Better error hanlding when parsing, added medical system
fixed grammar
This commit is contained in:
elvis
@ -44,15 +44,16 @@ match {
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"Products", "MaskProducts", "UncommonProducts", "UncommonMaskProducts",
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"Union", "MaskUnion", "UncommonUnion", "UncommonMaskUnion",
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"Difference", "MaskDifference",
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"UncommonDifference", "UncommonMaskDifference",
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"UncommonDifference", "UncommonMaskDifference",
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"EntitiesDeleted", "MaskEntitiesDeleted",
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"UncommonEntitiesDeleted", "UncommonMaskEntitiesDeleted",
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"EntitiesAdded", "MaskEntitiesAdded",
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"UncommonEntitiesAdded", "UncommonMaskEntitiesAdded",
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"label", "edge", "if", "then", "else", "let", "=", "return", "for", "in",
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"not", "rand", ".empty", ".length", ".tostr", ".source", ".target",
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"not", "rand", "empty", "length", "tostr", "source", "target",
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"&&", "||", "^^", "<=", ">=", "==", "!=", "+", "*", "/", "%",
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"::", "substr", "min", "max", "commonsubstr",
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"::",
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"substr", "min", "max", "commonsubstr",
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"SystemEntities", "SystemContext",
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"AvailableEntities", "AllReactants", "AllInhibitors",
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"relabel",
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@ -67,16 +68,96 @@ match {
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_
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}
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// matches words (letter followed by numbers, letters or _)
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Literal: String = {
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WORD => <>.to_string()
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WORD => <>.into(),
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};
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LiteralProcess: String = {
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Literal => <>,
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"true" => <>.into(),
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"false" => <>.into(),
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"Environment" => <>.into(),
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"Initial" => <>.into(),
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"Context" => <>.into(),
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"Reactions" => <>.into(),
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"Weights" => <>.into(),
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"Sets" => <>.into(),
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"Print" => <>.into(),
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"Save" => <>.into(),
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"Dot" => <>.into(),
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"GraphML" => <>.into(),
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"Serialize" => <>.into(),
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"Stats" => <>.into(),
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"Target" => <>.into(),
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"Run" => <>.into(),
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"Loop" => <>.into(),
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"Frequency" => <>.into(),
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"LimitFrequency" => <>.into(),
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"FastFrequency" => <>.into(),
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"Digraph" => <>.into(),
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"Bisimilarity" => <>.into(),
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"Deserialize" => <>.into(),
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"Hide" => <>.into(),
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"Entities" => <>.into(),
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"MaskEntities" => <>.into(),
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"UncommonEntities" => <>.into(),
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"UncommonMaskEntities" => <>.into(),
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"MaskContext" => <>.into(),
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"UncommonContext" => <>.into(),
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"UncommonMaskContext" => <>.into(),
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"Products" => <>.into(),
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"MaskProducts" => <>.into(),
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"UncommonProducts" => <>.into(),
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"UncommonMaskProducts" => <>.into(),
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"Union" => <>.into(),
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"MaskUnion" => <>.into(),
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"UncommonUnion" => <>.into(),
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"UncommonMaskUnion" => <>.into(),
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"Difference" => <>.into(),
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"MaskDifference" => <>.into(),
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"UncommonDifference" => <>.into(),
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"UncommonMaskDifference" => <>.into(),
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"EntitiesDeleted" => <>.into(),
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"MaskEntitiesDeleted" => <>.into(),
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"UncommonEntitiesDeleted" => <>.into(),
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"UncommonMaskEntitiesDeleted" => <>.into(),
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"EntitiesAdded" => <>.into(),
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"MaskEntitiesAdded" => <>.into(),
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"UncommonEntitiesAdded" => <>.into(),
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"UncommonMaskEntitiesAdded" => <>.into(),
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"label" => <>.into(),
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"edge" => <>.into(),
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"if" => <>.into(),
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"then" => <>.into(),
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"else" => <>.into(),
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"let" => <>.into(),
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"return" => <>.into(),
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"for" => <>.into(),
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"in" => <>.into(),
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"not" => <>.into(),
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"rand" => <>.into(),
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"empty" => <>.into(),
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"length" => <>.into(),
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"tostr" => <>.into(),
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"source" => <>.into(),
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"target" => <>.into(),
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"substr" => <>.into(),
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"min" => <>.into(),
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"max" => <>.into(),
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"commonsubstr" => <>.into(),
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"SystemEntities" => <>.into(),
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"SystemContext" => <>.into(),
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"AvailableEntities" => <>.into(),
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"AllReactants" => <>.into(),
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"AllInhibitors" => <>.into(),
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"relabel" => <>.into(),
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};
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// all numbers are i64
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Num: i64 = {
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NUMBER =>? i64::from_str(<>)
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.map_err(|_| ParseError::User { error: "Number is too big" })
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.map_err(|_| ParseError::User { error: "Number is too big" })
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};
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Path: String = {
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@ -124,7 +205,10 @@ pub Reactions: Vec<RSreaction> = {
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}
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Reaction: RSreaction = {
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#[precedence(level="1")]
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"[" <r: Set> "," <i: Set> "," <p: Set> "]" => RSreaction::from(r, i, p),
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#[precedence(level="0")]
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"[" "r:" <r: Set> "," "i:" <i: Set> "," "p:" <p: Set> "]" =>
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RSreaction::from(r, i, p),
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}
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@ -145,18 +229,26 @@ Boxed_CTX_process: Rc<RSprocess> = {
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CTX_process: RSprocess = {
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"nill" => RSprocess::Nill,
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<c: Set_of_entities> "." <k: CTX_process> =>
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RSprocess::EntitySet{ entities: c, next_process: Rc::new(k) },
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"(" <k: CTX_process> ")" => k,
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"(" <k: Separated<CTX_process, "+">> ")" =>
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RSprocess::Summation{
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children: k.into_iter().map(Rc::new).collect::<Vec<_>>()
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},
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"<" <n: Num> <k1: CTX_process> ">" "." <k: CTX_process> =>
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"?" <r: Reaction> "?" "." <k: CTX_process> =>
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RSprocess::Guarded{ reaction: r, next_process: Rc::new(k) },
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"<" <n: Num> "," <k1: CTX_process> ">" "." <k: CTX_process> =>
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RSprocess::WaitEntity{ repeat: n,
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repeated_process: Rc::new(k1),
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next_process: Rc::new(k) },
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<identifier: Literal> =>
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<identifier: LiteralProcess> =>
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RSprocess::RecursiveIdentifier{
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identifier: translator.encode(identifier)
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}
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@ -172,7 +264,7 @@ pub Environment: Box<RSenvironment> = {
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};
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Env_term: (IdType, RSprocess) = {
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<identifier: Literal> "=" <k: CTX_process> =>
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<identifier: LiteralProcess> "=" <k: CTX_process> =>
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(translator.encode(identifier), k)
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};
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@ -192,61 +284,78 @@ AssertTree: rsassert::Tree = {
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}
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AssertTree2: rsassert::Tree = {
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#[precedence(level="1")]
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"if" <e: AssertExpression>
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"then" "{" <t: AssertTree> "}" =>
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rsassert::Tree::If(Box::new(e), Box::new(t)),
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#[precedence(level="0")]
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"if" <e: AssertExpression>
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"then" "{" <t1: AssertTree> "}"
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"else" "{" <t2: AssertTree> "}" =>
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rsassert::Tree::IfElse(Box::new(e), Box::new(t1), Box::new(t2)),
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#[precedence(level="2")]
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"let" <v: AssertVariable> <q: AssertQualifier?> "=" <e: AssertExpression> =>
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rsassert::Tree::Assignment(v, q, Box::new(e)),
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#[precedence(level="3")]
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"return" <e: AssertExpression> =>
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rsassert::Tree::Return(Box::new(e)),
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#[precedence(level="4")]
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"for" <v: AssertVariable> "in" <r: AssertRange> "{" <t: AssertTree> "}" =>
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rsassert::Tree::For(v, r, Box::new(t)),
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}
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AssertVariable: rsassert::Variable = {
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#[precedence(level="0")]
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"label" => rsassert::Variable::Special(rsassert::Special::Label),
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#[precedence(level="1")]
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"edge" => rsassert::Variable::Special(rsassert::Special::Edge),
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#[precedence(level="2")]
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<v: Literal> => rsassert::Variable::Id(v),
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}
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AssertExpression: rsassert::Expression = {
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// Unary
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#[precedence(level="0")]
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<unp: AssertUnaryPrefix> <e: AssertExpression> =>
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rsassert::Expression::Unary(unp, Box::new(e)),
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"(" <e: AssertExpression> ")" <uns: AssertUnarySuffix> =>
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#[precedence(level="2")]
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<e: AssertExpression> <uns: AssertUnarySuffix> =>
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rsassert::Expression::Unary(uns, Box::new(e)),
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// binary
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"(" <e1: AssertExpression> <b: AssertBinary> <e2: AssertExpression> ")" =>
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#[precedence(level="3")] #[assoc(side="left")]
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<e1: AssertExpression> <b: AssertBinary> <e2: AssertExpression> =>
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rsassert::Expression::Binary(b, Box::new(e1), Box::new(e2)),
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#[precedence(level="1")]
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<b: AssertBinaryPrefix>
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"(" <e1: AssertExpression> "," <e2: AssertExpression> ")" =>
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rsassert::Expression::Binary(b, Box::new(e1), Box::new(e2)),
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#[precedence(level="4")]
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"(" <e: AssertExpression> ")" => e,
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"true" => rsassert::Expression::True,
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"false" => rsassert::Expression::False,
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#[precedence(level="5")]
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<v: AssertVariable> => rsassert::Expression::Var(v),
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// If changing IntegerType in assert.rs, also change from Num to another
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// similar parser with different return type
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#[precedence(level="6")]
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<i: Num> => rsassert::Expression::Integer(i),
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#[precedence(level="7")]
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<lab: AssertLabel> => rsassert::Expression::Label(Box::new(lab)),
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<set: Set_of_entities> => rsassert::Expression::Set(set),
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"'" <el: Literal> "'" => rsassert::Expression::Element(translator.encode(el)),
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// strings
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#[precedence(level="8")]
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PATH => rsassert::Expression::String(<>.trim_end_matches("\"")
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.trim_start_matches("\"")
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.to_string()),
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@ -264,11 +373,13 @@ AssertUnaryPrefix: rsassert::Unary = {
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}
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AssertUnarySuffix: rsassert::Unary = {
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".empty" => rsassert::Unary::Empty,
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".length" => rsassert::Unary::Length,
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".tostr" => rsassert::Unary::ToStr,
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".toel" => rsassert::Unary::ToEl,
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#[precedence(level="0")]
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"." "empty" => rsassert::Unary::Empty,
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"." "length" => rsassert::Unary::Length,
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"." "tostr" => rsassert::Unary::ToStr,
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"." "toel" => rsassert::Unary::ToEl,
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#[precedence(level="1")]
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"." <q: AssertQualifier> => rsassert::Unary::Qualifier(q),
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}
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@ -377,7 +488,6 @@ AssertLabel: RSlabel = {
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// system
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// a system is an environment, a set of entities as initial state, a context and
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// a set of reaction rules.
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pub System: RSsystem = {
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"Environment" ":" <delta: Environment>
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"Initial Entities" ":" <available_entities: Set>
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@ -392,7 +502,6 @@ pub System: RSsystem = {
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// experiment
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// an experiment is composed by a sequence of weights and a sequence of sets of
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// entities of equal length.
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pub Experiment: (Vec<u32>, Vec<RSset>) = {
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"Weights" ":" <w: Separated_Or<Num, ",">>
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"Sets" ":" <s: Separated_Or<Set_of_entities, ",">>
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@ -749,14 +858,17 @@ Instruction: presets::Instruction = {
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}
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pub Run: presets::Instructions = {
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#[precedence(level="0")]
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<sys: System> <instr: Separated_Or<Instruction, ",">> =>
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Instructions { system: presets::System::RSsystem { sys },
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instructions: instr },
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#[precedence(level="1")]
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<sys: System> =>
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Instructions { system: presets::System::RSsystem { sys },
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instructions: vec![] },
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#[precedence(level="2")]
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"Deserialize" "(" <path: Path> ")"
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<instr: Separated_Or<Instruction, ",">> =>
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Instructions { system: presets::System::Deserialize { path },
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