search

PRIDE-Archive / pride-curation-scripts

Useful PRIDE Pipelines curation scripts
0 stars 0 forks source link

Xml Schema Validation error #17

Closed deeptijk closed 5 years ago

deeptijk commented 5 years ago

Removed the special character from the element "<run id" but still gives the error.

Error - ================= Xml schema validation ===============

FILE: 27Dec2017_Suping_ShoExp1.mzML VALIDATION MESSAGE: (1) Non-fatal XML Parsing error detected on line 1, (2) Error message: cvc-attribute.3: The value '27Dec2017SupingShoExp118Feb2019' of attribute 'id' on element 'run' is not valid with respect to its type, 'ID'., (3) Error message: cvc-datatype-valid.1.2.1: '27Dec2017SupingShoExp118Feb2019' is not a valid value for 'NCName'.

Ticket number - 1-20190306-35424-RESUB1

sureshhewabi commented 5 years ago

An xsd:ID value must be an NCName. This means that it must start with a letter or underscore, and can only contain letters, digits, underscores, hyphens, and periods.

Substitute string in Mac:

sed -i .bak 's/27Dec2017SupingShoExp118Feb2019/Dec2017SupingShoExp118Feb2019/g' 27Dec2017_Suping_ShoExp1_edited.mzML

Validate XML file against Schema(XSD) file:

xmllint --noout --schema mzML1.1.0.xsd 27Dec2017_Suping_ShoExp1_edited.mzML

sureshhewabi commented 5 years ago

@deeptijk Did we manage to solve this issue or do you need any help on this?