diff --git a/src/reader/cif/schema/utils.ts b/src/reader/cif/schema/utils.ts
index 27a5174fa8fcb3a91bf818766867f67545a2ebed..072257addba3f27eae13deb2b03b4042de50684b 100644
--- a/src/reader/cif/schema/utils.ts
+++ b/src/reader/cif/schema/utils.ts
@@ -1,17 +1,16 @@
// 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}`
}
diff --git a/src/script.ts b/src/script.ts
index fa3b8f3b6a018c1654fa76eb047e1531de0b162a..c10a3e1bd579544c51b1f0a0915e20b76315a95f 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -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 => {