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Commit c624d302 authored by David Sehnal's avatar David Sehnal
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Merge branch 'master' into structure-data-model

parents 4a39a389 3157bff8
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src/reader/cif/schema/utils.ts
+ 79
− 44
View file @ c624d302
// import dic from './dic'
import { Field, FrameSchema } from '../schema'
import * as Data from '../data-model'
const pooledStr = Field.pooledStr()
const str = Field.str()
const int = Field.int()
const float = Field.float()
export function getFieldType (type: string) {
export function getFieldType (type: string, values?: string[]) {
switch (type) {
case 'code':
case 'ucode':
if (values && values.length) {
return `str as Field.Schema<'${values.join("'|'")}'>`
} else {
return 'str'
}
case 'line':
case 'uline':
case 'text':
......@@ -47,32 +46,32 @@ export function getFieldType (type: string) {
case 'boolean':
case 'symmetry_operation':
case 'date_dep':
return str
return 'str'
case 'uchar3':
case 'uchar1':
case 'symop':
return pooledStr
return 'pooledStr'
case 'int':
case 'non_negative_int':
case 'positive_int':
return int
return 'int'
case 'float':
return float
return 'float'
}
console.log(`unknown type '${type}'`)
return str
return 'str'
}
type SafeFrameCategories = { [category: string]: Data.Frame }
type SafeFrameLinks = { [k: string]: string }
type FrameCategories = { [category: string]: Data.Frame }
type FrameLinks = { [k: string]: string }
interface SafeFrameData {
categories: SafeFrameCategories
links: SafeFrameLinks
interface FrameData {
categories: FrameCategories
links: FrameLinks
}
// get field from given or linked category
function getField ( category: string, field: string, d: Data.Frame, ctx: SafeFrameData): Data.Field|undefined {
function getField ( category: string, field: string, d: Data.Frame, ctx: FrameData): Data.Field|undefined {
const { categories, links } = ctx
const cat = d.categories[category]
......@@ -87,43 +86,64 @@ function getField ( category: string, field: string, d: Data.Frame, ctx: SafeFra
}
}
// function getEnums (d: Data.SafeFrame, ctx: SafeFrameData): string[]|undefined {
// const value = getField('_item_enumeration', 'value', d, ctx)
// if (value) {
// const enums: string[] = []
// for (let i = 0; i < value.rowCount; ++i) {
// enums.push(value.str(i))
// // console.log(value.str(i))
// }
// return enums
// } else {
// // console.log(`item_enumeration.value not found for '${d.header}'`)
// }
// }
function getCode (d: Data.Frame, ctx: SafeFrameData): string|undefined {
function getEnums (d: Data.Frame, ctx: FrameData): string[]|undefined {
const value = getField('_item_enumeration', 'value', d, ctx)
if (value) {
const enums: string[] = []
for (let i = 0; i < value.rowCount; ++i) {
enums.push(value.str(i))
// console.log(value.str(i))
}
return enums
} else {
// console.log(`item_enumeration.value not found for '${d.header}'`)
}
}
function getCode (d: Data.Frame, ctx: FrameData): [string, string[]]|undefined {
const code = getField('_item_type', 'code', d, ctx)
if (code) {
let c = code.str(0)
// if (c === 'ucode') {
// const enums = getEnums(d, ctx)
// if (enums) c += `: ${enums.join('|')}`
// }
return c
let e = []
if (c === 'ucode') {
const enums = getEnums(d, ctx)
if (enums) e.push(...enums)
}
return [c, e]
} else {
console.log(`item_type.code not found for '${d.header}'`)
}
}
export function getSchema (dic: Data.Block) { // todo Block needs to be specialized with safe frames as well
const schema: FrameSchema = {} // { [category: string]: Category.Schema } = {}
const header = `/**
* Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Your friendly code generator
*/
import { Field, TypedFrame } from '../schema'
const pooledStr = Field.pooledStr();
const str = Field.str();
const int = Field.int();
const float = Field.float();`
const footer = `
type mmCIF = TypedFrame<typeof mmCIF>
export default mmCIF;`
export function generateSchema (dic: Data.Block) { // todo Block needs to be specialized with safe frames as well
// const schema: FrameSchema = {} // { [category: string]: Category.Schema } = {}
const schema: { [category: string]: { [field: string]: string } } = {}
const codeLines: string[] = []
// TODO: for fields with finite allowed values, generate:
// type FieldValue = 'a' | 'b' | 'c'
// const catetegory = { field: <type> as Field.Schema<FieldValue> }
const categories: SafeFrameCategories = {}
const links: SafeFrameLinks = {}
const categories: FrameCategories = {}
const links: FrameLinks = {}
dic.saveFrames.forEach(d => {
if (d.header[0] !== '_') return
categories[d.header] = d
......@@ -158,11 +178,26 @@ export function getSchema (dic: Data.Block) { // todo Block needs to be special
const code = getCode(d, { categories, links })
if (code) {
fields[itemName] = getFieldType(code)
fields[itemName] = getFieldType(code[0], code[1])
} else {
console.log(`could not determine code for '${d.header}'`)
}
})
return schema;
schema.entry = { id: 'str' }
codeLines.push(`const mmCIF = {`)
Object.keys(schema).forEach(category => {
codeLines.push(`\t${category}: {`)
const fields = schema[category]
Object.keys(fields).forEach(field => {
const type = fields[field]
// TODO: check if quoting is required
codeLines.push(`\t\t'${field}': ${type},`)
})
codeLines.push('\t},')
})
codeLines.push('}')
return `${header}\n\n${codeLines.join('\n')}\n${footer}`
}
src/script.ts
+ 18
− 15
View file @ c624d302
......@@ -10,12 +10,13 @@ import * as fs from 'fs'
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
const writeFileAsync = util.promisify(fs.writeFile);
import Gro from './reader/gro/parser'
import CIF from './reader/cif/index'
import { toTypedFrame as applySchema } from './reader/cif/schema'
import { getSchema } from './reader/cif/schema/utils'
// import { toTypedFrame as applySchema } from './reader/cif/schema'
import { generateSchema } from './reader/cif/schema/utils'
const file = '1crn.gro'
// const file = 'water.gro'
......@@ -109,16 +110,16 @@ async function runCIF(input: string | Uint8Array) {
console.log(mmcif.entity.type.toArray());
console.log(mmcif.pdbx_struct_oper_list.matrix.value(0));
const schema = await _dic()
if (schema) {
const mmcif2 = applySchema(schema, data)
// console.log(util.inspect(mmcif2.atom_site, {showHidden: false, depth: 3}))
console.log(mmcif2.atom_site.Cartn_x.value(0));
console.log(mmcif2.entity.type.toArray());
// console.log(mmcif2.pdbx_struct_oper_list.matrix.value(0)); // TODO
} else {
console.log('error getting mmcif schema from dic')
}
// const schema = await _dic()
// if (schema) {
// const mmcif2 = applySchema(schema, data)
// // console.log(util.inspect(mmcif2.atom_site, {showHidden: false, depth: 3}))
// console.log(mmcif2.atom_site.Cartn_x.value(0));
// console.log(mmcif2.entity.type.toArray());
// // console.log(mmcif2.pdbx_struct_oper_list.matrix.value(0)); // TODO
// } else {
// console.log('error getting mmcif schema from dic')
// }
}
export async function _cif() {
......@@ -153,10 +154,12 @@ async function runDic(input: string | Uint8Array) {
return;
}
const schema = getSchema(parsed.result.blocks[0])
console.log(util.inspect(schema, {showHidden: false, depth: 3}))
const schema = generateSchema(parsed.result.blocks[0])
// console.log(schema)
// console.log(util.inspect(Object.keys(schema).length, {showHidden: false, depth: 1}))
await writeFileAsync('./src/reader/cif/schema/mmcif-gen.ts', schema, 'utf8')
return schema
}
......@@ -168,7 +171,7 @@ export async function _dic() {
return runDic(input);
}
// _dic();
_dic();
import Computation from './utils/computation'
const comp = Computation.create(async ctx => {
......
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