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deviser/pytest_files/test_tex/test-tex/testsbxml/apdx-validation.tex
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| % -*- TeX-master: "main"; fill-column: 72 -*- | ||
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| \section{Validation of SBML documents} | ||
| \label{apdx-validation} | ||
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| \subsection{Validation and consistency rules} | ||
| \label{validation-rules} | ||
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| This section summarizes all the conditions that must (or in some cases, | ||
| at least \emph{should}) be true of an SBML Level~1 Version~1 model that | ||
| uses the \TestTSBXMLLibraryPackage. We use the same conventions as are | ||
| used in the SBML Level~1 Version~1 Core specification document. In | ||
| particular, there are different degrees of rule strictness. Formally, | ||
| the differences are expressed in the statement of a rule: either a rule | ||
| states that a condition \emph{must} be true, or a rule states that it | ||
| \emph{should} be true. Rules of the former kind are strict SBML | ||
| validation rules---a model encoded in SBML must conform to all of them | ||
| in order to be considered valid. Rules of the latter kind are | ||
| consistency rules. To help highlight these differences, we use the | ||
| following three symbols next to the rule numbers: | ||
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| \begin{description} | ||
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| \item[\hspace*{6.5pt}\vSymbol\vsp] A \vSymbolName indicates a | ||
| \emph{requirement} for SBML conformance. If a model does not follow this | ||
| rule, it does not conform to the \TestTSBXMLLibraryPackage | ||
| specification. (Mnemonic intention behind the choice of symbol: ``This | ||
| must be checked.'') | ||
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| \item[\hspace*{6.5pt}\cSymbol\csp] A \cSymbolName indicates a | ||
| \emph{recommendation} for model consistency. If a model does not follow | ||
| this rule, it is not considered strictly invalid as far as the | ||
| \TestTSBXMLLibraryPackage specification is concerned; however, it | ||
| indicates that the model contains a physical or conceptual | ||
| inconsistency. (Mnemonic intention behind the choice of symbol: ``This | ||
| is a cause for warning.'') | ||
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| \item[\hspace*{6.5pt}\mSymbol\msp] A \mSymbolName indicates a strong | ||
| recommendation for good modeling practice. This rule is not strictly a | ||
| matter of SBML encoding, but the recommendation comes from logical | ||
| reasoning. As in the previous case, if a model does not follow this | ||
| rule, it is not strictly considered an invalid SBML encoding. (Mnemonic | ||
| intention behind the choice of symbol: ``You're a star if you heed | ||
| this.'') | ||
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| \end{description} | ||
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| The validation rules listed in the following subsections are all stated | ||
| or implied in the rest of this specification document. They are | ||
| enumerated here for convenience. Unless explicitly stated, all | ||
| validation rules concern objects and attributes specifically defined in | ||
| the \TestTSBXMLLibraryPackage package. | ||
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| For \notice convenience and brevity, we use the shorthand | ||
| ``\token{:\-x}'' to stand for an attribute or element name \token{x} in | ||
| the namespace for the \TestTSBXMLLibraryPackage package, using the | ||
| namespace prefix \token{}. In reality, the prefix string may be | ||
| different from the literal ``\token{}'' used here (and indeed, it can be | ||
| any valid XML namespace prefix that the modeler or software chooses). We | ||
| use ``\token{:\-x}'' because it is shorter than to write a full | ||
| explanation everywhere we refer to an attribute or element in the | ||
| \TestTSBXMLLibraryPackage namespace. | ||
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| \subsubsection*{General rules about this package} | ||
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| \validRule{tsb-10101}{To conform to the \TestTSBXMLLibrary specification | ||
| for TSB Level~1 Version~1, an TSB document must declare | ||
| \uri{http://testsbxml.org/l1v1} as the XMLNamespace to use for elements | ||
| of this package. (Reference: TSB Level~1 Specification for Test TSB XML | ||
| Library, Version~1 \sec{xml-namespace}.)} | ||
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| \validRule{tsb-10102}{Wherever they appear in a TSB document, elements | ||
| and attributes from the \TestTSBXMLLibrary must use the | ||
| \uri{http://testsbxml.org/l1v1} namespace, declaring so either | ||
| explicitly or implicitly. (Reference: TSB Level~1 Specification for Test | ||
| TSB XML Library, Version~1 \sec{xml-namespace}.)} | ||
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| \subsubsection*{General rules about identifiers} | ||
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| \validRule{tsb-10201}{The value of a \token{metaid} must conform to the | ||
| syntax of the XML Type ID (Reference: metaid)} | ||
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| \subsubsection*{General rules for \TestAnnotation elements} | ||
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| \validRule{tsb-10301}{Every top-level XML element within an | ||
| \TestAnnotation object must have an XML namespace declared. (Reference: | ||
| TSB Level~1 Specification for Test TSB XML Library, Version~1 | ||
| \sec{annotation-use}.)} | ||
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| \validRule{tsb-10302}{A given XML namespace cannot be the namespace of | ||
| more than one top-levelelement within a given \TestAnnotation object. | ||
| (Reference: TSB Level~1 Specification for Test TSB XML Library, | ||
| Version~1 \sec{annotation-use}.)} | ||
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| \validRule{tsb-10303}{A given TSB element may contain at most one | ||
| \TestAnnotation subobject. (Reference: TSB Level~1 Specification for | ||
| Test TSB XML Library, Version~1 \sec{annotation-use}.)} | ||
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| \subsubsection*{General rules for \notes elements} | ||
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| \validRule{tsb-10401}{The contents of a \Notes object must be explicitly | ||
| placed in the XHTML XML namespace. (Reference: TSB Level~1 Specification | ||
| for Test TSB XML Library, Version~1 \sec{notes}.)} | ||
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| \validRule{tsb-10402}{The contents of a \Notes object must not contain | ||
| an XML declaration, \ie a string of the form \val{<?xml version="1.0" | ||
| encoding="UTF-8"?>} or similar. (Reference: TSB Level~1 Specification | ||
| for Test TSB XML Library, Version~1 \sec{notes}.)} | ||
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| \validRule{tsb-10403}{The content of a \Notes object must not contain an | ||
| XML DOCTYPE declaration, \ie a string beginning with the characters | ||
| \val{<!DOCTYPE}. (Reference: TSB Level~1 Specification for Test TSB XML | ||
| Library, Version~1 \sec{notes}.)} | ||
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| \validRule{tsb-10404}{A given TSB element may contain at most one \Notes | ||
| subobject. (Reference: TSB Level~1 Specification for Test TSB XML | ||
| Library, Version~1 \sec{notes}.)} | ||
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| \subsubsection*{Rules for \class{TSBDocument} object} | ||
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| \validRule{tsb-20101}{A \TSBDocument object must have the required | ||
| attributes \token{tsb:\-level} and \token{tsb:\-version}, and may have | ||
| the optional attribute \token{tsb:\-metaid}. No other attributes from | ||
| the TSB Level~1 Version~1 namespaces are permitted on a \TSBDocument | ||
| object. (Reference: TSB Level~1 Specification for Test TSB XML Library, | ||
| Version~1, \sec{tsbdocument-class}.)} | ||
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| \validRule{tsb-20102}{Apart from the general \Notes and \TestAnnotation | ||
| subobjects permitted on all TSB components, A \TSBDocument object may | ||
| contain one and only one instance of the \ListOfComments element. No | ||
| other objects from the TSB Level~1 Version~1 namespaces are permitted on | ||
| a \TSBDocument object. (Reference: TSB Level~1 Specification for Test | ||
| TSB XML Library, Version~1, \sec{tsbdocument-class}.)} | ||
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| \validRule{tsb-20103}{The attribute \token{level} on a \TSBDocument must | ||
| have a value of data type \token{integer}, and must be non negative. | ||
| (Reference: TSB Level~1 Specification for Test TSB XML Library, | ||
| Version~1, \sec{tsbdocument-class}.)} | ||
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| \validRule{tsb-20104}{The attribute \token{version} on a \TSBDocument | ||
| must have a value of data type \token{integer}, and must be non | ||
| negative. (Reference: TSB Level~1 Specification for Test TSB XML | ||
| Library, Version~1, \sec{tsbdocument-class}.)} | ||
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| \subsubsection*{Rules for \class{ListOfComments} object} | ||
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| \validRule{tsb-20201}{Apart from the general \notes and \TestAnnotation | ||
| subobjects permitted on all TSB objects, a \ListOfComments container | ||
| object may only contain \Comment objects. (Reference: TSB Level~1 | ||
| Specification for Test TSB XML Library, Version~1, | ||
| \sec{listofcomments-class}.)} | ||
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| \validRule{tsb-20202}{A \ListOfComments object may have the optional | ||
| attribute \token{metaid}. No other attributes from the TSB Level~1 | ||
| Version~1 namespaces are permitted on a \ListOfComments object. | ||
| (Reference: TSB Level~1 Specification for Test TSB XML Library, | ||
| Version~1, \sec{listofcomments-class}.)} | ||
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| \subsubsection*{Rules for \class{Comment} object} | ||
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| \validRule{tsb-20301}{A \Comment object must have the required | ||
| attributes \token{tsb:\-contributor} and \token{tsb:\-number}, and may | ||
| have the optional attributes \token{tsb:\-point} and | ||
| \token{tsb:\-metaid}. No other attributes from the TSB Level~1 Version~1 | ||
| namespaces are permitted on a \Comment object. (Reference: TSB Level~1 | ||
| Specification for Test TSB XML Library, Version~1, | ||
| \sec{comment-class}.)} | ||
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| \validRule{tsb-20302}{The attribute \token{contributor} on a \Comment | ||
| must have a value of data type \token{string}. (Reference: TSB Level~1 | ||
| Specification for Test TSB XML Library, Version~1, | ||
| \sec{comment-class}.)} | ||
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| \validRule{tsb-20303}{The attribute \token{number} on a \Comment must | ||
| have a value of data type \token{double}. (Reference: TSB Level~1 | ||
| Specification for Test TSB XML Library, Version~1, | ||
| \sec{comment-class}.)} | ||
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| \validRule{tsb-20304}{The attribute \token{point} on a \Comment must | ||
| have a value of data type \token{string}. (Reference: TSB Level~1 | ||
| Specification for Test TSB XML Library, Version~1, | ||
| \sec{comment-class}.)} | ||
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deviser/pytest_files/test_tex/test-tex/testsbxml/macros.tex
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| % \newcommand{\fixttspace}{\hspace*{1pt}} | ||
| \newcommand{\const}[1]{\texttt{ #1}} | ||
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| \newcommand{\TestTSBXMLLibrary}{\textsf{Test TSB XML Library}\xspace} | ||
| \newcommand{\Tsb}{\textsf{Test TSB XML Library}\xspace} | ||
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| \newcommand{\TODO}[1]{\colorbox{blue}{\textcolor{white}{TODO: #1}}} | ||
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| % commands for classes | ||
| \newcommand{\TSBDocument}{\defRef{TSBDocument}{tsbdocument-class}} | ||
| \newcommand{\Comment}{\defRef{Comment}{comment-class}} | ||
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| % commands for listOfClasses | ||
| \newcommand{\ListOfComments}{\defRef{ListOfComments}{listofcomments-class}} | ||
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| % commands for types | ||
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| % commands for plugins |
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