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Commit 6629c0b5 authored by Alexander Rose's avatar Alexander Rose
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improved schema generation and moved to apps folder

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with 49 additions and 27 deletions
src/scripts/generate-schema.ts → src/apps/schema-generator/generate-typescript.ts
+ 2
− 2
View file @ 6629c0b5
/** /**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
import * as argparse from 'argparse' import * as argparse from 'argparse'
import * as fs from 'fs' import * as fs from 'fs'
import { generate } from './schema-generation/generate' import { generate } from './util/generate'
function generateSchema (name: string, path: string) { function generateSchema (name: string, path: string) {
const str = fs.readFileSync(path, 'utf8') const str = fs.readFileSync(path, 'utf8')
......
src/scripts/schema-from-mmcif-dic.ts → src/apps/schema-generator/schema-from-mmcif-dic.ts
+ 30
− 14
View file @ 6629c0b5
/** /**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
...@@ -11,9 +11,9 @@ import fetch from 'node-fetch' ...@@ -11,9 +11,9 @@ import fetch from 'node-fetch'
import Csv from 'mol-io/reader/csv/parser' import Csv from 'mol-io/reader/csv/parser'
import CIF from 'mol-io/reader/cif' import CIF from 'mol-io/reader/cif'
import { generateSchema } from './schema-generation/cif-dic' import { generateSchema } from './util/cif-dic'
import { generate } from './schema-generation/generate' import { generate } from './util/generate'
import { Filter, mergeFilters } from './schema-generation/json-schema' import { Filter, mergeFilters } from './util/json-schema'
async function runGenerateSchema(name: string, fieldNamesPath?: string, minCount = 0, typescript = false, out?: string) { async function runGenerateSchema(name: string, fieldNamesPath?: string, minCount = 0, typescript = false, out?: string) {
await ensureMmcifDicAvailable() await ensureMmcifDicAvailable()
...@@ -21,12 +21,21 @@ async function runGenerateSchema(name: string, fieldNamesPath?: string, minCount ...@@ -21,12 +21,21 @@ async function runGenerateSchema(name: string, fieldNamesPath?: string, minCount
const parsed = await comp(); const parsed = await comp();
if (parsed.isError) throw parsed if (parsed.isError) throw parsed
let filter = await getUsageCountsFilter(minCount) console.log(fieldNamesPath, minCount)
// console.log(util.inspect(filter, {showHidden: false, depth: 3}))
if (fieldNamesPath) { let filter: Filter | undefined
filter = mergeFilters(filter, await getFieldNamesFilter(fieldNamesPath)) if (minCount && fieldNamesPath) {
filter = mergeFilters(
await getUsageCountsFilter(minCount),
await getFieldNamesFilter(fieldNamesPath)
)
} else if (minCount) {
filter = await getUsageCountsFilter(minCount)
} else if (fieldNamesPath) {
console.log('MOIN')
filter = await getFieldNamesFilter(fieldNamesPath)
} }
// console.log(util.inspect(filter, {showHidden: false, depth: 3}))
const schema = generateSchema(parsed.result.blocks[0]) const schema = generateSchema(parsed.result.blocks[0])
const output = typescript ? generate(name, schema, filter) : JSON.stringify(schema, undefined, 4) const output = typescript ? generate(name, schema, filter) : JSON.stringify(schema, undefined, 4)
...@@ -49,10 +58,12 @@ async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> { ...@@ -49,10 +58,12 @@ async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
const filter: Filter = {} const filter: Filter = {}
fieldNames.forEach((name, i) => { fieldNames.forEach((name, i) => {
const [ category, field ] = name.substr(1).split('.') const [ category, field ] = name.split('.')
console.log(category, field)
if (!filter[ category ]) filter[ category ] = {} if (!filter[ category ]) filter[ category ] = {}
filter[ category ][ field ] = true filter[ category ][ field ] = true
}) })
console.log(filter)
return filter return filter
} }
...@@ -82,18 +93,22 @@ async function ensureMmcifDicAvailable() { ...@@ -82,18 +93,22 @@ async function ensureMmcifDicAvailable() {
if (FORCE_MMCIF_DOWNLOAD || !fs.existsSync(MMCIF_DIC_PATH)) { if (FORCE_MMCIF_DOWNLOAD || !fs.existsSync(MMCIF_DIC_PATH)) {
console.log('downloading mmcif dic...') console.log('downloading mmcif dic...')
const data = await fetch(MMCIF_DIC_URL) const data = await fetch(MMCIF_DIC_URL)
if (!fs.existsSync(MMCIF_DIC_DIR)){
fs.mkdirSync(MMCIF_DIC_DIR);
}
fs.writeFileSync(MMCIF_DIC_PATH, await data.text()) fs.writeFileSync(MMCIF_DIC_PATH, await data.text())
console.log('done downloading mmcif dic') console.log('done downloading mmcif dic')
} }
} }
const MMCIF_USAGE_COUNTS_PATH = './data/mmcif-usage-counts.txt' const MMCIF_USAGE_COUNTS_PATH = './data/mmcif-usage-counts.txt'
const MMCIF_DIC_PATH = './build/dics/mmcif_pdbx_v50.dic' const MMCIF_DIC_DIR = './build/dics'
const MMCIF_DIC_PATH = `${MMCIF_DIC_DIR}/mmcif_pdbx_v50.dic`
const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic' const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic'
const parser = new argparse.ArgumentParser({ const parser = new argparse.ArgumentParser({
addHelp: true, addHelp: true,
description: 'Create schema from mmcif dictionary' description: 'Create schema from mmcif dictionary (v50, downloaded from wwPDB)'
}); });
parser.addArgument([ '--name', '-n' ], { parser.addArgument([ '--name', '-n' ], {
defaultValue: 'mmCIF', defaultValue: 'mmCIF',
...@@ -107,11 +122,12 @@ parser.addArgument([ '--typescript', '-ts' ], { ...@@ -107,11 +122,12 @@ parser.addArgument([ '--typescript', '-ts' ], {
help: 'Output schema as TypeScript instead of as JSON' help: 'Output schema as TypeScript instead of as JSON'
}); });
parser.addArgument([ '--minFieldUsageCount', '-mc' ], { parser.addArgument([ '--minFieldUsageCount', '-mc' ], {
defaultValue: 1, defaultValue: 0,
type: parseInt,
help: 'Minimum mmcif field usage counts' help: 'Minimum mmcif field usage counts'
}); });
parser.addArgument([ '--fieldNamesPath', '-fn' ], { parser.addArgument([ '--fieldNamesPath', '-fn' ], {
defaultValue: 1, defaultValue: '',
help: 'Field names to include' help: 'Field names to include'
}); });
parser.addArgument([ '--forceMmcifDicDownload', '-f' ], { parser.addArgument([ '--forceMmcifDicDownload', '-f' ], {
......
src/scripts/schema-generation/cif-dic.ts → src/apps/schema-generator/util/cif-dic.ts
+ 2
− 1
View file @ 6629c0b5
/** /**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
...@@ -48,6 +48,7 @@ export function getFieldType (type: string, values?: string[]): Column { ...@@ -48,6 +48,7 @@ export function getFieldType (type: string, values?: string[]): Column {
case 'point_symmetry': case 'point_symmetry':
case 'id_list': case 'id_list':
case '4x3_matrix': case '4x3_matrix':
case '3x4_matrices':
case 'point_group': case 'point_group':
case 'point_group_helical': case 'point_group_helical':
case 'boolean': case 'boolean':
......
src/scripts/schema-generation/generate.ts → src/apps/schema-generator/util/generate.ts
+ 11
− 6
View file @ 6629c0b5
/** /**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
...@@ -7,13 +7,13 @@ ...@@ -7,13 +7,13 @@
import { validate } from './validate' import { validate } from './validate'
import { Database, getTypeAndArgs, Filter } from './json-schema' import { Database, getTypeAndArgs, Filter } from './json-schema'
function header (name: string, importDatabasePath = 'mol-base/collections/database') { function header (name: string, importDatabasePath = 'mol-data/db') {
return `/** return `/**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* Code-generated '${name}' schema file * Code-generated '${name}' schema file
* *
* @author mol-star package (src/scripts/schema-generation/generate) * @author mol-star package (src/apps/schema-generator/generate)
*/ */
import { Database, Column } from '${importDatabasePath}' import { Database, Column } from '${importDatabasePath}'
...@@ -48,6 +48,11 @@ const value: { [k: string]: (...args: any[]) => string } = { ...@@ -48,6 +48,11 @@ const value: { [k: string]: (...args: any[]) => string } = {
} }
} }
const reSafePropertyName = /^[a-zA-Z_$][0-9a-zA-Z_$]*$/
function safePropertyString(name: string) {
return name.match(reSafePropertyName) ? name : `'${name}'`
}
export function generate (name: string, schema: Database, fields?: Filter, importDatabasePath?: string) { export function generate (name: string, schema: Database, fields?: Filter, importDatabasePath?: string) {
const validationResult = validate(schema) const validationResult = validate(schema)
if (validationResult !== true) { if (validationResult !== true) {
...@@ -59,7 +64,7 @@ export function generate (name: string, schema: Database, fields?: Filter, impor ...@@ -59,7 +64,7 @@ export function generate (name: string, schema: Database, fields?: Filter, impor
codeLines.push(`export const ${name}_Schema = {`) codeLines.push(`export const ${name}_Schema = {`)
Object.keys(schema).forEach(table => { Object.keys(schema).forEach(table => {
if (fields && !fields[ table ]) return if (fields && !fields[ table ]) return
codeLines.push(`\t'${table}': {`) codeLines.push(`\t${safePropertyString(table)}: {`)
const columns = schema[ table ] const columns = schema[ table ]
Object.keys(columns).forEach(columnName => { Object.keys(columns).forEach(columnName => {
if (fields && !fields[ table ][ columnName ]) return if (fields && !fields[ table ][ columnName ]) return
...@@ -71,7 +76,7 @@ export function generate (name: string, schema: Database, fields?: Filter, impor ...@@ -71,7 +76,7 @@ export function generate (name: string, schema: Database, fields?: Filter, impor
} else { } else {
typeDef = fieldType typeDef = fieldType
} }
codeLines.push(`\t\t'${columnName}': ${typeDef},`) codeLines.push(`\t\t${safePropertyString(columnName)}: ${typeDef},`)
}) })
codeLines.push('\t},') codeLines.push('\t},')
}) })
......
src/scripts/schema-generation/json-schema.ts → src/apps/schema-generator/util/json-schema.ts
+ 1
− 1
View file @ 6629c0b5
/** /**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
......
src/scripts/schema-generation/validate.ts → src/apps/schema-generator/util/validate.ts
+ 1
− 1
View file @ 6629c0b5
/** /**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
......
src/scripts/validate-schema.ts → src/apps/schema-generator/validate-schema.ts
+ 2
− 2
View file @ 6629c0b5
/** /**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
import * as argparse from 'argparse' import * as argparse from 'argparse'
import * as fs from 'fs' import * as fs from 'fs'
import { validate } from './schema-generation/validate' import { validate } from './util/validate'
function runValidateSchema (path: string) { function runValidateSchema (path: string) {
const str = fs.readFileSync(path, 'utf8') const str = fs.readFileSync(path, 'utf8')
......
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