diff --git a/package-lock.json b/package-lock.json
index e4144a016c1a7ebdb30a33ef67553d6cf351de40..a182e4106aefca0f6398e10d764ad3072ddcab85 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index a6d47ae62eacfae1ed86cf3a366589a0d5b6e663..c0338722ff1886873e60d13c82fad01e9fc1da23 100644
--- a/package.json
+++ b/package.json
@@ -88,54 +88,54 @@
],
"license": "MIT",
"devDependencies": {
- "@graphql-codegen/add": "^2.0.2",
- "@graphql-codegen/cli": "^1.19.4",
- "@graphql-codegen/time": "^2.0.2",
- "@graphql-codegen/typescript": "^1.19.0",
- "@graphql-codegen/typescript-graphql-files-modules": "^1.18.1",
- "@graphql-codegen/typescript-graphql-request": "^2.0.3",
- "@graphql-codegen/typescript-operations": "^1.17.12",
- "@types/cors": "^2.8.8",
- "@typescript-eslint/eslint-plugin": "^4.9.1",
- "@typescript-eslint/parser": "^4.9.1",
+ "@graphql-codegen/add": "^3.1.0",
+ "@graphql-codegen/cli": "^2.2.0",
+ "@graphql-codegen/time": "^3.1.0",
+ "@graphql-codegen/typescript": "^2.2.2",
+ "@graphql-codegen/typescript-graphql-files-modules": "^2.1.0",
+ "@graphql-codegen/typescript-graphql-request": "^4.1.4",
+ "@graphql-codegen/typescript-operations": "^2.1.4",
+ "@types/cors": "^2.8.12",
+ "@typescript-eslint/eslint-plugin": "^4.31.0",
+ "@typescript-eslint/parser": "^4.31.0",
"benchmark": "^2.1.4",
- "concurrently": "^5.3.0",
- "cpx2": "^3.0.0",
+ "concurrently": "^6.2.1",
+ "cpx2": "^3.0.2",
"crypto-browserify": "^3.12.0",
- "css-loader": "^5.0.1",
- "eslint": "^7.15.0",
+ "css-loader": "^6.2.0",
+ "eslint": "^7.32.0",
"extra-watch-webpack-plugin": "^1.0.3",
"file-loader": "^6.2.0",
- "fs-extra": "^9.0.1",
- "graphql": "^15.4.0",
- "http-server": "^0.12.3",
- "jest": "^26.6.3",
- "mini-css-extract-plugin": "^1.3.2",
- "node-sass": "^6.0.0",
+ "fs-extra": "^10.0.0",
+ "graphql": "^15.5.3",
+ "http-server": "^13.0.1",
+ "jest": "^27.1.1",
+ "mini-css-extract-plugin": "^2.3.0",
+ "node-sass": "^6.0.1",
"path-browserify": "^1.0.1",
"raw-loader": "^4.0.2",
- "sass-loader": "^11.1.1",
- "simple-git": "^2.25.0",
+ "sass-loader": "^12.1.0",
+ "simple-git": "^2.45.1",
"stream-browserify": "^3.0.0",
- "style-loader": "^2.0.0",
- "ts-jest": "^26.4.4",
- "typescript": "^4.4.2",
- "webpack": "^5.37.1",
- "webpack-cli": "^4.7.0",
+ "style-loader": "^3.2.1",
+ "ts-jest": "^27.0.5",
+ "typescript": "^4.4.3",
+ "webpack": "^5.52.1",
+ "webpack-cli": "^4.8.0",
"webpack-version-file-plugin": "^0.4.0"
},
"dependencies": {
- "@types/argparse": "^1.0.38",
- "@types/benchmark": "^2.1.0",
- "@types/compression": "1.7.0",
- "@types/express": "^4.17.9",
- "@types/jest": "^26.0.18",
- "@types/node": "^14.14.11",
- "@types/node-fetch": "^2.5.7",
- "@types/react": "^17.0.0",
- "@types/react-dom": "^17.0.0",
- "@types/swagger-ui-dist": "3.30.0",
- "argparse": "^1.0.10",
+ "@types/argparse": "^2.0.10",
+ "@types/benchmark": "^2.1.1",
+ "@types/compression": "1.7.2",
+ "@types/express": "^4.17.13",
+ "@types/jest": "^27.0.1",
+ "@types/node": "^16.9.1",
+ "@types/node-fetch": "^2.5.12",
+ "@types/react": "^17.0.20",
+ "@types/react-dom": "^17.0.9",
+ "@types/swagger-ui-dist": "3.30.1",
+ "argparse": "^2.0.1",
"body-parser": "^1.19.0",
"compression": "^1.7.4",
"cors": "^2.8.5",
@@ -143,13 +143,13 @@
"h264-mp4-encoder": "^1.0.12",
"immer": "^9.0.6",
"immutable": "^3.8.2",
- "node-fetch": "^2.6.1",
+ "node-fetch": "^2.6.2",
"react": "^17.0.2",
"react-dom": "^17.0.2",
"rxjs": "^7.3.0",
- "swagger-ui-dist": "^3.37.2",
+ "swagger-ui-dist": "^3.52.1",
"tslib": "^2.3.1",
- "util.promisify": "^1.0.1",
- "xhr2": "^0.2.0"
+ "util.promisify": "^1.1.1",
+ "xhr2": "^0.2.1"
}
}
diff --git a/src/cli/chem-comp-dict/create-ions.ts b/src/cli/chem-comp-dict/create-ions.ts
index d2c5a27f0ef345824d75a50d0bf30d0919d52d75..2c0ed76b46b1b25334100e58a9539ea02a8ccabc 100644
--- a/src/cli/chem-comp-dict/create-ions.ts
+++ b/src/cli/chem-comp-dict/create-ions.ts
@@ -54,20 +54,20 @@ async function run(out: string, forceDownload = false) {
}
const parser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: 'Extract and save IonNames from CCD.'
});
-parser.addArgument('out', {
+parser.add_argument('out', {
help: 'Generated file output path.'
});
-parser.addArgument([ '--forceDownload', '-f' ], {
- action: 'storeTrue',
+parser.add_argument('--forceDownload', '-f', {
+ action: 'store_true',
help: 'Force download of CCD and PVCD.'
});
interface Args {
out: string,
forceDownload?: boolean,
}
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
run(args.out, args.forceDownload);
diff --git a/src/cli/chem-comp-dict/create-table.ts b/src/cli/chem-comp-dict/create-table.ts
index f20af5933515312cce4663262436f1de07e55e8b..03da1a3ee772f5e1a890329456f77bea9ca4c76b 100644
--- a/src/cli/chem-comp-dict/create-table.ts
+++ b/src/cli/chem-comp-dict/create-table.ts
@@ -265,21 +265,21 @@ const CCB_TABLE_NAME = 'CHEM_COMP_BONDS';
const CCA_TABLE_NAME = 'CHEM_COMP_ATOMS';
const parser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: 'Create a cif file with one big table of all chem_comp_bond entries from the CCD and PVCD.'
});
-parser.addArgument('out', {
+parser.add_argument('out', {
help: 'Generated file output path.'
});
-parser.addArgument([ '--forceDownload', '-f' ], {
- action: 'storeTrue',
+parser.add_argument('--forceDownload', '-f', {
+ action: 'store_true',
help: 'Force download of CCD and PVCD.'
});
-parser.addArgument([ '--binary', '-b' ], {
- action: 'storeTrue',
+parser.add_argument('--binary', '-b', {
+ action: 'store_true',
help: 'Output as BinaryCIF.'
});
-parser.addArgument(['--ccaOut', '-a'], {
+parser.add_argument('--ccaOut', '-a', {
help: 'Optional generated file output path for chem_comp_atom data.',
required: false
});
@@ -289,6 +289,6 @@ interface Args {
binary?: boolean,
ccaOut?: string
}
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
run(args.out, args.binary, args.forceDownload, args.ccaOut);
diff --git a/src/cli/cif2bcif/index.ts b/src/cli/cif2bcif/index.ts
index bcf5dbab2b670f14b5f3597892931fefcb80b2b5..5dcd39af50cfa70dd78abb516e8e1c9c86e7ccc1 100644
--- a/src/cli/cif2bcif/index.ts
+++ b/src/cli/cif2bcif/index.ts
@@ -37,20 +37,20 @@ function run(args: Args) {
}
const parser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: 'Convert any CIF file to a BCIF file'
});
-parser.addArgument([ 'src' ], {
+parser.add_argument('src', {
help: 'Source CIF path'
});
-parser.addArgument([ 'out' ], {
+parser.add_argument('out', {
help: 'Output BCIF path'
});
-parser.addArgument([ '-c', '--config' ], {
+parser.add_argument('-c', '--config', {
help: 'Optional encoding strategy/precision config path',
required: false
});
-parser.addArgument([ '-f', '--filter' ], {
+parser.add_argument('-f', '--filter', {
help: 'Optional filter whitelist/blacklist path',
required: false
});
@@ -61,7 +61,7 @@ interface Args {
config?: string
filter?: string
}
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
if (args) {
run(args);
diff --git a/src/cli/cifschema/index.ts b/src/cli/cifschema/index.ts
index d3846e7a34466ed4d374e03d130096efd8222811..bfcdf04f719057032a2ff2633903335d38b083bf 100644
--- a/src/cli/cifschema/index.ts
+++ b/src/cli/cifschema/index.ts
@@ -178,44 +178,44 @@ const CIF_CORE_ATTR_PATH = `${DIC_DIR}/templ_attr.cif`;
const CIF_CORE_ATTR_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_attr.cif';
const parser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: 'Create schema from mmcif dictionary (v50 plus IHM and entity_branch extensions, downloaded from wwPDB)'
});
-parser.addArgument([ '--preset', '-p' ], {
- defaultValue: '',
+parser.add_argument('--preset', '-p', {
+ default: '',
choices: ['', 'mmCIF', 'CCD', 'BIRD', 'CifCore'],
help: 'Preset name'
});
-parser.addArgument([ '--name', '-n' ], {
- defaultValue: '',
+parser.add_argument('--name', '-n', {
+ default: '',
help: 'Schema name'
});
-parser.addArgument([ '--out', '-o' ], {
+parser.add_argument('--out', '-o', {
help: 'Generated schema output path, if not given printed to stdout'
});
-parser.addArgument([ '--targetFormat', '-tf' ], {
- defaultValue: 'typescript-molstar',
+parser.add_argument('--targetFormat', '-tf', {
+ default: 'typescript-molstar',
choices: ['typescript-molstar', 'json-internal'],
help: 'Target format'
});
-parser.addArgument([ '--dicPath', '-d' ], {
- defaultValue: '',
+parser.add_argument('--dicPath', '-d', {
+ default: '',
help: 'Path to dictionary'
});
-parser.addArgument([ '--fieldNamesPath', '-fn' ], {
- defaultValue: '',
+parser.add_argument('--fieldNamesPath', '-fn', {
+ default: '',
help: 'Field names to include'
});
-parser.addArgument([ '--forceDicDownload', '-f' ], {
- action: 'storeTrue',
+parser.add_argument('--forceDicDownload', '-f', {
+ action: 'store_true',
help: 'Force download of dictionaries'
});
-parser.addArgument([ '--moldataImportPath', '-mip' ], {
- defaultValue: 'molstar/lib/mol-data',
+parser.add_argument('--moldataImportPath', '-mip', {
+ default: 'molstar/lib/mol-data',
help: 'mol-data import path (for typescript target only)'
});
-parser.addArgument([ '--addAliases', '-aa' ], {
- action: 'storeTrue',
+parser.add_argument('--addAliases', '-aa', {
+ action: 'store_true',
help: 'Add field name/path aliases'
});
interface Args {
@@ -230,7 +230,7 @@ interface Args {
moldataImportPath: string
addAliases: boolean
}
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
const FORCE_DIC_DOWNLOAD = args.forceDicDownload;
diff --git a/src/cli/lipid-params/index.ts b/src/cli/lipid-params/index.ts
index d0895a12e7b938bc7753ab5e21cb50b2dbe43790..ee1bf4ad58c4b24ed613c86ce2a47a8dfc403a6a 100644
--- a/src/cli/lipid-params/index.ts
+++ b/src/cli/lipid-params/index.ts
@@ -70,21 +70,21 @@ export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g,
}
const parser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: 'Create lipid params (from martini lipids itp)'
});
-parser.addArgument([ '--out', '-o' ], {
+parser.add_argument('--out', '-o', {
help: 'Generated lipid params output path, if not given printed to stdout'
});
-parser.addArgument([ '--forceDownload', '-f' ], {
- action: 'storeTrue',
+parser.add_argument('--forceDownload', '-f', {
+ action: 'store_true',
help: 'Force download of martini lipids itp'
});
interface Args {
out: string
forceDownload: boolean
}
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
const FORCE_DOWNLOAD = args.forceDownload;
diff --git a/src/cli/structure-info/model.ts b/src/cli/structure-info/model.ts
index c909b9d91a2871420e8693390c7881b01e94e661..d42c67187e2e8a256b180fd6a5e5103a0601d4c4 100644
--- a/src/cli/structure-info/model.ts
+++ b/src/cli/structure-info/model.ts
@@ -230,21 +230,21 @@ async function runFile(filename: string, args: Args) {
}
const parser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: 'Print info about a structure, mainly to test and showcase the mol-model module'
});
-parser.addArgument(['--download', '-d'], { help: 'Pdb entry id' });
-parser.addArgument(['--file', '-f'], { help: 'filename' });
-
-parser.addArgument(['--models'], { help: 'print models info', action: 'storeTrue' });
-parser.addArgument(['--seq'], { help: 'print sequence', action: 'storeTrue' });
-parser.addArgument(['--units'], { help: 'print units', action: 'storeTrue' });
-parser.addArgument(['--sym'], { help: 'print symmetry', action: 'storeTrue' });
-parser.addArgument(['--rings'], { help: 'print rings', action: 'storeTrue' });
-parser.addArgument(['--intraBonds'], { help: 'print intra unit bonds', action: 'storeTrue' });
-parser.addArgument(['--interBonds'], { help: 'print inter unit bonds', action: 'storeTrue' });
-parser.addArgument(['--mod'], { help: 'print modified residues', action: 'storeTrue' });
-parser.addArgument(['--sec'], { help: 'print secoundary structure', action: 'storeTrue' });
+parser.add_argument('--download', '-d', { help: 'Pdb entry id' });
+parser.add_argument('--file', '-f', { help: 'filename' });
+
+parser.add_argument('--models', { help: 'print models info', action: 'store_true' });
+parser.add_argument('--seq', { help: 'print sequence', action: 'store_true' });
+parser.add_argument('--units', { help: 'print units', action: 'store_true' });
+parser.add_argument('--sym', { help: 'print symmetry', action: 'store_true' });
+parser.add_argument('--rings', { help: 'print rings', action: 'store_true' });
+parser.add_argument('--intraBonds', { help: 'print intra unit bonds', action: 'store_true' });
+parser.add_argument('--interBonds', { help: 'print inter unit bonds', action: 'store_true' });
+parser.add_argument('--mod', { help: 'print modified residues', action: 'store_true' });
+parser.add_argument('--sec', { help: 'print secoundary structure', action: 'store_true' });
interface Args {
download?: string,
file?: string,
@@ -260,7 +260,7 @@ interface Args {
mod?: boolean,
sec?: boolean,
}
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
if (args.download) runDL(args.download, args);
else if (args.file) runFile(args.file, args);
diff --git a/src/cli/structure-info/volume.ts b/src/cli/structure-info/volume.ts
index 27b13ba0ef4d3da9acaa077a5d8e825655f01f9b..4e3ad62cd2a8887a8a631bc8ed9f9109d658c57d 100644
--- a/src/cli/structure-info/volume.ts
+++ b/src/cli/structure-info/volume.ts
@@ -75,13 +75,13 @@ async function run(url: string, meshFilename: string) {
}
const parser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: 'Info about VolumeData from mol-model module'
});
-parser.addArgument([ '--emdb', '-e' ], {
+parser.add_argument('--emdb', '-e', {
help: 'EMDB id, for example 8116',
});
-parser.addArgument([ '--mesh' ], {
+parser.add_argument('--mesh', {
help: 'Mesh filename',
required: true
});
@@ -89,6 +89,6 @@ interface Args {
emdb?: string,
mesh: string
}
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
run(`https://ds.litemol.org/em/emd-${args.emdb}/cell?detail=4`, args.mesh);
\ No newline at end of file
diff --git a/src/extensions/rcsb/graphql/codegen.yml b/src/extensions/rcsb/graphql/codegen.yml
index a6d7ebd1720ee984e7f136f927ce03c6c69d403b..d5d458bde1d80705a88f1d8b9b2717cfeabb7d34 100644
--- a/src/extensions/rcsb/graphql/codegen.yml
+++ b/src/extensions/rcsb/graphql/codegen.yml
@@ -1,12 +1,13 @@
schema: https://data.rcsb.org/graphql
documents: './src/extensions/rcsb/graphql/symmetry.gql.ts'
generates:
- './src/extensions/rcsb/graphql/types.ts':
- plugins:
- - add: '/* eslint-disable */'
- - time
- - typescript
- - typescript-operations
- config:
- immutableTypes: true
- skipTypename: true
\ No newline at end of file
+ './src/extensions/rcsb/graphql/types.ts':
+ plugins:
+ - add:
+ content: '/* eslint-disable */'
+ - time
+ - typescript
+ - typescript-operations
+ config:
+ immutableTypes: true
+ skipTypename: true
\ No newline at end of file
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index 4231f8bda35836acdc37d334db1f30b9478fdbdc..32e9cff781369ef5341d7d81d9d39670cf312100 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -68,7 +68,7 @@ export async function testQ() {
const { structure } = await getModelsAndStructure(frame);
const model = structure.models[0];
- const rawData = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${model.entryId.toLowerCase()}`, { timeout: 1500 });
+ const rawData = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${model.entryId.toLowerCase()}`);
const data = StructureQualityReport.fromJson(model, await rawData.json());
StructureQualityReportProvider.set(model, { serverUrl: '' }, data);
diff --git a/src/servers/model/config.ts b/src/servers/model/config.ts
index 7de2563951883e5cd502caefcda147d16a357d6b..0cfd9d6b42edfd409a408707d0aef441728715e5 100644
--- a/src/servers/model/config.ts
+++ b/src/servers/model/config.ts
@@ -117,65 +117,65 @@ export let mapSourceAndIdToFilename: (source: string, id: string) => [string, Mo
};
function addServerArgs(parser: argparse.ArgumentParser) {
- parser.addArgument([ '--apiPrefix' ], {
- defaultValue: DefaultModelServerConfig.apiPrefix,
+ parser.add_argument('--apiPrefix', {
+ default: DefaultModelServerConfig.apiPrefix,
metavar: 'PREFIX',
help: `Specify the prefix of the API, i.e. <host>/<apiPrefix>/<API queries>`
});
- parser.addArgument([ '--defaultPort' ], {
- defaultValue: DefaultModelServerConfig.defaultPort,
+ parser.add_argument('--defaultPort', {
+ default: DefaultModelServerConfig.defaultPort,
metavar: 'PORT',
type: 'int',
help: `Specify the port the server is running on`
});
- parser.addArgument([ '--cacheMaxSizeInBytes' ], {
- defaultValue: DefaultModelServerConfig.cacheMaxSizeInBytes,
+ parser.add_argument('--cacheMaxSizeInBytes', {
+ default: DefaultModelServerConfig.cacheMaxSizeInBytes,
metavar: 'CACHE_SIZE',
type: 'int',
help: `0 for off.`
});
- parser.addArgument([ '--cacheEntryTimeoutMs' ], {
- defaultValue: DefaultModelServerConfig.cacheEntryTimeoutMs,
+ parser.add_argument('--cacheEntryTimeoutMs', {
+ default: DefaultModelServerConfig.cacheEntryTimeoutMs,
metavar: 'CACHE_TIMEOUT',
type: 'int',
help: `Specify in ms how long to keep entries in cache.`
});
- parser.addArgument([ '--requestTimeoutMs' ], {
- defaultValue: DefaultModelServerConfig.requestTimeoutMs,
+ parser.add_argument('--requestTimeoutMs', {
+ default: DefaultModelServerConfig.requestTimeoutMs,
metavar: 'REQUEST_TIMEOUT',
type: 'int',
help: `The maximum number of ms the server spends on a request.`
});
- parser.addArgument([ '--queryTimeoutMs' ], {
- defaultValue: DefaultModelServerConfig.queryTimeoutMs,
+ parser.add_argument('--queryTimeoutMs', {
+ default: DefaultModelServerConfig.queryTimeoutMs,
metavar: 'QUERY_TIMEOUT',
type: 'int',
help: `The maximum time the server dedicates to executing a query in ms.\nDoes not include the time it takes to read and export the data.`
});
- parser.addArgument([ '--shutdownTimeoutMinutes' ], {
- defaultValue: DefaultModelServerConfig.shutdownTimeoutMinutes,
+ parser.add_argument('--shutdownTimeoutMinutes', {
+ default: DefaultModelServerConfig.shutdownTimeoutMinutes,
metavar: 'TIME',
type: 'int',
help: `0 for off, server will shut down after this amount of minutes.`
});
- parser.addArgument([ '--shutdownTimeoutVarianceMinutes' ], {
- defaultValue: DefaultModelServerConfig.shutdownTimeoutVarianceMinutes,
+ parser.add_argument('--shutdownTimeoutVarianceMinutes', {
+ default: DefaultModelServerConfig.shutdownTimeoutVarianceMinutes,
metavar: 'VARIANCE',
type: 'int',
help: `modifies the shutdown timer by +/- timeoutVarianceMinutes (to avoid multiple instances shutting at the same time)`
});
- parser.addArgument([ '--maxQueryManyQueries' ], {
- defaultValue: DefaultModelServerConfig.maxQueryManyQueries,
+ parser.add_argument('--maxQueryManyQueries', {
+ default: DefaultModelServerConfig.maxQueryManyQueries,
metavar: 'QUERY_MANY_LIMIT',
type: 'int',
help: `maximum number of queries allowed by the query-many at a time`
});
- parser.addArgument([ '--defaultSource' ], {
- defaultValue: DefaultModelServerConfig.defaultSource,
+ parser.add_argument('--defaultSource', {
+ default: DefaultModelServerConfig.defaultSource,
metavar: 'DEFAULT_SOURCE',
help: `modifies which 'sourceMap' source to use by default`
});
- parser.addArgument([ '--sourceMap' ], {
+ parser.add_argument('--sourceMap', {
nargs: 2,
action: 'append',
metavar: ['SOURCE', 'PATH'] as any,
@@ -188,7 +188,7 @@ function addServerArgs(parser: argparse.ArgumentParser) {
`Supported formats: ${ModelServerFetchFormats.join(', ')}`
].join('\n'),
});
- parser.addArgument([ '--sourceMapUrl' ], {
+ parser.add_argument('--sourceMapUrl', {
nargs: 3,
action: 'append',
metavar: ['SOURCE', 'PATH', 'SOURCE_MAP_FORMAT'] as any,
@@ -224,15 +224,15 @@ interface ServerJsonConfig {
}
function addJsonConfigArgs(parser: argparse.ArgumentParser) {
- parser.addArgument(['--cfg'], {
+ parser.add_argument('--cfg', {
help: [
'JSON config file path',
'If a property is not specified, cmd line param/OS variable/default value are used.'
].join('\n'),
required: false
});
- parser.addArgument(['--printCfg'], { help: 'Print current config for validation and exit.', required: false, nargs: 0 });
- parser.addArgument(['--cfgTemplate'], { help: 'Prints default JSON config template to be modified and exits.', required: false, nargs: 0 });
+ parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, nargs: 0 });
+ parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, nargs: 0 });
}
function setConfig(config: ModelServerConfig) {
@@ -260,13 +260,12 @@ function validateConfigAndSetupSourceMap() {
function parseConfigArguments() {
const parser = new argparse.ArgumentParser({
- version: VERSION,
- addHelp: true,
+ add_help: true,
description: `ModelServer ${VERSION}, (c) 2018-2020, Mol* contributors`
});
addJsonConfigArgs(parser);
addServerArgs(parser);
- return parser.parseArgs() as ModelServerConfig & ServerJsonConfig;
+ return parser.parse_args() as ModelServerConfig & ServerJsonConfig;
}
export function configureServer() {
diff --git a/src/servers/model/preprocess.ts b/src/servers/model/preprocess.ts
index 6da907e4a6083cd40f2e0ece8e2b43e5ea7c93a3..9a4b4efd9904df8c1d198261b85812659ead4af3 100644
--- a/src/servers/model/preprocess.ts
+++ b/src/servers/model/preprocess.ts
@@ -5,10 +5,10 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as cluster from 'cluster';
+import cluster from 'cluster';
import { runChild } from './preprocess/parallel';
-if (cluster.isMaster) {
+if (cluster.isPrimary) {
require('./preprocess/master');
} else {
runChild();
diff --git a/src/servers/model/preprocess/master.ts b/src/servers/model/preprocess/master.ts
index 687b9fe41931fbc50c7bbd61af8d11c2b857944d..d16875bd7308c0e338dc93053a7932e8c9165adf 100644
--- a/src/servers/model/preprocess/master.ts
+++ b/src/servers/model/preprocess/master.ts
@@ -29,18 +29,18 @@ function description() {
}
const cmdParser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: description()
});
-cmdParser.addArgument(['--input', '-i'], { help: 'Input filename', required: false });
-cmdParser.addArgument(['--outCIF', '-oc'], { help: 'Output CIF filename', required: false });
-cmdParser.addArgument(['--outBCIF', '-ob'], { help: 'Output BinaryCIF filename', required: false });
+cmdParser.add_argument('--input', '-i', { help: 'Input filename', required: false });
+cmdParser.add_argument('--outCIF', '-oc', { help: 'Output CIF filename', required: false });
+cmdParser.add_argument('--outBCIF', '-ob', { help: 'Output BinaryCIF filename', required: false });
// TODO: add back? cmdParser.addArgument(['--bulk', '-b'], { help: 'Bulk JSON ({ numProcesses?: number, entries: { source: string, cif?: string, bcif?: string }[] })', required: false });
-cmdParser.addArgument(['--cfg', '-c'], { help: 'Config file path', required: false });
-cmdParser.addArgument(['--folderIn', '-fin'], { help: 'Convert folder', required: false });
-cmdParser.addArgument(['--folderOutCIF', '-foc'], { help: 'Convert folder text output', required: false });
-cmdParser.addArgument(['--folderOutBCIF', '-fob'], { help: 'Convert folder binary output', required: false });
-cmdParser.addArgument(['--folderNumProcesses', '-fp'], { help: 'Convert folder num processes', required: false });
+cmdParser.add_argument('--cfg', '-c', { help: 'Config file path', required: false });
+cmdParser.add_argument('--folderIn', '-fin', { help: 'Convert folder', required: false });
+cmdParser.add_argument('--folderOutCIF', '-foc', { help: 'Convert folder text output', required: false });
+cmdParser.add_argument('--folderOutBCIF', '-fob', { help: 'Convert folder binary output', required: false });
+cmdParser.add_argument('--folderNumProcesses', '-fp', { help: 'Convert folder num processes', required: false });
interface CmdArgs {
// bulk?: string,
@@ -61,10 +61,10 @@ export interface PreprocessConfig {
customProperties?: ModelPropertyProviderConfig | string
}
-const cmdArgs = cmdParser.parseArgs() as CmdArgs;
+const cmdArgs = cmdParser.parse_args() as CmdArgs;
if (Object.keys(cmdArgs).filter(k => (cmdArgs as any)[k] !== null).length === 0 || typeof cmdArgs.help !== 'undefined') {
- cmdParser.printHelp();
+ cmdParser.print_help();
process.exit(0);
}
diff --git a/src/servers/model/preprocess/parallel.ts b/src/servers/model/preprocess/parallel.ts
index 399e06c920378a7b76d4df3abaaa207f46960d4d..e20e665b7b0b691d8ac9fb60be2bb8ae05e64a7d 100644
--- a/src/servers/model/preprocess/parallel.ts
+++ b/src/servers/model/preprocess/parallel.ts
@@ -5,7 +5,7 @@
*/
import * as path from 'path';
-import * as cluster from 'cluster';
+import cluster from 'cluster';
import { now } from '../../../mol-util/now';
import { PerformanceMonitor } from '../../../mol-util/performance-monitor';
import { preprocessFile } from './preprocess';
diff --git a/src/servers/model/properties/providers/pdbe.ts b/src/servers/model/properties/providers/pdbe.ts
index 09f818bf3c3c352959955bf1ec95fa281b42d1ed..adaf0a7ff2a73ff98bad88ddf2f7af3b3ea4dd26 100644
--- a/src/servers/model/properties/providers/pdbe.ts
+++ b/src/servers/model/properties/providers/pdbe.ts
@@ -77,12 +77,12 @@ function apiQueryProvider(urlPrefix: string, cache: any) {
const rawData = await fetchRetry(`${urlPrefix}/${model.entryId.toLowerCase()}`, 1500, 5);
// TODO: is this ok?
if (rawData.status !== 200) return { };
- const json = (await rawData.json())[model.entryId.toLowerCase()] || { };
+ const json = ((await rawData.json()) as any)[model.entryId.toLowerCase()] || { };
cache[cacheKey] = json;
return json;
} catch (e) {
// TODO: handle better
- ConsoleLogger.warn('Props', `Count not retrieve prop @${`${urlPrefix}/${model.entryId.toLowerCase()}`}`);
+ ConsoleLogger.warn('Props', `Could not retrieve prop @${`${urlPrefix}/${model.entryId.toLowerCase()}`}`);
return { };
}
};
diff --git a/src/servers/model/utils/fetch-props-pdbe.ts b/src/servers/model/utils/fetch-props-pdbe.ts
index a08094e07d2e51ab6eca43011b231f2e254ace3e..2da0804507c30f23cceea224e612b6d7265ebe0e 100644
--- a/src/servers/model/utils/fetch-props-pdbe.ts
+++ b/src/servers/model/utils/fetch-props-pdbe.ts
@@ -13,19 +13,19 @@ import { now } from '../../../mol-util/now';
import { PerformanceMonitor } from '../../../mol-util/performance-monitor';
const cmdParser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: 'Download JSON data from PDBe API'
});
-cmdParser.addArgument(['--in'], { help: 'Input folder', required: true });
-cmdParser.addArgument(['--out'], { help: 'Output folder', required: true });
+cmdParser.add_argument('--in', { help: 'Input folder', required: true });
+cmdParser.add_argument('--out', { help: 'Output folder', required: true });
interface CmdArgs {
in: string,
out: string
}
-const cmdArgs = cmdParser.parseArgs() as CmdArgs;
+const cmdArgs = cmdParser.parse_args() as CmdArgs;
function getPDBid(name: string) {
let idx = name.indexOf('_');
@@ -73,7 +73,7 @@ async function process() {
for (let ee of e.entries) {
const query = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${ee}`);
try {
- if (query.status === 200) data[ee] = (await query.json())[ee] || { };
+ if (query.status === 200) data[ee] = ((await query.json()) as any)[ee] || { };
else console.error(ee, query.status);
} catch (e) {
console.error(ee, '' + e);
diff --git a/src/servers/model/utils/fetch-retry.ts b/src/servers/model/utils/fetch-retry.ts
index 4ce146bb6bc50ad9987cbe1d86084f0bdb004827..9ba80b1121c6b1cfdd531c3520c112d15cb1ffe6 100644
--- a/src/servers/model/utils/fetch-retry.ts
+++ b/src/servers/model/utils/fetch-retry.ts
@@ -17,15 +17,16 @@ function isRetriableNetworkError(error: any) {
}
export async function fetchRetry(url: string, timeout: number, retryCount: number, onRetry?: () => void): Promise<Response> {
- const result = await retryIf(() => fetch(url, { timeout }), {
- retryThenIf: r => r.status === 408 /** timeout */ || r.status === 429 /** too mant requests */ || (r.status >= 500 && r.status < 600),
+ const controller = new AbortController();
+ const id = setTimeout(() => controller.abort(), timeout);
+ const result = await retryIf(() => fetch(url, { signal: controller.signal }), {
+ retryThenIf: r => r.status === 408 /** timeout */ || r.status === 429 /** too many requests */ || (r.status >= 500 && r.status < 600),
// TODO test retryCatchIf
retryCatchIf: e => isRetriableNetworkError(e),
onRetry,
retryCount
});
+ clearTimeout(id);
return result;
- // if (result.status >= 200 && result.status < 300) return result;
- // throw new Error(result.statusText);
}
diff --git a/src/servers/plugin-state/config.ts b/src/servers/plugin-state/config.ts
index 38ecd7667bf88590647b486621ff1d1a0d39770b..e89dbefbf12add0e5f08313d3b8329e6dfcfc935 100644
--- a/src/servers/plugin-state/config.ts
+++ b/src/servers/plugin-state/config.ts
@@ -15,14 +15,14 @@ export interface Config {
export function getConfig() {
const cmdParser = new argparse.ArgumentParser({
- addHelp: true
+ add_help: true
});
- cmdParser.addArgument(['--working-folder'], { help: 'Working forlder path.', required: true });
- cmdParser.addArgument(['--port'], { help: 'Server port. Altenatively use ENV variable PORT.', type: 'int', required: false });
- cmdParser.addArgument(['--api-prefix'], { help: 'Server API prefix.', defaultValue: '', required: false });
- cmdParser.addArgument(['--max-states'], { help: 'Maxinum number of states that could be saved.', defaultValue: 40, type: 'int', required: false });
+ cmdParser.add_argument('--working-folder', { help: 'Working forlder path.', required: true });
+ cmdParser.add_argument('--port', { help: 'Server port. Altenatively use ENV variable PORT.', type: 'int', required: false });
+ cmdParser.add_argument('--api-prefix', { help: 'Server API prefix.', default: '', required: false });
+ cmdParser.add_argument('--max-states', { help: 'Maxinum number of states that could be saved.', default: 40, type: 'int', required: false });
- const config = cmdParser.parseArgs() as Config;
+ const config = cmdParser.parse_args() as Config;
if (!config.port) config.port = process.env.port || 1339;
return config;
}
diff --git a/src/servers/volume/config.ts b/src/servers/volume/config.ts
index b1ac9db61a63b6cb92b46253d432579a845fe8c1..53d247d7205284c441f20ba1eef93fa728c6f69c 100644
--- a/src/servers/volume/config.ts
+++ b/src/servers/volume/config.ts
@@ -7,7 +7,7 @@
import * as argparse from 'argparse';
import { ObjectKeys } from '../../mol-util/type-helpers';
-import { VOLUME_SERVER_HEADER, VOLUME_SERVER_VERSION } from './server/version';
+import { VOLUME_SERVER_HEADER } from './server/version';
import * as fs from 'fs';
const DefaultServerConfig = {
@@ -19,22 +19,22 @@ const DefaultServerConfig = {
};
function addLimitsArgs(parser: argparse.ArgumentParser) {
- parser.addArgument([ '--maxRequestBlockCount' ], {
- defaultValue: DefaultLimitsConfig.maxRequestBlockCount,
+ parser.add_argument('--maxRequestBlockCount', {
+ default: DefaultLimitsConfig.maxRequestBlockCount,
metavar: 'COUNT',
help: `Maximum number of blocks that could be read in 1 query.
This is somewhat tied to the maxOutputSizeInVoxelCountByPrecisionLevel
in that the <maximum number of voxel> = maxRequestBlockCount * <block size>^3.
The default block size is 96 which corresponds to 28,311,552 voxels with 32 max blocks.`
});
- parser.addArgument([ '--maxFractionalBoxVolume' ], {
- defaultValue: DefaultLimitsConfig.maxFractionalBoxVolume,
+ parser.add_argument('--maxFractionalBoxVolume', {
+ default: DefaultLimitsConfig.maxFractionalBoxVolume,
metavar: 'VOLUME',
help: `The maximum fractional volume of the query box (to prevent queries that are too big).`
});
- parser.addArgument([ '--maxOutputSizeInVoxelCountByPrecisionLevel' ], {
+ parser.add_argument('--maxOutputSizeInVoxelCountByPrecisionLevel', {
nargs: '+',
- defaultValue: DefaultLimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel,
+ default: DefaultLimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel,
metavar: 'LEVEL',
help: `What is the (approximate) maximum desired size in voxel count by precision level
Rule of thumb: <response gzipped size> in [<voxel count> / 8, <voxel count> / 4].
@@ -43,31 +43,31 @@ The maximum number of voxels is tied to maxRequestBlockCount.`
}
function addServerArgs(parser: argparse.ArgumentParser) {
- parser.addArgument([ '--apiPrefix' ], {
- defaultValue: DefaultServerConfig.apiPrefix,
+ parser.add_argument('--apiPrefix', {
+ default: DefaultServerConfig.apiPrefix,
metavar: 'PREFIX',
help: `Specify the prefix of the API, i.e. <host>/<apiPrefix>/<API queries>`
});
- parser.addArgument([ '--defaultPort' ], {
- defaultValue: DefaultServerConfig.defaultPort,
+ parser.add_argument('--defaultPort', {
+ default: DefaultServerConfig.defaultPort,
metavar: 'PORT',
type: 'int',
help: `Specify the port the server is running on`
});
- parser.addArgument([ '--shutdownTimeoutMinutes' ], {
- defaultValue: DefaultServerConfig.shutdownTimeoutMinutes,
+ parser.add_argument('--shutdownTimeoutMinutes', {
+ default: DefaultServerConfig.shutdownTimeoutMinutes,
metavar: 'TIME',
type: 'int',
help: `0 for off, server will shut down after this amount of minutes.`
});
- parser.addArgument([ '--shutdownTimeoutVarianceMinutes' ], {
- defaultValue: DefaultServerConfig.shutdownTimeoutVarianceMinutes,
+ parser.add_argument('--shutdownTimeoutVarianceMinutes', {
+ default: DefaultServerConfig.shutdownTimeoutVarianceMinutes,
metavar: 'VARIANCE',
type: 'int',
help: `modifies the shutdown timer by +/- timeoutVarianceMinutes (to avoid multiple instances shutting at the same time)`
});
- parser.addArgument([ '--idMap' ], {
+ parser.add_argument('--idMap', {
nargs: 2,
action: 'append',
metavar: ['TYPE', 'PATH'] as any,
@@ -84,15 +84,15 @@ function addServerArgs(parser: argparse.ArgumentParser) {
}
function addJsonConfigArgs(parser: argparse.ArgumentParser) {
- parser.addArgument(['--cfg'], {
+ parser.add_argument('--cfg', {
help: [
'JSON config file path',
'If a property is not specified, cmd line param/OS variable/default value are used.'
].join('\n'),
required: false
});
- parser.addArgument(['--printCfg'], { help: 'Print current config for validation and exit.', required: false, nargs: 0 });
- parser.addArgument(['--cfgTemplate'], { help: 'Prints default JSON config template to be modified and exits.', required: false, nargs: 0 });
+ parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, nargs: 0 });
+ parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, nargs: 0 });
}
export interface ServerJsonConfig {
@@ -156,14 +156,14 @@ const ServerConfigTemplate: FullServerConfig = {
export function configureServer() {
const parser = new argparse.ArgumentParser({
- version: VOLUME_SERVER_VERSION,
- addHelp: true,
+ // version: VOLUME_SERVER_VERSION,
+ add_help: true,
description: VOLUME_SERVER_HEADER
});
addJsonConfigArgs(parser);
addServerArgs(parser);
addLimitsArgs(parser);
- const config = parser.parseArgs() as FullServerConfig & ServerJsonConfig;
+ const config = parser.parse_args() as FullServerConfig & ServerJsonConfig;
if (config.cfgTemplate !== null) {
console.log(JSON.stringify(ServerConfigTemplate, null, 2));
@@ -192,16 +192,16 @@ export function configureServer() {
export function configureLocal() {
const parser = new argparse.ArgumentParser({
- version: VOLUME_SERVER_VERSION,
- addHelp: true,
+ // version: VOLUME_SERVER_VERSION,
+ add_help: true,
description: VOLUME_SERVER_HEADER
});
- parser.addArgument(['--jobs'], { help: `Path to a JSON file with job specification.`, required: false });
- parser.addArgument(['--jobsTemplate'], { help: 'Print example template for jobs.json and exit.', required: false, nargs: 0 });;
+ parser.add_argument('--jobs', { help: `Path to a JSON file with job specification.`, required: false });
+ parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, nargs: 0 });;
addJsonConfigArgs(parser);
addLimitsArgs(parser);
- const config = parser.parseArgs() as LimitsConfig & ServerJsonConfig;
+ const config = parser.parse_args() as LimitsConfig & ServerJsonConfig;
if (config.cfgTemplate !== null) {
console.log(JSON.stringify(DefaultLimitsConfig, null, 2));
diff --git a/src/servers/volume/pack.ts b/src/servers/volume/pack.ts
index f77a930dd3f6a292d58ec35bba0701f7013bf4ae..343bb772ecc29a6a242f2ef4a53d6c7fe1ffa229 100644
--- a/src/servers/volume/pack.ts
+++ b/src/servers/volume/pack.ts
@@ -63,31 +63,31 @@ interface EmArgs extends GeneralArgs {
type Args = XrayArgs | EmArgs
const parser = new argparse.ArgumentParser({
- addHelp: true,
+ add_help: true,
description: `VolumeServer Packer ${VERSION}, (c) 2018-2019, Mol* contributors`
});
-const subparsers = parser.addSubparsers({
+const subparsers = parser.add_subparsers({
title: 'Packing modes',
dest: 'mode'
});
function addGeneralArgs(parser: argparse.ArgumentParser) {
- parser.addArgument(['output'], { help: `Output path.` });
- parser.addArgument(['--blockSizeInMB'], { defaultValue: 96, help: `Maximum block size.`, metavar: 'SIZE' });
- parser.addArgument(['--format'], { defaultValue: 'ccp4', help: `Input file format.` });
+ parser.add_argument('output', { help: `Output path.` });
+ parser.add_argument('--blockSizeInMB', { default: 96, help: `Maximum block size.`, metavar: 'SIZE' });
+ parser.add_argument('--format', { default: 'ccp4', help: `Input file format.` });
}
-const xrayParser = subparsers.addParser('xray', { addHelp: true });
-xrayParser.addArgument(['input2fofc'], { help: `Path to 2fofc file.`, metavar: '2FOFC' });
-xrayParser.addArgument(['inputFofc'], { help: `Path to fofc file.`, metavar: 'FOFC' });
+const xrayParser = subparsers.add_parser('xray', { add_help: true });
+xrayParser.add_argument('input2fofc', { help: `Path to 2fofc file.`, metavar: '2FOFC' });
+xrayParser.add_argument('inputFofc', { help: `Path to fofc file.`, metavar: 'FOFC' });
addGeneralArgs(xrayParser);
-const emParser = subparsers.addParser('em', { addHelp: true });
-emParser.addArgument(['inputEm'], { help: `Path to EM density file.`, metavar: 'EM' });
+const emParser = subparsers.add_parser('em', { add_help: true });
+emParser.add_argument('inputEm', { help: `Path to EM density file.`, metavar: 'EM' });
addGeneralArgs(emParser);
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
const config = getConfig(args);
pack(config.input, config.blockSizeInMB, config.isPeriodic, config.outputFilename, config.format);