeyType is "SubjectUUID", then return the SubjectName
return self.subjectname
else:
return self.subjectkey | python | def subject_name(self):
"""
Get the subject name consistently
:rtype str
:return: The Subject ID for the subject
.. note::
* If the `SubjectKeyType` is `SubjectUUID` then the subject name lives in the `mdsol:SubjectName` attribute
* If the `SubjectKeyType` is `SubjectName` then the subject name lives in the `SubjectKey` attribute
"""
if self.subjectkeytype and self.subjectkeytype == "SubjectUUID".lower():
# if the SubjectKeyType is "SubjectUUID", then return the SubjectName
return self.subjectname
else:
return self.subjectkey | [
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mdsol/rwslib | rwslib/rwsobjects.py | RWSSubjectListItem.fromElement | def fromElement(cls, elem):
"""
Read properties from an XML Element
"""
self = cls()
self.studyoid = elem.get("StudyOID")
self.metadataversionoid = elem.get("MetaDataVersionOID")
e_subjectdata = elem.findall(ODM_NS + "SubjectData")[0]
self.subjectkey = e_subjectdata.get("SubjectKey")
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e_links = e_subjectdata.findall(MEDI_NS + "Link")
for e_link in e_links:
self.links.append(e_link.get(XLINK_NS + "href"))
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for prop in RWSSubjectListItem.STATUS_PROPERTIES:
val = e_subjectdata.get(MEDI_NS + prop, "").lower()
setattr(self, prop.lower(), decodes.get(val, val))
# By default we only get back active and non-deleted subjects
self.active = decodes[
e_subjectdata.get(MEDI_NS + "SubjectActive", "yes").lower()
]
self.deleted = decodes[e_subjectdata.get(MEDI_NS + "Deleted", "no").lower()]
return self | python | def fromElement(cls, elem):
"""
Read properties from an XML Element
"""
self = cls()
self.studyoid = elem.get("StudyOID")
self.metadataversionoid = elem.get("MetaDataVersionOID")
e_subjectdata = elem.findall(ODM_NS + "SubjectData")[0]
self.subjectkey = e_subjectdata.get("SubjectKey")
e_siteref = e_subjectdata.findall(ODM_NS + "SiteRef")[0]
self.locationoid = e_siteref.get("LocationOID")
e_links = e_subjectdata.findall(MEDI_NS + "Link")
for e_link in e_links:
self.links.append(e_link.get(XLINK_NS + "href"))
decodes = {"yes": True, "no": False, "": None}
for prop in RWSSubjectListItem.STATUS_PROPERTIES:
val = e_subjectdata.get(MEDI_NS + prop, "").lower()
setattr(self, prop.lower(), decodes.get(val, val))
# By default we only get back active and non-deleted subjects
self.active = decodes[
e_subjectdata.get(MEDI_NS + "SubjectActive", "yes").lower()
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self.deleted = decodes[e_subjectdata.get(MEDI_NS + "Deleted", "no").lower()]
return self | [
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mdsol/rwslib | rwslib/builders/common.py | make_element | def make_element(builder, tag, content):
"""Make an element with this tag and text content"""
builder.start(tag, {})
builder.data(content) # Must be UTF-8 encoded
builder.end(tag) | python | def make_element(builder, tag, content):
"""Make an element with this tag and text content"""
builder.start(tag, {})
builder.data(content) # Must be UTF-8 encoded
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mdsol/rwslib | rwslib/builders/common.py | ODMElement.set_single_attribute | def set_single_attribute(self, other, trigger_klass, property_name):
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# Check property exists
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"""Used to set guard the setting of an attribute which is singular and can't be set twice"""
if isinstance(other, trigger_klass):
# Check property exists
if not hasattr(self, property_name):
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mdsol/rwslib | rwslib/builders/common.py | ODMElement.set_list_attribute | def set_list_attribute(self, other, trigger_klass, property_name):
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mdsol/rwslib | rwslib/builders/common.py | TransactionalElement.transaction_type | def transaction_type(self, value):
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if value is not None:
if value not in self.ALLOWED_TRANSACTION_TYPES:
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"""Set the TransactionType (with Input Validation)"""
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mdsol/rwslib | rwslib/builders/admindata.py | AdminData.build | def build(self, builder):
"""Build XML by appending to builder"""
params = {}
if self.study_oid:
params.update(dict(StudyOID=self.study_oid))
builder.start("AdminData", params)
for user in self.users:
user.build(builder)
for location in self.locations:
location.build(builder)
builder.end("AdminData") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = {}
if self.study_oid:
params.update(dict(StudyOID=self.study_oid))
builder.start("AdminData", params)
for user in self.users:
user.build(builder)
for location in self.locations:
location.build(builder)
builder.end("AdminData") | [
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mdsol/rwslib | rwslib/builders/admindata.py | MetaDataVersionRef.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(StudyOID=self.study_oid,
MetaDataVersionOID=self.metadata_version_oid,
EffectiveDate=dt_to_iso8601(self.effective_date))
builder.start("MetaDataVersionRef", params)
builder.end("MetaDataVersionRef") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(StudyOID=self.study_oid,
MetaDataVersionOID=self.metadata_version_oid,
EffectiveDate=dt_to_iso8601(self.effective_date))
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mdsol/rwslib | rwslib/builders/admindata.py | Location.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(OID=self.oid,
Name=self.name)
if self.location_type:
params.update(dict(LocationType=self.location_type.value))
# mixins
self.mixin()
self.mixin_params(params)
builder.start("Location", params)
for mdv in self.metadata_versions:
mdv.build(builder)
builder.end("Location") | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(OID=self.oid,
Name=self.name)
if self.location_type:
params.update(dict(LocationType=self.location_type.value))
# mixins
self.mixin()
self.mixin_params(params)
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mdsol/rwslib | rwslib/builders/admindata.py | Address.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict()
builder.start(self.__class__.__name__, params)
for street in self.street_names:
street.build(builder)
# build the children
for child in ('city', 'country', 'state_prov', 'postal_code', 'other_text'):
if getattr(self, child) is not None:
getattr(self, child).build(builder)
builder.end(self.__class__.__name__) | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict()
builder.start(self.__class__.__name__, params)
for street in self.street_names:
street.build(builder)
# build the children
for child in ('city', 'country', 'state_prov', 'postal_code', 'other_text'):
if getattr(self, child) is not None:
getattr(self, child).build(builder)
builder.end(self.__class__.__name__) | [
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mdsol/rwslib | rwslib/builders/admindata.py | User.build | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(OID=self.oid)
if self.user_type:
params.update(dict(UserType=self.user_type.value))
builder.start(self.__class__.__name__, params)
# build the children
for child in ('login_name', 'display_name', 'full_name', 'first_name', 'last_name',
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if getattr(self, child) is not None:
getattr(self, child).build(builder)
for address in self.addresses:
address.build(builder)
for email in self.emails:
email.build(builder)
for phone in self.phones:
phone.build(builder)
for location in self.locations:
location.build(builder)
builder.end(self.__class__.__name__) | python | def build(self, builder):
"""Build XML by appending to builder"""
params = dict(OID=self.oid)
if self.user_type:
params.update(dict(UserType=self.user_type.value))
builder.start(self.__class__.__name__, params)
# build the children
for child in ('login_name', 'display_name', 'full_name', 'first_name', 'last_name',
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for email in self.emails:
email.build(builder)
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phone.build(builder)
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location.build(builder)
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mdsol/rwslib | rwslib/builders/admindata.py | Country.build | def build(self, builder):
"""
Build this element
:param builder:
:return:
"""
builder.start(self.__class__.__name__)
builder.data(self.country_code)
builder.end(self.__class__.__name__) | python | def build(self, builder):
"""
Build this element
:param builder:
:return:
"""
builder.start(self.__class__.__name__)
builder.data(self.country_code)
builder.end(self.__class__.__name__) | [
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mdsol/rwslib | rwslib/extras/audit_event/main.py | ODMAdapter.get_next_start_id | def get_next_start_id(self):
"""If link for next result set has been passed, extract it and get the next set start id"""
link = self.rws_connection.last_result.links.get("next", None)
if link:
link = link['url']
p = urlparse(link)
start_id = int(parse_qs(p.query)['startid'][0])
return start_id
return None | python | def get_next_start_id(self):
"""If link for next result set has been passed, extract it and get the next set start id"""
link = self.rws_connection.last_result.links.get("next", None)
if link:
link = link['url']
p = urlparse(link)
start_id = int(parse_qs(p.query)['startid'][0])
return start_id
return None | [
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mdsol/rwslib | rwslib/__init__.py | RWSConnection.send_request | def send_request(self, request_object, timeout=None, retries=1, **kwargs):
"""Send request to RWS endpoint. The request object passed provides the URL endpoint and the HTTP method.
Takes the text response from RWS and allows the request object to modify it for return. This allows the request
object to return text, an XML document object, a CSV file or anything else that can be generated from the text
response from RWS.
A timeout, in seconds, can be optionally passed into send_request.
"""
if not isinstance(request_object, RWSRequest):
raise ValueError("Request object must be a subclass of RWSRequest")
# Construct a URL from the object and make a call
full_url = make_url(self.base_url, request_object.url_path())
if request_object.requires_authorization:
kwargs["auth"] = self.auth
# TODO: Look at different connect and read timeouts?
kwargs["timeout"] = timeout
kwargs.update(request_object.args())
# Explicit use of requests library here. Could alter in future to inject library to use in case
# requests not available.
# Get a session that allows us to customize HTTP requests
session = requests.Session()
# Mount a custom adapter that retries failed connections for HTTP and HTTPS requests.
for scheme in ["http://", "https://"]:
session.mount(scheme, requests.adapters.HTTPAdapter(max_retries=retries))
action = {"GET": session.get, "POST": session.post}[request_object.method]
start_time = time.time()
try:
r = action(full_url, **kwargs) # type: requests.models.Response
except (
requests.exceptions.ConnectTimeout,
requests.exceptions.ReadTimeout,
) as exc:
if isinstance(exc, (requests.exceptions.ConnectTimeout,)):
raise RWSException(
"Server Connection Timeout",
"Connection timeout for {}".format(full_url),
)
elif isinstance(exc, (requests.exceptions.ReadTimeout,)):
raise RWSException(
"Server Read Timeout", "Read timeout for {}".format(full_url)
)
self.request_time = time.time() - start_time
self.last_result = r # see also r.elapsed for timedelta object.
if r.status_code in [400, 404]:
# Is it a RWS response?
if r.text.startswith("<Response"):
error = RWSErrorResponse(r.text)
raise RWSException(error.errordescription, error)
elif "<html" in r.text:
raise RWSException("IIS Error", r.text)
else:
error = RWSError(r.text)
raise RWSException(error.errordescription, error)
elif r.status_code == 500:
raise RWSException("Server Error (500)", r.text)
elif r.status_code == 401:
# Either you didn't supply auth header and it was required OR your credentials were wrong
# RWS handles each differently
# You didn't supply auth (text response from RWS)
if r.text == "Authorization Header not provided":
raise AuthorizationException(r.text)
if "<h2>HTTP Error 401.0 - Unauthorized</h2>" in r.text:
raise RWSException("Unauthorized.", r.text)
# Check if the content_type is text/xml. Use startswith
# in case the charset is also specified:
# content-type: text/xml; charset=utf-8
if r.headers.get("content-type").startswith("text/xml"):
# XML response
if r.text.startswith("<Response"):
error = RWSErrorResponse(r.text)
elif "ODM" in r.text:
error = RWSError(r.text)
else:
# There was some problem with your credentials (XML response from RWS)
error = RWSErrorResponse(r.text)
raise RWSException(error.errordescription, error)
# Catch all.
if r.status_code != 200:
if "<" in r.text:
# XML like
if r.text.strip().startswith("<Response"):
error = RWSErrorResponse(r.text)
elif "ODM" in r.text:
error = RWSError(r.text)
else:
# IIS error page as an example
raise RWSException(
"Unexpected Status Code ({0.status_code})".format(r), r.text
)
else:
# not XML like, better to be safe than blow up
# example response: 'HTTP 503 Service Temporarily Unavailable'
raise RWSException(
"Unexpected Status Code ({0.status_code})".format(r), r.text
)
raise RWSException(error.errordescription, error)
return request_object.result(r) | python | def send_request(self, request_object, timeout=None, retries=1, **kwargs):
"""Send request to RWS endpoint. The request object passed provides the URL endpoint and the HTTP method.
Takes the text response from RWS and allows the request object to modify it for return. This allows the request
object to return text, an XML document object, a CSV file or anything else that can be generated from the text
response from RWS.
A timeout, in seconds, can be optionally passed into send_request.
"""
if not isinstance(request_object, RWSRequest):
raise ValueError("Request object must be a subclass of RWSRequest")
# Construct a URL from the object and make a call
full_url = make_url(self.base_url, request_object.url_path())
if request_object.requires_authorization:
kwargs["auth"] = self.auth
# TODO: Look at different connect and read timeouts?
kwargs["timeout"] = timeout
kwargs.update(request_object.args())
# Explicit use of requests library here. Could alter in future to inject library to use in case
# requests not available.
# Get a session that allows us to customize HTTP requests
session = requests.Session()
# Mount a custom adapter that retries failed connections for HTTP and HTTPS requests.
for scheme in ["http://", "https://"]:
session.mount(scheme, requests.adapters.HTTPAdapter(max_retries=retries))
action = {"GET": session.get, "POST": session.post}[request_object.method]
start_time = time.time()
try:
r = action(full_url, **kwargs) # type: requests.models.Response
except (
requests.exceptions.ConnectTimeout,
requests.exceptions.ReadTimeout,
) as exc:
if isinstance(exc, (requests.exceptions.ConnectTimeout,)):
raise RWSException(
"Server Connection Timeout",
"Connection timeout for {}".format(full_url),
)
elif isinstance(exc, (requests.exceptions.ReadTimeout,)):
raise RWSException(
"Server Read Timeout", "Read timeout for {}".format(full_url)
)
self.request_time = time.time() - start_time
self.last_result = r # see also r.elapsed for timedelta object.
if r.status_code in [400, 404]:
# Is it a RWS response?
if r.text.startswith("<Response"):
error = RWSErrorResponse(r.text)
raise RWSException(error.errordescription, error)
elif "<html" in r.text:
raise RWSException("IIS Error", r.text)
else:
error = RWSError(r.text)
raise RWSException(error.errordescription, error)
elif r.status_code == 500:
raise RWSException("Server Error (500)", r.text)
elif r.status_code == 401:
# Either you didn't supply auth header and it was required OR your credentials were wrong
# RWS handles each differently
# You didn't supply auth (text response from RWS)
if r.text == "Authorization Header not provided":
raise AuthorizationException(r.text)
if "<h2>HTTP Error 401.0 - Unauthorized</h2>" in r.text:
raise RWSException("Unauthorized.", r.text)
# Check if the content_type is text/xml. Use startswith
# in case the charset is also specified:
# content-type: text/xml; charset=utf-8
if r.headers.get("content-type").startswith("text/xml"):
# XML response
if r.text.startswith("<Response"):
error = RWSErrorResponse(r.text)
elif "ODM" in r.text:
error = RWSError(r.text)
else:
# There was some problem with your credentials (XML response from RWS)
error = RWSErrorResponse(r.text)
raise RWSException(error.errordescription, error)
# Catch all.
if r.status_code != 200:
if "<" in r.text:
# XML like
if r.text.strip().startswith("<Response"):
error = RWSErrorResponse(r.text)
elif "ODM" in r.text:
error = RWSError(r.text)
else:
# IIS error page as an example
raise RWSException(
"Unexpected Status Code ({0.status_code})".format(r), r.text
)
else:
# not XML like, better to be safe than blow up
# example response: 'HTTP 503 Service Temporarily Unavailable'
raise RWSException(
"Unexpected Status Code ({0.status_code})".format(r), r.text
)
raise RWSException(error.errordescription, error)
return request_object.result(r) | [
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mdsol/rwslib | rwslib/builders_example.py | example_clinical_data | def example_clinical_data(study_name, environment):
"""Test demonstrating building clinical data"""
odm = ODM("test system")(
ClinicalData("Mediflex", "DEV")(
SubjectData("MDSOL", "IJS TEST4", transaction_type="Insert")(
StudyEventData("SUBJECT")(
FormData("EN", transaction_type="Update")(
# Although Signature is ODM1.3.1 RWS does not support it inbound currently
# RWSBuilders do support outbound generation of Signature at FormData level
# Signature()(
# UserRef("isparks"),
# LocationRef("MDSOL"),
# SignatureRef("APPROVED"),
# DateTimeStamp(datetime(2015, 9, 11, 10, 15, 22, 80))
# ),
ItemGroupData()(
ItemData("SUBJINIT", "AAA")(
AuditRecord(edit_point=AuditRecord.EDIT_DATA_MANAGEMENT,
used_imputation_method= False,
identifier='X2011',
include_file_oid=False)(
UserRef("isparks"),
LocationRef("MDSOL"),
ReasonForChange("Data Entry Error"),
DateTimeStamp(datetime(2015, 9, 11, 10, 15, 22, 80))
),
MdsolQuery(value="Subject initials should be 2 chars only.", recipient="Site from System",
status=QueryStatusType.Open)
),
ItemData("SUBJID", '001')
)
)
)
)
)
)
return odm | python | def example_clinical_data(study_name, environment):
"""Test demonstrating building clinical data"""
odm = ODM("test system")(
ClinicalData("Mediflex", "DEV")(
SubjectData("MDSOL", "IJS TEST4", transaction_type="Insert")(
StudyEventData("SUBJECT")(
FormData("EN", transaction_type="Update")(
# Although Signature is ODM1.3.1 RWS does not support it inbound currently
# RWSBuilders do support outbound generation of Signature at FormData level
# Signature()(
# UserRef("isparks"),
# LocationRef("MDSOL"),
# SignatureRef("APPROVED"),
# DateTimeStamp(datetime(2015, 9, 11, 10, 15, 22, 80))
# ),
ItemGroupData()(
ItemData("SUBJINIT", "AAA")(
AuditRecord(edit_point=AuditRecord.EDIT_DATA_MANAGEMENT,
used_imputation_method= False,
identifier='X2011',
include_file_oid=False)(
UserRef("isparks"),
LocationRef("MDSOL"),
ReasonForChange("Data Entry Error"),
DateTimeStamp(datetime(2015, 9, 11, 10, 15, 22, 80))
),
MdsolQuery(value="Subject initials should be 2 chars only.", recipient="Site from System",
status=QueryStatusType.Open)
),
ItemData("SUBJID", '001')
)
)
)
)
)
)
return odm | [
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mdsol/rwslib | rwslib/builders_example.py | example_metadata | def example_metadata(study_name, draft_name):
"""Example of building a metadata doc"""
odm = ODM("SYSTEM_NAME", filetype=ODM.FILETYPE_SNAPSHOT)
study = Study(study_name, project_type=Study.PROJECT)
# Push study element into odm
odm << study
# Create global variables and set them into study.
study << GlobalVariables(study_name) #Expected that protocol name will match the Study OID.
# Create some basic definitions
bd = BasicDefinitions()
# Add some measurement units to the basic definitions. This time using the call () syntax:
bd(
MeasurementUnit("KG", "Kilograms")(
Symbol()(TranslatedText("Kilograms"))
),
MeasurementUnit("CM", "Centimeters")(
Symbol()(TranslatedText("Centimeters"))
)
)
# Add basic definitions to study
study << bd
# Now metadata which will contain all our form and field defs eventually
meta = MetaDataVersion('META1', draft_name)
study << meta
# Protocol contains StudyEventRefs
protocol = Protocol()
# Add some StudyEventRefs
protocol << StudyEventRef("FLDR1", 1, True) # Order 1, Mandatory
# protocol << StudyEventRef("FLDR2", 2, False) # Order 2, Not Mandatory
# protocol << StudyEventRef("AE", 3, True)
meta << protocol
# Add Study Event Defs with some child FormRefs
fldr1 = StudyEventDef("FLDR1", "Folder 1", False, StudyEventDef.SCHEDULED)
fldr1 << FormRef("DM", 1, True)
fldr1 << FormRef("VS", 2, True)
meta << fldr1
meta << StudyEventDef("FLDR2", "Folder 2", False, StudyEventDef.UNSCHEDULED)(
FormRef("VS", 1, True)
)
meta << StudyEventDef("AE", "Adverse Events", False, StudyEventDef.COMMON)(
FormRef("AE", 1, False)
)
dm_form = FormDef("DM","Demography")
dm_form << MdsolHelpText("en","Some help text for Demography")
dm_form << MdsolViewRestriction('Data Manager')
dm_form << MdsolEntryRestriction('Batch Upload')
dm_form << ItemGroupRef("DM_IG1", 1)
dm_form << ItemGroupRef("DM_IG2", 2)
# Add to metadata
meta << dm_form
# Define item group
meta << ItemGroupDef("DM_IG1", "DM Item Group 1")(
MdsolLabelRef("LBL1", 1),
ItemRef("SEX", 2)(
MdsolAttribute("Standards","CDASH","SEX"),
MdsolAttribute("Standards","STDNUMBER","1120")
),
ItemRef("RACE", 3),
ItemRef("RACE_OTH", 4),
ItemRef("DOB", 5),
ItemRef("AGE", 6)
)
# Add the ItemDefs
meta << ItemDef("SEX", "Gender", DataType.Text, 1, control_type=ControlType.RadioButton
)(
Question()(TranslatedText("Gender at Birth")),
CodeListRef("CL_SEX")
)
meta << ItemDef("RACE", "Race", DataType.Text, 2,
control_type=ControlType.RadioButtonVertical
)(
Question()(TranslatedText("Race")),
CodeListRef("CL_RACE")
)
meta << ItemDef("RACE_OTH", "RaceOther", DataType.Text, 20) \
<< Question() << TranslatedText("If Race Other, please specify")
meta << ItemDef("DOB", "DateOfBirth", DataType.Date, 10,
control_type=ControlType.DateTime,
date_time_format="dd/mm/yyyy"
)(
Question()(TranslatedText("Date of Birth")),
MdsolHelpText("en","If month unknown, enter January")
)
meta << ItemDef("AGE", "Age in Years", DataType.Integer, 4, significant_digits=3, control_type=ControlType.Text
)(
Question()(TranslatedText("Age in Years")),
RangeCheck(RangeCheckComparatorType.GreaterThanEqualTo, RangeCheckType.Soft) (
CheckValue("18")
),
RangeCheck(RangeCheckComparatorType.LessThanEqualTo, RangeCheckType.Soft) (
CheckValue("65")
)
)
# Add a Label
meta.add(MdsolLabelDef("LBL1", "Label1")(TranslatedText("Please answer all questions.")))
# As well as () and << you can use add()
meta.add(
CodeList("CL_SEX", "SEX", datatype=DataType.Text)(
CodeListItem("M").add(
Decode().add(
TranslatedText("Male"))
),
CodeListItem("F").add(
Decode().add(
TranslatedText("Female"))
),
),
CodeList("CL_RACE", "RACE", datatype=DataType.Text)(
CodeListItem("AS")(Decode()(TranslatedText("Asian"))),
CodeListItem("CA")(Decode()(TranslatedText("White"))),
CodeListItem("OT")(Decode()(TranslatedText("Other"))),
)
)
meta.add(MdsolEditCheckDef('CHECK1')(
# Static value required to make this stick, gets ignored but won't load without it
MdsolCheckStep(form_oid="DM", field_oid="RACE", data_format='CodedValue', static_value="1"),
MdsolCheckStep(static_value="OT", data_format="$2"),
MdsolCheckStep(function=StepType.IsEqualTo),
MdsolCheckStep(form_oid="DM", field_oid="RACE_OTH"),
MdsolCheckStep(function=StepType.IsEmpty),
MdsolCheckStep(function=StepType.And),
MdsolCheckAction(form_oid="DM", field_oid="RACE_OTH",
check_action_type=ActionType.OpenQuery,
check_string="Race is set as OTHER but not specified. Please correct.",
check_options="Site from System,RequiresResponse,RequiresManualClose"
)
),
MdsolEditCheckDef('CHECK2')
)
meta.add(MdsolCustomFunctionDef("CF1","SELECT 1,2 FROM DataPoints", language="SQ"))
meta.add(MdsolCustomFunctionDef("CF2","return true;", language="C#"))
meta.add(
# Variable OID required
MdsolDerivationDef("AGE", form_oid="DM", field_oid="AGE")(
# Variable OID required to be identified as a data step
MdsolDerivationStep(form_oid="DM", field_oid="DOB", data_format="StandardValue", variable_oid="DOB"),
MdsolDerivationStep(function=StepType.Age)
)
)
return odm | python | def example_metadata(study_name, draft_name):
"""Example of building a metadata doc"""
odm = ODM("SYSTEM_NAME", filetype=ODM.FILETYPE_SNAPSHOT)
study = Study(study_name, project_type=Study.PROJECT)
# Push study element into odm
odm << study
# Create global variables and set them into study.
study << GlobalVariables(study_name) #Expected that protocol name will match the Study OID.
# Create some basic definitions
bd = BasicDefinitions()
# Add some measurement units to the basic definitions. This time using the call () syntax:
bd(
MeasurementUnit("KG", "Kilograms")(
Symbol()(TranslatedText("Kilograms"))
),
MeasurementUnit("CM", "Centimeters")(
Symbol()(TranslatedText("Centimeters"))
)
)
# Add basic definitions to study
study << bd
# Now metadata which will contain all our form and field defs eventually
meta = MetaDataVersion('META1', draft_name)
study << meta
# Protocol contains StudyEventRefs
protocol = Protocol()
# Add some StudyEventRefs
protocol << StudyEventRef("FLDR1", 1, True) # Order 1, Mandatory
# protocol << StudyEventRef("FLDR2", 2, False) # Order 2, Not Mandatory
# protocol << StudyEventRef("AE", 3, True)
meta << protocol
# Add Study Event Defs with some child FormRefs
fldr1 = StudyEventDef("FLDR1", "Folder 1", False, StudyEventDef.SCHEDULED)
fldr1 << FormRef("DM", 1, True)
fldr1 << FormRef("VS", 2, True)
meta << fldr1
meta << StudyEventDef("FLDR2", "Folder 2", False, StudyEventDef.UNSCHEDULED)(
FormRef("VS", 1, True)
)
meta << StudyEventDef("AE", "Adverse Events", False, StudyEventDef.COMMON)(
FormRef("AE", 1, False)
)
dm_form = FormDef("DM","Demography")
dm_form << MdsolHelpText("en","Some help text for Demography")
dm_form << MdsolViewRestriction('Data Manager')
dm_form << MdsolEntryRestriction('Batch Upload')
dm_form << ItemGroupRef("DM_IG1", 1)
dm_form << ItemGroupRef("DM_IG2", 2)
# Add to metadata
meta << dm_form
# Define item group
meta << ItemGroupDef("DM_IG1", "DM Item Group 1")(
MdsolLabelRef("LBL1", 1),
ItemRef("SEX", 2)(
MdsolAttribute("Standards","CDASH","SEX"),
MdsolAttribute("Standards","STDNUMBER","1120")
),
ItemRef("RACE", 3),
ItemRef("RACE_OTH", 4),
ItemRef("DOB", 5),
ItemRef("AGE", 6)
)
# Add the ItemDefs
meta << ItemDef("SEX", "Gender", DataType.Text, 1, control_type=ControlType.RadioButton
)(
Question()(TranslatedText("Gender at Birth")),
CodeListRef("CL_SEX")
)
meta << ItemDef("RACE", "Race", DataType.Text, 2,
control_type=ControlType.RadioButtonVertical
)(
Question()(TranslatedText("Race")),
CodeListRef("CL_RACE")
)
meta << ItemDef("RACE_OTH", "RaceOther", DataType.Text, 20) \
<< Question() << TranslatedText("If Race Other, please specify")
meta << ItemDef("DOB", "DateOfBirth", DataType.Date, 10,
control_type=ControlType.DateTime,
date_time_format="dd/mm/yyyy"
)(
Question()(TranslatedText("Date of Birth")),
MdsolHelpText("en","If month unknown, enter January")
)
meta << ItemDef("AGE", "Age in Years", DataType.Integer, 4, significant_digits=3, control_type=ControlType.Text
)(
Question()(TranslatedText("Age in Years")),
RangeCheck(RangeCheckComparatorType.GreaterThanEqualTo, RangeCheckType.Soft) (
CheckValue("18")
),
RangeCheck(RangeCheckComparatorType.LessThanEqualTo, RangeCheckType.Soft) (
CheckValue("65")
)
)
# Add a Label
meta.add(MdsolLabelDef("LBL1", "Label1")(TranslatedText("Please answer all questions.")))
# As well as () and << you can use add()
meta.add(
CodeList("CL_SEX", "SEX", datatype=DataType.Text)(
CodeListItem("M").add(
Decode().add(
TranslatedText("Male"))
),
CodeListItem("F").add(
Decode().add(
TranslatedText("Female"))
),
),
CodeList("CL_RACE", "RACE", datatype=DataType.Text)(
CodeListItem("AS")(Decode()(TranslatedText("Asian"))),
CodeListItem("CA")(Decode()(TranslatedText("White"))),
CodeListItem("OT")(Decode()(TranslatedText("Other"))),
)
)
meta.add(MdsolEditCheckDef('CHECK1')(
# Static value required to make this stick, gets ignored but won't load without it
MdsolCheckStep(form_oid="DM", field_oid="RACE", data_format='CodedValue', static_value="1"),
MdsolCheckStep(static_value="OT", data_format="$2"),
MdsolCheckStep(function=StepType.IsEqualTo),
MdsolCheckStep(form_oid="DM", field_oid="RACE_OTH"),
MdsolCheckStep(function=StepType.IsEmpty),
MdsolCheckStep(function=StepType.And),
MdsolCheckAction(form_oid="DM", field_oid="RACE_OTH",
check_action_type=ActionType.OpenQuery,
check_string="Race is set as OTHER but not specified. Please correct.",
check_options="Site from System,RequiresResponse,RequiresManualClose"
)
),
MdsolEditCheckDef('CHECK2')
)
meta.add(MdsolCustomFunctionDef("CF1","SELECT 1,2 FROM DataPoints", language="SQ"))
meta.add(MdsolCustomFunctionDef("CF2","return true;", language="C#"))
meta.add(
# Variable OID required
MdsolDerivationDef("AGE", form_oid="DM", field_oid="AGE")(
# Variable OID required to be identified as a data step
MdsolDerivationStep(form_oid="DM", field_oid="DOB", data_format="StandardValue", variable_oid="DOB"),
MdsolDerivationStep(function=StepType.Age)
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return odm | [
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mdsol/rwslib | rwslib/extras/local_cv.py | BaseDBAdapter.getCSVReader | def getCSVReader(data, reader_type=csv.DictReader):
"""Take a Rave CSV output ending with a line with just EOF on it and return a DictReader"""
f = StringIO(data[:-4]) # Remove \nEOF
return reader_type(f) | python | def getCSVReader(data, reader_type=csv.DictReader):
"""Take a Rave CSV output ending with a line with just EOF on it and return a DictReader"""
f = StringIO(data[:-4]) # Remove \nEOF
return reader_type(f) | [
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mdsol/rwslib | rwslib/extras/local_cv.py | BaseDBAdapter._setDatasets | def _setDatasets(self, metadata):
"""Extract dataset definitions from CSV metadata"""
# Pull the lot into a list
cols = list(self.getCSVReader(metadata))
# sort the cols by view name and ordinal (they come sorted, but lets be sure)
cols.sort(key=lambda x: [x['viewname'], int(x['ordinal'])])
# Now group them by their viewname
for key, grp in groupby(cols, key=lambda x: x["viewname"]):
self.datasets[key] = list(grp) | python | def _setDatasets(self, metadata):
"""Extract dataset definitions from CSV metadata"""
# Pull the lot into a list
cols = list(self.getCSVReader(metadata))
# sort the cols by view name and ordinal (they come sorted, but lets be sure)
cols.sort(key=lambda x: [x['viewname'], int(x['ordinal'])])
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mdsol/rwslib | rwslib/extras/local_cv.py | BaseDBAdapter.processFormData | def processFormData(self, data, dataset_name):
"""Take a string of form data as CSV and convert to insert statements, return template and data values"""
# Get the cols for this dataset
cols = self.datasets[dataset_name]
reader = self.getCSVReader(data, reader_type=csv.reader)
# Get fieldnames from first line of reader, what is left is set of rows
fieldnames = next(reader)
# Check columns
for col in cols:
varname = col["varname"]
if varname not in fieldnames:
raise ValueError("Column %s not found in data for dataset %s" % (varname, dataset_name,))
# Now call overrideen methods of base classes to process this data
self._processDML(dataset_name, cols, reader) | python | def processFormData(self, data, dataset_name):
"""Take a string of form data as CSV and convert to insert statements, return template and data values"""
# Get the cols for this dataset
cols = self.datasets[dataset_name]
reader = self.getCSVReader(data, reader_type=csv.reader)
# Get fieldnames from first line of reader, what is left is set of rows
fieldnames = next(reader)
# Check columns
for col in cols:
varname = col["varname"]
if varname not in fieldnames:
raise ValueError("Column %s not found in data for dataset %s" % (varname, dataset_name,))
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mdsol/rwslib | rwslib/extras/local_cv.py | SQLLiteDBAdapter._processDDL | def _processDDL(self):
"""Generate and process table SQL, SQLLite version"""
sql_statements = self._generateDDL()
logging.info('Generating sqllite tables')
for stmt in sql_statements:
c = self.conn.cursor()
c.execute(stmt)
self.conn.commit() | python | def _processDDL(self):
"""Generate and process table SQL, SQLLite version"""
sql_statements = self._generateDDL()
logging.info('Generating sqllite tables')
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mdsol/rwslib | rwslib/extras/local_cv.py | SQLLiteDBAdapter._generateDDL | def _generateDDL(self):
"""Generate DDL statements for SQLLite"""
sql = []
# Next convert each set of columns into a table structure
for dataset_name in sorted(self.datasets.keys()):
# SQL to drop the table if it already exists
sql.append('''drop table if exists %s;''' % dataset_name)
# Generate the SQL for the cols
cols = self.datasets[dataset_name]
col_defs = []
for col in cols:
sql_datatype = self.getSQLDataType(col["vartype"])
col_defs.append("%s %s" % (col["varname"], sql_datatype,))
stmt = 'CREATE TABLE %s (%s)' % (dataset_name, ','.join(col_defs))
sql.append(stmt)
return sql | python | def _generateDDL(self):
"""Generate DDL statements for SQLLite"""
sql = []
# Next convert each set of columns into a table structure
for dataset_name in sorted(self.datasets.keys()):
# SQL to drop the table if it already exists
sql.append('''drop table if exists %s;''' % dataset_name)
# Generate the SQL for the cols
cols = self.datasets[dataset_name]
col_defs = []
for col in cols:
sql_datatype = self.getSQLDataType(col["vartype"])
col_defs.append("%s %s" % (col["varname"], sql_datatype,))
stmt = 'CREATE TABLE %s (%s)' % (dataset_name, ','.join(col_defs))
sql.append(stmt)
return sql | [
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mdsol/rwslib | rwslib/extras/local_cv.py | SQLLiteDBAdapter._processDML | def _processDML(self, dataset_name, cols, reader):
"""Overridden version of create DML for SQLLite"""
sql_template = self._generateInsertStatement(dataset_name, cols)
# Now insert in batch, reader is a list of rows to insert at this point
c = self.conn.cursor()
c.executemany(sql_template, reader)
self.conn.commit() | python | def _processDML(self, dataset_name, cols, reader):
"""Overridden version of create DML for SQLLite"""
sql_template = self._generateInsertStatement(dataset_name, cols)
# Now insert in batch, reader is a list of rows to insert at this point
c = self.conn.cursor()
c.executemany(sql_template, reader)
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mdsol/rwslib | rwslib/extras/local_cv.py | SQLLiteDBAdapter._generateInsertStatement | def _generateInsertStatement(self, dataset_name, cols):
"""Generates a sql INSERT template"""
col_names = [col["varname"] for col in cols]
# Generate question mark placeholders
qms = ','.join(['?' for x in col_names])
return 'INSERT INTO %s (%s) values (%s)' % (dataset_name, ','.join(col_names), qms) | python | def _generateInsertStatement(self, dataset_name, cols):
"""Generates a sql INSERT template"""
col_names = [col["varname"] for col in cols]
# Generate question mark placeholders
qms = ','.join(['?' for x in col_names])
return 'INSERT INTO %s (%s) values (%s)' % (dataset_name, ','.join(col_names), qms) | [
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mdsol/rwslib | rwslib/extras/local_cv.py | LocalCVBuilder.name_type_from_viewname | def name_type_from_viewname(viewname):
"""Have format V_<studyname>_<view>[_RAW], return name and view type REGULAR or RAW"""
matched = VIEW_REX.match(viewname)
return matched.group('view'), matched.group('type') or 'REGULAR' | python | def name_type_from_viewname(viewname):
"""Have format V_<studyname>_<view>[_RAW], return name and view type REGULAR or RAW"""
matched = VIEW_REX.match(viewname)
return matched.group('view'), matched.group('type') or 'REGULAR' | [
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mdsol/rwslib | rwslib/extras/local_cv.py | LocalCVBuilder.execute | def execute(self):
"""Generate local DB, pulling metadata and data from RWSConnection"""
logging.info('Requesting view metadata for project %s' % self.project_name)
project_csv_meta = self.rws_connection.send_request(ProjectMetaDataRequest(self.project_name))
# Process it into a set of tables
self.db_adapter.processMetaData(project_csv_meta)
# Get the data for the study
for dataset_name in self.db_adapter.datasets.keys():
logging.info('Requesting data from dataset %s' % dataset_name)
form_name, _type = self.name_type_from_viewname(dataset_name)
form_data = self.rws_connection.send_request(
FormDataRequest(self.project_name, self.environment, _type, form_name))
# Now process the form_data into the db of choice
logging.info('Populating dataset %s' % dataset_name)
self.db_adapter.processFormData(form_data, dataset_name)
logging.info('Process complete') | python | def execute(self):
"""Generate local DB, pulling metadata and data from RWSConnection"""
logging.info('Requesting view metadata for project %s' % self.project_name)
project_csv_meta = self.rws_connection.send_request(ProjectMetaDataRequest(self.project_name))
# Process it into a set of tables
self.db_adapter.processMetaData(project_csv_meta)
# Get the data for the study
for dataset_name in self.db_adapter.datasets.keys():
logging.info('Requesting data from dataset %s' % dataset_name)
form_name, _type = self.name_type_from_viewname(dataset_name)
form_data = self.rws_connection.send_request(
FormDataRequest(self.project_name, self.environment, _type, form_name))
# Now process the form_data into the db of choice
logging.info('Populating dataset %s' % dataset_name)
self.db_adapter.processFormData(form_data, dataset_name)
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mdsol/rwslib | rwslib/extras/rwscmd/data_scrambler.py | typeof_rave_data | def typeof_rave_data(value):
"""Function to duck-type values, not relying on standard Python functions because, for example,
a string of '1' should be typed as an integer and not as a string or float
since we're trying to replace like with like when scrambling."""
# Test if value is a date
for format in ['%d %b %Y', '%b %Y', '%Y', '%d %m %Y', '%m %Y', '%d/%b/%Y', '%b/%Y', '%d/%m/%Y', '%m/%Y']:
try:
datetime.datetime.strptime(value, format)
if len(value) == 4 and (int(value) < 1900 or int(value) > 2030):
break
return ('date', format)
except ValueError:
pass
except TypeError:
pass
# Test if value is a time
for format in ['%H:%M:%S', '%H:%M', '%I:%M:%S', '%I:%M', '%I:%M:%S %p', '%I:%M %p']:
try:
datetime.datetime.strptime(value, format)
return ('time', format)
except ValueError:
pass
except TypeError:
pass
# Test if value is a integer
try:
if ((isinstance(value, str) and isinstance(int(value), int)) \
or isinstance(value, int)):
return ('int', None)
except ValueError:
pass
except TypeError:
pass
# Test if value is a float
try:
float(value)
return ('float', None)
except ValueError:
pass
except TypeError:
pass
# If no match on anything else, assume its a string
return ('string', None) | python | def typeof_rave_data(value):
"""Function to duck-type values, not relying on standard Python functions because, for example,
a string of '1' should be typed as an integer and not as a string or float
since we're trying to replace like with like when scrambling."""
# Test if value is a date
for format in ['%d %b %Y', '%b %Y', '%Y', '%d %m %Y', '%m %Y', '%d/%b/%Y', '%b/%Y', '%d/%m/%Y', '%m/%Y']:
try:
datetime.datetime.strptime(value, format)
if len(value) == 4 and (int(value) < 1900 or int(value) > 2030):
break
return ('date', format)
except ValueError:
pass
except TypeError:
pass
# Test if value is a time
for format in ['%H:%M:%S', '%H:%M', '%I:%M:%S', '%I:%M', '%I:%M:%S %p', '%I:%M %p']:
try:
datetime.datetime.strptime(value, format)
return ('time', format)
except ValueError:
pass
except TypeError:
pass
# Test if value is a integer
try:
if ((isinstance(value, str) and isinstance(int(value), int)) \
or isinstance(value, int)):
return ('int', None)
except ValueError:
pass
except TypeError:
pass
# Test if value is a float
try:
float(value)
return ('float', None)
except ValueError:
pass
except TypeError:
pass
# If no match on anything else, assume its a string
return ('string', None) | [
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mdsol/rwslib | rwslib/extras/rwscmd/data_scrambler.py | Scramble.scramble_float | def scramble_float(self, length, sd=0):
"""Return random float in specified format"""
if sd == 0:
return str(fake.random_number(length))
else:
return str(fake.pyfloat(length - sd, sd, positive=True)) | python | def scramble_float(self, length, sd=0):
"""Return random float in specified format"""
if sd == 0:
return str(fake.random_number(length))
else:
return str(fake.pyfloat(length - sd, sd, positive=True)) | [
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mdsol/rwslib | rwslib/extras/rwscmd/data_scrambler.py | Scramble.scramble_date | def scramble_date(self, value, format='%d %b %Y'):
"""Return random date """
# faker method signature changed
if value == '':
# handle the empty string by defaulting to 'now' and 1 year ago
end_date = 'now'
start_date = '-1y'
else:
# specified end date, and one year prior
end_date = datetime.datetime.strptime(value, format).date()
start_date = end_date - datetime.timedelta(days=365)
fake_date = fake.date_time_between(start_date=start_date,
end_date=end_date).strftime(format).upper()
return fake_date | python | def scramble_date(self, value, format='%d %b %Y'):
"""Return random date """
# faker method signature changed
if value == '':
# handle the empty string by defaulting to 'now' and 1 year ago
end_date = 'now'
start_date = '-1y'
else:
# specified end date, and one year prior
end_date = datetime.datetime.strptime(value, format).date()
start_date = end_date - datetime.timedelta(days=365)
fake_date = fake.date_time_between(start_date=start_date,
end_date=end_date).strftime(format).upper()
return fake_date | [
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"fake_date",
"=",
"fake",
".",
"date_time_between",
"(",
"start_date",
"=",
"start_date",
",",
"end_date",
"=",
"end_date",
")",
".",
"strftime",
"(",
"format",
")",
".",
"upper",
"(",
")",
"return",
"fake_date"
] | Return random date | [
"Return",
"random",
"date"
] | train | https://github.com/mdsol/rwslib/blob/1a86bc072d408c009ed1de8bf6e98a1769f54d18/rwslib/extras/rwscmd/data_scrambler.py#L83-L96 |
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