This commit is contained in:
alex-s168
2024-10-28 18:53:53 +01:00
parent 234a682f7e
commit f0b2736af5
18 changed files with 799 additions and 232 deletions

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@@ -12,7 +12,7 @@ repositories {
}
dependencies {
implementation("me.alex_s168:blitz:0.21")
implementation("me.alex_s168:blitz:0.22h2")
}
```

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@@ -5,7 +5,7 @@ plugins {
}
group = "me.alex_s168"
version = "0.20"
version = "0.22h2"
repositories {
mavenCentral()
@@ -15,9 +15,6 @@ dependencies {
testImplementation("org.jetbrains.kotlin:kotlin-test")
implementation("org.jetbrains.kotlinx:kotlinx-io-core:0.3.1")
implementation("org.jetbrains.kotlinx:kotlinx-io-bytestring:0.3.1")
// https://mvnrepository.com/artifact/org.json/json
implementation("org.json:json:20240303")
}
tasks.test {

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@@ -114,3 +114,11 @@ fun <A: Any, BA: Any, BB: Any> Either<A, Either<BA, BB>>.getBAOrNull(): BA? =
fun <A: Any, BA: Any, BB: Any> Either<A, Either<BA, BB>>.getBBOrNull(): BB? =
b?.b
inline fun <A: Any, B: Any, RA: Any, RB: Any> Either<A, B>.map(fa: (A) -> RA, fb: (B) -> RB): Either<RA, RB> =
if (a != null) Either.ofA(fa(a!!))
else Either.ofB(fb(b!!))
inline fun <A: Any, B: Any, R> Either<A, B>.flatMap(fa: (A) -> R, fb: (B) -> R): R =
if (a != null) fa(a!!)
else fb(b!!)

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@@ -0,0 +1,26 @@
package blitz
data class SwitchCase<C, T: Any, R>(
val cond: (C) -> Pair<Boolean, T?>,
val then: (T) -> R,
)
inline infix fun <C, T: Any, R> ((C)->Pair<Boolean, T?>).case(noinline then: (T) -> R) =
SwitchCase(this, then)
infix fun <R> Regex.startsWithCase(then: (MatchResult) -> R): SwitchCase<String, MatchResult, R> =
{ it: String ->
this.matchAt(it, 0)?.let {
true to it
} ?: (false to null)
} case then
inline fun <T, R> T.switch(vararg cases: SwitchCase<T, *, R>, default: (T) -> R): R {
cases.forEach { (cond, then) ->
val (b, v) = cond(this)
if (b) {
return (then as (Any) -> R)(v!!)
}
}
return default(this)
}

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@@ -0,0 +1,7 @@
package blitz
fun unreachable(): Nothing =
error("this should be unreachable")
inline fun <reified R> Any?.cast(): R? =
this?.let { if (it is R) it else null }

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@@ -18,6 +18,9 @@ class ByteVec(private val initCap: Int = 0): Vec<Byte>, ByteBatchSequence {
}
}
fun unsafeBackingArr(): ByteArray =
array
fun copyAsArray(): ByteArray =
array.copyOfRange(0, size)

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@@ -0,0 +1,156 @@
package blitz.collections
import kotlin.contracts.ExperimentalContracts
import kotlin.contracts.contract
class CharVec(private val initCap: Int = 0): Vec<Char>, BatchSequence<Char> {
override var size = 0
private var cap = initCap
private var array = CharArray(initCap)
override fun clear() {
size = 0
if (array.size <= initCap) {
cap = array.size
} else {
cap = initCap
array = CharArray(initCap)
}
}
fun copyAsArray(): CharArray =
array.copyOfRange(0, size)
fun copyIntoArray(arr: CharArray, destOff: Int = 0, startOff: Int = 0) =
array.copyInto(arr, destOff, startOff, size)
override fun copy(): CharVec =
CharVec(size).also {
copyIntoArray(it.array)
}
override fun reserve(amount: Int) {
if (amount > 0 && cap - size >= amount)
return
array = array.copyOf(size + amount)
cap = size + amount
}
override fun reserve(need: Int, wantIfRealloc: Int) {
if (need > 0 && cap - size >= need)
return
cap = size + wantIfRealloc
array = array.copyOf(cap)
}
override fun popBack(): Char =
array[size - 1].also {
reserve(-1)
size --
}
fun tryPopPack(dest: CharArray, destOff: Int = 0): Int {
val can = kotlin.math.min(size, dest.size - destOff)
copyIntoArray(dest, destOff, size - can)
reserve(-can)
size -= can
return can
}
fun popBack(dest: CharArray, destOff: Int = 0) {
val destCopySize = dest.size - destOff
require(size >= destCopySize)
copyIntoArray(dest, destOff, size - destCopySize)
reserve(-destCopySize)
size -= destCopySize
}
@OptIn(ExperimentalContracts::class)
inline fun consumePopBack(batching: CharArray, fn: (CharArray, Int) -> Unit) {
contract {
callsInPlace(fn)
}
while (true) {
val rem = tryPopPack(batching)
if (rem == 0) break
fn(batching, rem)
}
}
inline fun consumePopBack(batching: CharArray, fn: (Char) -> Unit) =
consumePopBack(batching) { batch, count ->
repeat(count) {
fn(batch[it])
}
}
@OptIn(ExperimentalContracts::class)
inline fun consumePopBackSlicedBatches(batching: CharArray, fn: (CharArray) -> Unit) {
contract {
callsInPlace(fn)
}
while (true) {
val rem = tryPopPack(batching)
if (rem == 0) break
if (rem == batching.size)
fn(batching)
else
fn(batching.copyOf(rem))
}
}
override fun get(index: Int): Char =
array[index]
override fun flip() {
array = array.reversedArray()
}
fun pushBack(arr: CharArray) {
reserve(arr.size)
arr.copyInto(array, size)
size += arr.size
}
override fun pushBack(elem: Char) {
reserve(1, 8)
array[size] = elem
size ++
}
override fun iterator(): BatchIterator<Char> =
array.asSequence().asBatch().iterator()
override fun toString(): String =
String(array, 0, size)
fun subViewToString(from: Int, num: Int = size - from): String =
String(array, from, num)
override fun set(index: Int, value: Char) {
array[index] = value
}
companion object {
fun from(data: String) =
CharVec(data.length).also {
data.toCharArray().copyInto(it.array)
it.size = data.length
}
fun from(bytes: CharArray) =
CharVec(bytes.size).also {
bytes.copyInto(it.array)
it.size += bytes.size
}
fun from(bytes: Sequence<Char>) =
CharVec().also { bv ->
bytes.forEach(bv::pushBack)
}
}
}

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@@ -0,0 +1,23 @@
package blitz.collections
fun <T> List<T>.containsAt(at: Int, other: List<T>): Boolean {
if (at + other.size > size)
return false
for (i in at..<at+other.size)
if (this[i] != other[i-at])
return false
return true
}
fun <T> List<T>.startsWith(other: List<T>): Boolean =
containsAt(0, other)
fun String.startsWith(re: Regex): Boolean =
re.matchesAt(this, 0)
fun String.substringAfter(m: MatchResult): String =
this.drop(m.value.length)
fun String.substringAfter(re: Regex): String? =
re.matchAt(this, 0)
?.let(this::substringAfter)

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@@ -0,0 +1,147 @@
package blitz.collections
import kotlin.contracts.ExperimentalContracts
import kotlin.contracts.contract
class IntVec(private val initCap: Int = 0): Vec<Int>, BatchSequence<Int> {
override var size = 0
private var cap = initCap
private var array = IntArray(initCap)
override fun clear() {
size = 0
if (array.size <= initCap) {
cap = array.size
} else {
cap = initCap
array = IntArray(initCap)
}
}
fun copyAsArray(): IntArray =
array.copyOfRange(0, size)
fun copyIntoArray(arr: IntArray, destOff: Int = 0, startOff: Int = 0) =
array.copyInto(arr, destOff, startOff, size)
override fun copy(): IntVec =
IntVec(size).also {
copyIntoArray(it.array)
}
override fun reserve(amount: Int) {
if (amount > 0 && cap - size >= amount)
return
array = array.copyOf(size + amount)
cap = size + amount
}
override fun reserve(need: Int, wantIfRealloc: Int) {
if (need > 0 && cap - size >= need)
return
cap = size + wantIfRealloc
array = array.copyOf(cap)
}
override fun popBack(): Int =
array[size - 1].also {
reserve(-1)
size --
}
fun tryPopPack(dest: IntArray, destOff: Int = 0): Int {
val can = kotlin.math.min(size, dest.size - destOff)
copyIntoArray(dest, destOff, size - can)
reserve(-can)
size -= can
return can
}
fun popBack(dest: IntArray, destOff: Int = 0) {
val destCopySize = dest.size - destOff
require(size >= destCopySize)
copyIntoArray(dest, destOff, size - destCopySize)
reserve(-destCopySize)
size -= destCopySize
}
@OptIn(ExperimentalContracts::class)
inline fun consumePopBack(batching: IntArray, fn: (IntArray, Int) -> Unit) {
contract {
callsInPlace(fn)
}
while (true) {
val rem = tryPopPack(batching)
if (rem == 0) break
fn(batching, rem)
}
}
inline fun consumePopBack(batching: IntArray, fn: (Int) -> Unit) =
consumePopBack(batching) { batch, count ->
repeat(count) {
fn(batch[it])
}
}
@OptIn(ExperimentalContracts::class)
inline fun consumePopBackSlicedBatches(batching: IntArray, fn: (IntArray) -> Unit) {
contract {
callsInPlace(fn)
}
while (true) {
val rem = tryPopPack(batching)
if (rem == 0) break
if (rem == batching.size)
fn(batching)
else
fn(batching.copyOf(rem))
}
}
override fun get(index: Int): Int =
array[index]
override fun flip() {
array = array.reversedArray()
}
fun pushBack(arr: IntArray) {
reserve(arr.size)
arr.copyInto(array, size)
size += arr.size
}
override fun pushBack(elem: Int) {
reserve(1, 8)
array[size] = elem
size ++
}
override fun iterator(): BatchIterator<Int> =
array.asSequence().asBatch().iterator()
override fun toString(): String =
contents.toString()
override fun set(index: Int, value: Int) {
array[index] = value
}
companion object {
fun from(bytes: IntArray) =
IntVec(bytes.size).also {
bytes.copyInto(it.array)
it.size += bytes.size
}
fun from(bytes: Sequence<Int>) =
IntVec().also { bv ->
bytes.forEach(bv::pushBack)
}
}
}

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@@ -31,3 +31,39 @@ fun <T> MutableList<T>.addFront(value: T) =
fun <T: Any> Iterable<T?>.countNotNull() =
count { it != null }
fun <T> Iterable<Iterable<T>>.intersections(dest: MutableList<T> = mutableListOf()): MutableList<T> =
reduce { acc, li -> acc.intersect(li) }
.forEach { dest += it }
.let { dest }
fun <T> Iterable<T>.removeAtIndexes(idc: Iterable<Int>, dest: MutableList<T> = mutableListOf()): MutableList<T> =
filterIndexedTo(dest) { index, _ -> index !in idc }
fun <T> List<T>.gather(idc: Iterable<Int>): MutableList<T> {
val dest = mutableListOf<T>()
idc.forEach {
dest += get(it)
}
return dest
}
fun <T> List<T>.before(idx: Int): List<T> =
take(idx)
fun <T> List<T>.after(idx: Int): List<T> =
drop(idx + 1)
inline fun <I, reified O> Collection<I>.mapToArray(fn: (I) -> O): Array<O> {
val iter = this.iterator()
return Array(this.size) {
fn(iter.next())
}
}
inline fun <I, reified O> Collection<I>.mapIndexedToArray(fn: (Int, I) -> O): Array<O> {
val iter = this.iterator()
return Array(this.size) {
fn(it, iter.next())
}
}

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@@ -0,0 +1,147 @@
package blitz.collections
import kotlin.contracts.ExperimentalContracts
import kotlin.contracts.contract
class LongVec(private val initCap: Int = 0): Vec<Long>, BatchSequence<Long> {
override var size = 0
private var cap = initCap
private var array = LongArray(initCap)
override fun clear() {
size = 0
if (array.size <= initCap) {
cap = array.size
} else {
cap = initCap
array = LongArray(initCap)
}
}
fun copyAsArray(): LongArray =
array.copyOfRange(0, size)
fun copyIntoArray(arr: LongArray, destOff: Int = 0, startOff: Int = 0) =
array.copyInto(arr, destOff, startOff, size)
override fun copy(): LongVec =
LongVec(size).also {
copyIntoArray(it.array)
}
override fun reserve(amount: Int) {
if (amount > 0 && cap - size >= amount)
return
array = array.copyOf(size + amount)
cap = size + amount
}
override fun reserve(need: Int, wantIfRealloc: Int) {
if (need > 0 && cap - size >= need)
return
cap = size + wantIfRealloc
array = array.copyOf(cap)
}
override fun popBack(): Long =
array[size - 1].also {
reserve(-1)
size --
}
fun tryPopPack(dest: LongArray, destOff: Int = 0): Int {
val can = kotlin.math.min(size, dest.size - destOff)
copyIntoArray(dest, destOff, size - can)
reserve(-can)
size -= can
return can
}
fun popBack(dest: LongArray, destOff: Int = 0) {
val destCopySize = dest.size - destOff
require(size >= destCopySize)
copyIntoArray(dest, destOff, size - destCopySize)
reserve(-destCopySize)
size -= destCopySize
}
@OptIn(ExperimentalContracts::class)
inline fun consumePopBack(batching: LongArray, fn: (LongArray, Int) -> Unit) {
contract {
callsInPlace(fn)
}
while (true) {
val rem = tryPopPack(batching)
if (rem == 0) break
fn(batching, rem)
}
}
inline fun consumePopBack(batching: LongArray, fn: (Long) -> Unit) =
consumePopBack(batching) { batch, count ->
repeat(count) {
fn(batch[it])
}
}
@OptIn(ExperimentalContracts::class)
inline fun consumePopBackSlicedBatches(batching: LongArray, fn: (LongArray) -> Unit) {
contract {
callsInPlace(fn)
}
while (true) {
val rem = tryPopPack(batching)
if (rem == 0) break
if (rem == batching.size)
fn(batching)
else
fn(batching.copyOf(rem))
}
}
override fun get(index: Int): Long =
array[index]
override fun flip() {
array = array.reversedArray()
}
fun pushBack(arr: LongArray) {
reserve(arr.size)
arr.copyInto(array, size)
size += arr.size
}
override fun pushBack(elem: Long) {
reserve(1, 8)
array[size] = elem
size ++
}
override fun iterator(): BatchIterator<Long> =
array.asSequence().asBatch().iterator()
override fun toString(): String =
contents.toString()
override fun set(index: Int, value: Long) {
array[index] = value
}
companion object {
fun from(bytes: LongArray) =
LongVec(bytes.size).also {
bytes.copyInto(it.array)
it.size += bytes.size
}
fun from(bytes: Sequence<Long>) =
LongVec().also { bv ->
bytes.forEach(bv::pushBack)
}
}
}

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@@ -89,6 +89,18 @@ class RefVec<T>(private val initCap: Int = 0): Vec<T> {
(_array as Array<Any?>)[index] = value
}
inline fun <R, C: MutableCollection<R>> mapTo(dest: C, fn: (T) -> R): C {
_array?.let {
for (i in 0 until size) {
dest.add(fn(it[i] as T))
}
}
return dest
}
inline fun <R> map(fn: (T) -> R): MutableList<R> =
MutableList(size) { fn(this[it]) }
companion object {
fun <T> from(data: Array<T>) =
RefVec<T>(data.size).also {
@@ -102,8 +114,9 @@ class RefVec<T>(private val initCap: Int = 0): Vec<T> {
}
inline fun <T> of(vararg elements: T): RefVec<T> =
RefVec<T>(elements.size shl 2).also {
RefVec<T>(elements.size shl 1).also {
it._array?.let { elements.copyInto(it) }
it.size += elements.size
}
}
}

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@@ -0,0 +1,147 @@
package blitz.collections
import kotlin.contracts.ExperimentalContracts
import kotlin.contracts.contract
class ShortVec(private val initCap: Int = 0): Vec<Short>, BatchSequence<Short> {
override var size = 0
private var cap = initCap
private var array = ShortArray(initCap)
override fun clear() {
size = 0
if (array.size <= initCap) {
cap = array.size
} else {
cap = initCap
array = ShortArray(initCap)
}
}
fun copyAsArray(): ShortArray =
array.copyOfRange(0, size)
fun copyIntoArray(arr: ShortArray, destOff: Int = 0, startOff: Int = 0) =
array.copyInto(arr, destOff, startOff, size)
override fun copy(): ShortVec =
ShortVec(size).also {
copyIntoArray(it.array)
}
override fun reserve(amount: Int) {
if (amount > 0 && cap - size >= amount)
return
array = array.copyOf(size + amount)
cap = size + amount
}
override fun reserve(need: Int, wantIfRealloc: Int) {
if (need > 0 && cap - size >= need)
return
cap = size + wantIfRealloc
array = array.copyOf(cap)
}
override fun popBack(): Short =
array[size - 1].also {
reserve(-1)
size --
}
fun tryPopPack(dest: ShortArray, destOff: Int = 0): Int {
val can = kotlin.math.min(size, dest.size - destOff)
copyIntoArray(dest, destOff, size - can)
reserve(-can)
size -= can
return can
}
fun popBack(dest: ShortArray, destOff: Int = 0) {
val destCopySize = dest.size - destOff
require(size >= destCopySize)
copyIntoArray(dest, destOff, size - destCopySize)
reserve(-destCopySize)
size -= destCopySize
}
@OptIn(ExperimentalContracts::class)
inline fun consumePopBack(batching: ShortArray, fn: (ShortArray, Int) -> Unit) {
contract {
callsInPlace(fn)
}
while (true) {
val rem = tryPopPack(batching)
if (rem == 0) break
fn(batching, rem)
}
}
inline fun consumePopBack(batching: ShortArray, fn: (Short) -> Unit) =
consumePopBack(batching) { batch, count ->
repeat(count) {
fn(batch[it])
}
}
@OptIn(ExperimentalContracts::class)
inline fun consumePopBackSlicedBatches(batching: ShortArray, fn: (ShortArray) -> Unit) {
contract {
callsInPlace(fn)
}
while (true) {
val rem = tryPopPack(batching)
if (rem == 0) break
if (rem == batching.size)
fn(batching)
else
fn(batching.copyOf(rem))
}
}
override fun get(index: Int): Short =
array[index]
override fun flip() {
array = array.reversedArray()
}
fun pushBack(arr: ShortArray) {
reserve(arr.size)
arr.copyInto(array, size)
size += arr.size
}
override fun pushBack(elem: Short) {
reserve(1, 8)
array[size] = elem
size ++
}
override fun iterator(): BatchIterator<Short> =
array.asSequence().asBatch().iterator()
override fun toString(): String =
contents.toString()
override fun set(index: Int, value: Short) {
array[index] = value
}
companion object {
fun from(bytes: ShortArray) =
ShortVec(bytes.size).also {
bytes.copyInto(it.array)
it.size += bytes.size
}
fun from(bytes: Sequence<Short>) =
ShortVec().also { bv ->
bytes.forEach(bv::pushBack)
}
}
}

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@@ -0,0 +1,11 @@
package blitz.collections
inline fun <reified T> SmartVec(initCap: Int = 0): Vec<T> =
when (T::class.java) {
Char::class.java -> CharVec(initCap) as Vec<T>
Byte::class.java -> ByteVec(initCap) as Vec<T>
Short::class.java -> ShortVec(initCap) as Vec<T>
Int::class.java -> IntVec(initCap) as Vec<T>
Long::class.java -> LongVec(initCap) as Vec<T>
else -> RefVec(initCap)
}

View File

@@ -1,10 +1,9 @@
package blitz.parse
import blitz.collections.RefVec
import blitz.collections.contents
import blitz.parse.comb2.*
import org.json.JSONObject
import kotlin.math.min
import kotlin.system.measureNanoTime
import blitz.unreachable
object JSON {
@@ -27,8 +26,10 @@ object JSON {
val jsonArray: Parser<Char, Element> =
thenIgnore(
thenIgnore(
thenOverwrite(just('['),
mapValue(delimitedBy(jsonElement, just(',')), Element::newArr)),
thenOverwrite(
thenIgnore(just('['), whitespaces),
mapValue(delimitedBy(jsonElement,
chain(whitespaces, ignoreSeq(","), whitespaces)), Element::newArr)),
whitespaces),
just(']')
)
@@ -91,6 +92,17 @@ object JSON {
inline fun newObj(v: Map<String, Element>): Element =
Element(OBJ, _boxed = v)
}
override fun toString(): String =
when (kind) {
NUM -> uncheckedAsNum().toString()
BOOL -> uncheckedAsBool().toString()
NULL -> "null"
ARR -> uncheckedAsArr().contents.toString()
STR -> "\"${uncheckedAsStr()}\""
OBJ -> uncheckedAsObj().map { "${it.key}: ${it.value}" }.joinToString(prefix = "{", postfix = "}")
else -> unreachable()
}
}
inline fun Element.uncheckedAsNum(): Double =
@@ -129,211 +141,6 @@ object JSON {
return _boxed as Map<String, Element>
}
fun parse(string: String): ParseResult<Element> {
val ctx = ParseCtx(string.toList(), 0)
val v = jsonElement(ctx)
return v
}
}
fun main() {
val json = """
{
"clinical_study": {
"brief_summary": {
"textblock": "CLEAR SYNERGY is an international multi center 2x2 randomized placebo controlled trial of"
},
"brief_title": "CLEAR SYNERGY Neutrophil Substudy",
"overall_status": "Recruiting",
"eligibility": {
"study_pop": {
"textblock": "Patients who are randomized to the drug RCT portion of the CLEAR SYNERGY (OASIS 9) trial"
},
"minimum_age": "19 Years",
"sampling_method": "Non-Probability Sample",
"gender": "All",
"criteria": {
"textblock": "Inclusion Criteria:"
},
"healthy_volunteers": "No",
"maximum_age": "110 Years"
},
"number_of_groups": "2",
"source": "NYU Langone Health",
"location_countries": {
"country": "United States"
},
"study_design_info": {
"time_perspective": "Prospective",
"observational_model": "Other"
},
"last_update_submitted_qc": "September 10, 2019",
"intervention_browse": {
"mesh_term": "Colchicine"
},
"official_title": "Studies on the Effects of Colchicine on Neutrophil Biology in Acute Myocardial Infarction: A Substudy of the CLEAR SYNERGY (OASIS 9) Trial",
"primary_completion_date": {
"type": "Anticipated",
"content": "February 1, 2021"
},
"sponsors": {
"lead_sponsor": {
"agency_class": "Other",
"agency": "NYU Langone Health"
},
"collaborator": [
{
"agency_class": "Other",
"agency": "Population Health Research Institute"
},
{
"agency_class": "NIH",
"agency": "National Heart, Lung, and Blood Institute (NHLBI)"
}
]
},
"overall_official": {
"role": "Principal Investigator",
"affiliation": "NYU School of Medicine",
"last_name": "Binita Shah, MD"
},
"overall_contact_backup": {
"last_name": "Binita Shah, MD"
},
"condition_browse": {
"mesh_term": [
"Myocardial Infarction",
"ST Elevation Myocardial Infarction",
"Infarction"
]
},
"overall_contact": {
"phone": "646-501-9648",
"last_name": "Fatmira Curovic",
"email": "fatmira.curovic@nyumc.org"
},
"responsible_party": {
"responsible_party_type": "Principal Investigator",
"investigator_title": "Assistant Professor of Medicine",
"investigator_full_name": "Binita Shah",
"investigator_affiliation": "NYU Langone Health"
},
"study_first_submitted_qc": "March 12, 2019",
"start_date": {
"type": "Actual",
"content": "March 4, 2019"
},
"has_expanded_access": "No",
"study_first_posted": {
"type": "Actual",
"content": "March 14, 2019"
},
"arm_group": [
{
"arm_group_label": "Colchicine"
},
{
"arm_group_label": "Placebo"
}
],
"primary_outcome": {
"measure": "soluble L-selectin",
"time_frame": "between baseline and 3 months",
"description": "Change in soluble L-selectin between baseline and 3 mo after STEMI in the placebo vs. colchicine groups."
},
"secondary_outcome": [
{
"measure": "Other soluble markers of neutrophil activity",
"time_frame": "between baseline and 3 months",
"description": "Other markers of neutrophil activity will be evaluated at baseline and 3 months after STEMI (myeloperoxidase, matrix metalloproteinase-9, neutrophil gelatinase-associated lipocalin, neutrophil elastase, intercellular/vascular cellular adhesion molecules)"
},
{
"measure": "Markers of systemic inflammation",
"time_frame": "between baseline and 3 months",
"description": "Markers of systemic inflammation will be evaluated at baseline and 3 months after STEMI (high sensitive CRP, IL-1β)"
},
{
"measure": "Neutrophil-driven responses that may further propagate injury",
"time_frame": "between baseline and 3 months",
"description": "Neutrophil-driven responses that may further propagate injury will be evaluated at baseline and 3 months after STEMI (neutrophil extracellular traps, neutrophil-derived microparticles)"
}
],
"oversight_info": {
"is_fda_regulated_drug": "No",
"is_fda_regulated_device": "No",
"has_dmc": "No"
},
"last_update_posted": {
"type": "Actual",
"content": "September 12, 2019"
},
"id_info": {
"nct_id": "NCT03874338",
"org_study_id": "18-01323",
"secondary_id": "1R01HL146206"
},
"enrollment": {
"type": "Anticipated",
"content": "670"
},
"study_first_submitted": "March 12, 2019",
"condition": [
"Neutrophils.Hypersegmented | Bld-Ser-Plas",
"STEMI - ST Elevation Myocardial Infarction"
],
"study_type": "Observational",
"required_header": {
"download_date": "ClinicalTrials.gov processed this data on July 19, 2020",
"link_text": "Link to the current ClinicalTrials.gov record.",
"url": "https://clinicaltrials.gov/show/NCT03874338"
},
"last_update_submitted": "September 10, 2019",
"completion_date": {
"type": "Anticipated",
"content": "February 1, 2022"
},
"location": {
"contact": {
"phone": "646-501-9648",
"last_name": "Fatmira Curovic",
"email": "fatmira.curovic@nyumc.org"
},
"facility": {
"address": {
"zip": "10016",
"country": "United States",
"city": "New York",
"state": "New York"
},
"name": "NYU School of Medicine"
},
"status": "Recruiting",
"contact_backup": {
"last_name": "Binita Shah, MD"
}
},
"intervention": {
"intervention_type": "Drug",
"arm_group_label": [
"Colchicine",
"Placebo"
],
"description": "Participants in the main CLEAR SYNERGY trial are randomized to colchicine/spironolactone versus placebo in a 2x2 factorial design. The substudy is interested in the evaluation of biospecimens obtained from patients in the colchicine vs placebo group.",
"intervention_name": "Colchicine Pill"
},
"patient_data": {
"sharing_ipd": "No"
},
"verification_date": "September 2019"
}
}
""".trimIndent()
var minAlex = Long.MAX_VALUE
var minJson = Long.MAX_VALUE
while (true) {
minAlex = min(measureNanoTime { JSON.parse(json).a!! }, minAlex)
minJson = min(measureNanoTime { JSONObject(json) }, minJson)
println("alex: $minAlex ns, json-java: $minJson ns ; alex is ${ minJson.toFloat() / minAlex.toFloat() } times as fast as json-java")
}
fun parse(string: String): ParseResult<Element> =
jsonElement.run(string.toList())
}

View File

@@ -2,6 +2,8 @@ package blitz.parse.comb2
import blitz.*
import blitz.collections.RefVec
import blitz.collections.containsAt
import blitz.parse.JSON.jsonElement
import blitz.str.charsToString
data class ParseCtx<I>(
@@ -192,9 +194,29 @@ fun <I, O: Any> chain(parsers: List<Parser<I, O>>): Parser<I, RefVec<O>> =
else Either.ofA(results)
}
inline fun <I, O: Any> chain(vararg parsers: Parser<I, O>): Parser<I, RefVec<O>> =
chain(parsers.toList())
inline fun <I: Any> seq(want: List<I>): Parser<I, RefVec<I>> =
chain(want.map(::just))
inline fun seq(want: String): Parser<Char, RefVec<Char>> =
chain(want.map(::just))
inline fun ignoreSeq(want: String): Parser<Char, Unit> =
{ ctx ->
if (ctx.idx >= ctx.input.size) {
Either.ofB(ParseError(ctx.idx, "unexpected end of file"))
} else {
if (ctx.input.containsAt(ctx.idx, want.toList())) {
ctx.idx += want.length
Either.ofA(Unit)
} else {
Either.ofB(ParseError(ctx.idx, "expected $want"))
}
}
}
inline fun <I: Any> filter(msg: String, crossinline filter: (I) -> Boolean): Parser<I, I> =
{ ctx ->
if (ctx.idx >= ctx.input.size) {
@@ -254,3 +276,12 @@ fun <O: Any> regex(pattern: String, fn: (groups: MatchGroupCollection) -> O): Pa
regex(Regex(pattern), fn)
fun regex(pattern: String) = regex(pattern) { it[0]!!.value }
fun <O: Any> ParseResult<O>.unwrap(): O =
flatMap(
{ it },
{ throw Exception("at ${it.loc}: ${it.message}") }
)
fun <I, O: Any> Parser<I, O>.run(input: List<I>): ParseResult<O> =
this(ParseCtx(input, 0))

View File

@@ -14,24 +14,24 @@ val digit: Parser<Char, Char> =
filter("expected digit") { it >= '0' && it <= '9' }
val uintLit: Parser<Char, RefVec<Char>> =
verifyValueWithSpan(withSpan(repeated(digit)))
verifyValue(repeated(digit))
{ if (it.size == 0) "need digits after sign in num lit" else null }
val intLit: Parser<Char, Int> =
mapValue(then(choose<Char,Int> {
val intLit: Parser<Char, Long> =
mapValue(then(choose<Char, Int> {
it(mapValue(just('+')) { +1 })
it(mapValue(just('-')) { -1 })
it(value(+1))
}, uintLit))
{ (sign, v) -> sign * v.charsToString().toInt() }
{ (sign, v) -> sign * (v.charsToString().toLongOrNull() ?: Long.MAX_VALUE) }
val floatLit: Parser<Char, Double> =
mapValue(
then(
thenIgnore(
intLit,
just('.')),
orElseVal(uintLit, RefVec.of('0'))))
orElseVal(
thenOverwrite(just('.'), uintLit),
RefVec.of('0'))))
{ (pre, post) ->
var p = post.charsToString().toDouble()
while (p.absoluteValue >= 1) {

View File

@@ -1,13 +1,21 @@
package blitz.str
import blitz.collections.ByteVec
import blitz.collections.CharVec
import blitz.collections.Vec
fun Collection<Char>.charsToString(): String =
String(this.toCharArray())
fun Vec<Char>.charsToString(): String =
String(CharArray(size) { this[it] })
when (this) {
is CharVec -> subViewToString(0)
else -> String(CharArray(size) { this[it] })
}
@JvmName("charsToString_VecByte")
fun Vec<Byte>.charsToString(): String =
String(CharArray(size) { this[it].toInt().toChar() })
when (this) {
is ByteVec -> String(unsafeBackingArr())
else -> String(CharArray(size) { this[it].toInt().toChar() })
}