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Further fix to #274.
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The previous fix dealt with the crash. This deals with keeping chemistry inside of `mtd` in tables. The basic idea is that `mtd` is like `math` in that it potentially encapsulates chemistry.

Added a test.

Also fixed up a number of comments.
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@NSoiffer
NSoiffer committed Aug 18, 2024
1 parent d5dd2e1 commit d41b3eb
Showing 1 changed file with 211 additions and 21 deletions.
232 changes: 211 additions & 21 deletions src/chemistry.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@ pub fn clean_chemistry_mrow(mathml: Element) {
clean_mrow_children_mark_pass(&children);
}

/// Do some aggressive structural changes and if they make this look like a chemistry formula, make it as one else remove other marks
/// Do some aggressive structural changes and if they make this look like a chemistry formula, mark it as one else remove other marks
/// Note: the element is replaced with a new restructured element if it is marked as chemistry
/// Pass 1:
/// a) for any run of mi/mtext that can be re-split into chem elements, split them and mark them if it is at least 3 chars long.
Expand Down Expand Up @@ -398,7 +398,7 @@ pub fn convert_leaves_to_chem_elements(mathml: Element) -> Option<Vec<Element>>
/// If it is, it is marked with either data-chem-equation or data-chem-formula
/// This function assumes proper structure
///
/// Returns false if not chemistry -- added attrs, mrows, and leaves are removed in preparation for a second parse
/// Returns true if not chemistry -- added attrs, mrows, and leaves are removed in preparation for a second parse
pub fn scan_and_mark_chemistry(mathml: Element) -> bool {
if is_chemistry_off(mathml) {
return true;
Expand Down Expand Up @@ -455,7 +455,7 @@ fn get_marked_value(mathml: Element) -> Option<isize> {

/// Sets the attr 'chem'
/// Recurse through all the children that have MAYBE_CHEMISTRY set
pub fn set_marked_chemistry_attr(mathml: Element, chem: &str) {
fn set_marked_chemistry_attr(mathml: Element, chem: &str) {
let tag_name = name(&mathml);
if let Some(maybe_attr) = mathml.attribute(MAYBE_CHEMISTRY) {
maybe_attr.remove_from_parent();
Expand Down Expand Up @@ -498,7 +498,7 @@ pub fn set_marked_chemistry_attr(mathml: Element, chem: &str) {
}
}

/// returns true if no MAYBE_CHEMISTRY's occur within the element
/// returns true if MAYBE_CHEMISTRY's occur within the element
fn has_maybe_chemistry(mathml: Element) -> bool {
if mathml.attribute(MAYBE_CHEMISTRY).is_some() {
return true;
Expand Down Expand Up @@ -581,7 +581,18 @@ fn is_changed_after_unmarking_chemistry(mathml: Element) -> bool {
} else {
let mut answer = false;
for child in mathml.children() {
answer |= is_changed_after_unmarking_chemistry(as_element(child));
let child = as_element(child);
if name(&child) == "mtd" {
assert_eq!(child.children().len(), 1);
// let mtd_child = as_element(child.children()[0]);
// if mtd_child.attribute(CHEM_FORMULA).is_none() && mtd_child.attribute(CHEM_EQUATION).is_none() {
// } else {

// }
answer = true;
} else {
answer |= is_changed_after_unmarking_chemistry(child);
}
}
if name(&mathml) == "mrow" {
if let Some(changed_value) = mathml.attribute_value(CHANGED_ATTR) {
Expand Down Expand Up @@ -746,7 +757,7 @@ fn is_chemistry_sanity_check(mathml: Element) -> bool {
/// Looks at the children of the element and uses heuristics to decide whether this is a chemical equation.
/// This assumes canonicalization of characters has happened
fn likely_chem_equation(mathml: Element) -> isize {
if name(&mathml) != "mrow" {
if name(&mathml) != "mrow" && name(&mathml) != "mtd" {
return NOT_CHEMISTRY;
}

Expand Down Expand Up @@ -800,6 +811,23 @@ fn likely_chem_equation(mathml: Element) -> isize {
likely
}
},
// no need to check for mtr or mtd because they only exist in a table and the recursion is dealt with here.
"mtable" => {
for mrow in child.children() {
let mrow = as_element(mrow);
for mtd in mrow.children() {
let mtd = as_element(mtd);
let mut likely = likely_chem_formula(mtd);
if likely < CHEMISTRY_THRESHOLD {
likely = likely_chem_equation(mtd);
}
if likely < CHEMISTRY_THRESHOLD {
is_changed_after_unmarking_chemistry(mtd);
}
}
}
NOT_CHEMISTRY
},
"semantics" => {
likely_chem_equation(get_presentation_element(mathml).1)
},
Expand Down Expand Up @@ -957,20 +985,36 @@ fn likely_chem_formula(mathml: Element) -> isize {
likely_chem_formula(as_element(mathml.children()[0])); // set MAYBE_CHEMISTRY attribute
likely_adorned_chem_formula(mathml)
},
"semantics" => {
likely_chem_formula(get_presentation_element(mathml).1)
},
"mrow" => {
let chem_state = likely_chem_state(mathml);
if chem_state > 0 {
chem_state
} else {
likely_mrow_chem_formula(mathml)
}

},
"mtable" => {
for mrow in mathml.children() {
let mrow = as_element(mrow);
for mtd in mrow.children() {
let mtd = as_element(mtd);
let mut likely = likely_chem_formula(mtd);
if likely < CHEMISTRY_THRESHOLD {
likely = likely_chem_equation(mtd);
}
if likely < CHEMISTRY_THRESHOLD {
is_changed_after_unmarking_chemistry(mtd);
}
}
}
NOT_CHEMISTRY
},
"semantics" => {
likely_chem_formula(get_presentation_element(mathml).1)
},
_ => {
if !is_leaf(mathml) {
// mfrac, msqrt, etc
for child in mathml.children() {
let child = as_element(child);
let likelihood = likely_chem_formula(child);
Expand Down Expand Up @@ -1515,7 +1559,7 @@ pub fn likely_chem_state(mathml: Element) -> isize {
if contents_name == "mi" || contents_name == "mtext" {
let text = as_text(contents);
if text == "s" || text == "l" ||text == "g" ||text == "aq" {
return text.as_bytes().len() as isize; // hack to count chars -- works because all are ASCII
return text.as_bytes().len() as isize + 1; // hack to count chars -- works because all are ASCII
};
}
}
Expand Down Expand Up @@ -2227,15 +2271,15 @@ mod chem_tests {
<mrow><mo>(</mo><mrow><mi>aq</mi></mrow><mo>)</mo></mrow>
</mrow></math>";
let target = "<math>
<mrow data-chem-formula='10'>
<mrow data-chem-formula='11'>
<mi data-chem-element='3'>Fe</mi>
<mo data-changed='added' data-chem-formula-op='0'>&#x2063;</mo>
<msub data-chem-formula='3'>
<mi data-chem-element='3'>Cl</mi>
<mn>3</mn>
</msub>
<mo data-changed='added' data-chem-formula-op='0'>&#x2063;</mo>
<mrow data-chem-formula='2'>
<mrow data-chem-formula='3'>
<mo>(</mo>
<mi>aq</mi>
<mo>)</mo>
Expand All @@ -2253,15 +2297,15 @@ mod chem_tests {
<mi>(aq)</mi>
</mrow></math>";
let target = "<math>
<mrow data-chem-formula='10'>
<mrow data-chem-formula='11'>
<mi data-chem-element='3'>Fe</mi>
<mo data-changed='added' data-chem-formula-op='0'>&#x2063;</mo>
<msub data-chem-formula='3'>
<mi data-chem-element='3'>Cl</mi>
<mn>3</mn>
</msub>
<mo data-changed='added' data-chem-formula-op='0'>&#x2063;</mo>
<mrow data-chem-formula='2'>
<mrow data-chem-formula='3'>
<mo>(</mo>
<mi>aq</mi>
<mo>)</mo>
Expand Down Expand Up @@ -2451,14 +2495,14 @@ mod chem_tests {
</mrow>
</math>";
let target = "<math>
<mrow data-chem-formula='16'>
<mrow data-chem-formula='18'>
<mmultiscripts data-chem-formula='4'>
<mi data-chem-element='3'>Na</mi>
<none></none>
<mo>+</mo>
</mmultiscripts>
<mo data-changed='added' data-chem-formula-op='0'>&#x2063;</mo>
<mrow data-changed='added' data-chem-formula='2'>
<mrow data-changed='added' data-chem-formula='3'>
<mo stretchy='false'>(</mo>
<mi>aq</mi>
<mo stretchy='false'>)</mo>
Expand All @@ -2470,7 +2514,7 @@ mod chem_tests {
<mo>-</mo>
</mmultiscripts>
<mo data-changed='added' data-chem-formula-op='0'>&#x2063;</mo>
<mrow data-changed='added' data-chem-formula='2'>
<mrow data-changed='added' data-chem-formula='3'>
<mo stretchy='false' data-previous-space-width='0.111'>(</mo>
<mi>aq</mi>
<mo stretchy='false'>)</mo>
Expand Down Expand Up @@ -2620,15 +2664,15 @@ mod chem_tests {
</mrow>
</math>";
let target = "<math>
<mrow data-chem-formula='8'>
<mrow data-chem-formula='9'>
<mn>2</mn>
<mo data-changed='added' data-chem-formula-op='0'>&#x2062;</mo>
<mrow data-changed='added' data-chem-formula='8'>
<mrow data-changed='added' data-chem-formula='9'>
<mi mathvariant='normal' data-previous-space-width='0.167' data-chem-element='1'>H</mi>
<mo data-changed='added' data-chem-formula-op='0'>&#x2063;</mo>
<mi data-split='true' data-chem-element='3'>Cl</mi>
<mo data-changed='added' data-chem-formula-op='0'>&#x2063;</mo>
<mrow data-changed='added' data-chem-formula='2'>
<mrow data-changed='added' data-chem-formula='3'>
<mo stretchy='false' data-previous-space-width='0.111'>(</mo>
<mi>aq</mi>
<mo stretchy='false'>)</mo>
Expand Down Expand Up @@ -2829,4 +2873,150 @@ mod chem_tests {
assert!(are_strs_canonically_equal(test, target));
}


#[test]
fn merge_bug_274() {
init_logger();
let test = r#"
<math>
<mrow>
<mtable>
<mtr>
<mtd>
<mrow>
<msub><mtext>H</mtext><mn>2</mn></msub>
<mtext>g</mtext>
<mtext/>
<mtext>+</mtext>
<mtext/>
<msub><mrow><mtext>Cl</mtext></mrow><mn>2</mn></msub>
<mo stretchy="false">(</mo>
<mtext>g</mtext>
<mo stretchy="false">)</mo>
<mo>&#x2192;</mo>
<mn>2</mn>
<mtext>HCl(g)</mtext>
</mrow>
</mtd>
</mtr>
<mtr>
<mtd>
<mrow>
<mn>1</mn>
<mo>:</mo>
<mn>1</mn>
<mo>:</mo>
<mn>2</mn>
</mrow>
</mtd>
</mtr>
<mtr>
<mtd>
<mrow>
<mn>1</mn>
<mtext/>
<msub><mtext>H</mtext><mn>2</mn></msub>
<mtext/>
<mtext>to</mtext>
<mtext/>
<mn>1</mn>
<mtext/>
<msub><mrow><mtext>Cl</mtext></mrow><mn>2</mn></msub>
<mtext/>
<mtext>to</mtext>
<mtext/>
<mtext>2</mtext>
<mtext/>
<mtext>HCl</mtext>
</mrow>
</mtd>
</mtr>
</mtable>
</mrow>
</math>
"#;
let target = "
<math>
<mtable>
<mtr>
<mtd data-maybe-chemistry='9'>
<mrow data-maybe-chemistry='9'>
<mrow data-changed='added' data-maybe-chemistry='8'>
<mrow data-changed='added' data-maybe-chemistry='1'>
<msub data-maybe-chemistry='1'>
<mtext data-maybe-chemistry='1'>H</mtext>
<mn>2</mn>
</msub>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<mtext data-maybe-chemistry='0'>g</mtext>
</mrow>
<mo data-chem-equation-op='1' data-maybe-chemistry='1'>+</mo>
<mrow data-changed='added' data-maybe-chemistry='6'>
<msub data-maybe-chemistry='3'>
<mtext data-maybe-chemistry='3'>Cl</mtext>
<mn>2</mn>
</msub>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2063;</mo>
<mrow data-changed='added' data-maybe-chemistry='2'>
<mo stretchy='false'>(</mo>
<mtext>g</mtext>
<mo stretchy='false'>)</mo>
</mrow>
</mrow>
</mrow>
<mo data-chem-equation-op='1' data-maybe-chemistry='1'>→</mo>
<mrow data-changed='added' data-maybe-chemistry='0'>
<mn data-maybe-chemistry='0'>2</mn>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<mtext data-maybe-chemistry='0'>HCl(g)</mtext>
</mrow>
</mrow>
</mtd>
</mtr>
<mtr>
<mtd>
<mrow>
<mn>1</mn>
<mo>:</mo>
<mn>1</mn>
<mo>:</mo>
<mn>2</mn>
</mrow>
</mtd>
</mtr>
<mtr>
<mtd data-maybe-chemistry='7'>
<mrow data-maybe-chemistry='7'>
<mn data-maybe-chemistry='0'>1</mn>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<msub data-maybe-chemistry='1'>
<mtext data-maybe-chemistry='1'>H</mtext>
<mn>2</mn>
</msub>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<mtext data-maybe-chemistry='0'>to</mtext>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<mn data-maybe-chemistry='0'>1</mn>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<msub data-maybe-chemistry='3'>
<mtext data-maybe-chemistry='3'>Cl</mtext>
<mn>2</mn>
</msub>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<mtext data-maybe-chemistry='0'>to</mtext>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<mtext data-maybe-chemistry='0'>2</mtext>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<mi data-maybe-chemistry='1' mathvariant='normal'>H</mi>
<mo data-changed='added' data-maybe-chemistry='0'>&#x2062;</mo>
<mi data-maybe-chemistry='3' data-split='true'>Cl</mi>
</mrow>
</mtd>
</mtr>
</mtable>
</math>
";
assert!(are_strs_canonically_equal(test, target));
}

}

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