From 613cdc3145867ab7d37cdc5920905afec74efad5 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Mon, 25 May 2020 13:46:46 -0700
Subject: [PATCH] fix building of cli tools
---
.gitignore | 1 +
README.md | 14 ++---
package.json | 4 +-
.../chem-comp-bond/create-table.ts | 1 +
src/{apps => cli}/cif2bcif/converter.ts | 0
src/{apps => cli}/cif2bcif/index.ts | 1 +
src/{apps => cli}/cifschema/index.ts | 1 +
src/{apps => cli}/cifschema/util/cif-dic.ts | 0
src/{apps => cli}/cifschema/util/generate.ts | 0
src/{apps => cli}/cifschema/util/helper.ts | 0
src/{apps => cli}/cifschema/util/schema.ts | 0
src/cli/lipid-params/index.ts | 59 +++++++++++++++++++
src/{apps => cli}/state-docs/index.ts | 1 +
src/{apps => cli}/state-docs/pd-to-md.ts | 0
src/{apps => cli}/structure-info/helpers.ts | 0
src/{apps => cli}/structure-info/model.ts | 1 +
src/{apps => cli}/structure-info/volume.ts | 1 +
src/perf-tests/mol-script.ts | 2 +-
tsconfig.json | 2 +-
tsconfig.servers.json | 4 +-
20 files changed, 79 insertions(+), 13 deletions(-)
rename src/{apps => cli}/chem-comp-bond/create-table.ts (99%)
rename src/{apps => cli}/cif2bcif/converter.ts (100%)
rename src/{apps => cli}/cif2bcif/index.ts (98%)
rename src/{apps => cli}/cifschema/index.ts (99%)
rename src/{apps => cli}/cifschema/util/cif-dic.ts (100%)
rename src/{apps => cli}/cifschema/util/generate.ts (100%)
rename src/{apps => cli}/cifschema/util/helper.ts (100%)
rename src/{apps => cli}/cifschema/util/schema.ts (100%)
create mode 100644 src/cli/lipid-params/index.ts
rename src/{apps => cli}/state-docs/index.ts (99%)
rename src/{apps => cli}/state-docs/pd-to-md.ts (100%)
rename src/{apps => cli}/structure-info/helpers.ts (100%)
rename src/{apps => cli}/structure-info/model.ts (99%)
rename src/{apps => cli}/structure-info/volume.ts (99%)
diff --git a/.gitignore b/.gitignore
index 202483f20..d0ab23e57 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@ node_modules/
debug.log
npm-debug.log
tsconfig.tsbuildinfo
+tsconfig.servers.tsbuildinfo
*.sublime-workspace
.idea
diff --git a/README.md b/README.md
index d30244e44..ec482ded2 100644
--- a/README.md
+++ b/README.md
@@ -41,7 +41,7 @@ Moreover, the project contains the implementation of `servers`, including
- `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
- `servers/plugin-state` A basic server to store Mol* Plugin states.
-The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `apps` (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
+The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
## Previous Work
This project builds on experience from previous solutions:
@@ -90,10 +90,10 @@ and navigate to `build/viewer`
### Code generation
**CIF schemas**
- node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
- node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
- node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
- node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
+ node ./lib/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
+ node ./lib/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
+ node ./lib/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
+ node ./lib/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
**GraphQL schemas**
@@ -102,7 +102,7 @@ and navigate to `build/viewer`
### Other scripts
**Create chem comp bond table**
- node --max-old-space-size=4096 lib/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
+ node --max-old-space-size=4096 lib/cli/chem-comp-bond/create-table.js build/data/ccb.bcif -b
**Test model server**
@@ -120,7 +120,7 @@ To see all available commands, use ``node lib/servers/model/preprocess -h``.
Or
- node ./lib/apps/cif2bcif
+ node ./lib/cli/cif2bcif
## Development
diff --git a/package.json b/package.json
index c5aab99a0..72986faaf 100644
--- a/package.json
+++ b/package.json
@@ -43,8 +43,8 @@
"build/viewer/"
],
"bin": {
- "cif2bcif": "lib/apps/cif2bcif/index.js",
- "cifschema": "lib/apps/cifschema/index.js",
+ "cif2bcif": "lib/cli/cif2bcif/index.js",
+ "cifschema": "lib/cli/cifschema/index.js",
"model-server": "lib/servers/servers/model/server.js",
"model-server-query": "lib/servers/servers/model/query.js",
"model-server-preprocess": "lib/servers/servers/model/preprocess.js",
diff --git a/src/apps/chem-comp-bond/create-table.ts b/src/cli/chem-comp-bond/create-table.ts
similarity index 99%
rename from src/apps/chem-comp-bond/create-table.ts
rename to src/cli/chem-comp-bond/create-table.ts
index ef09d66cc..1837028e6 100644
--- a/src/apps/chem-comp-bond/create-table.ts
+++ b/src/cli/chem-comp-bond/create-table.ts
@@ -1,3 +1,4 @@
+#!/usr/bin/env node
/**
* Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
diff --git a/src/apps/cif2bcif/converter.ts b/src/cli/cif2bcif/converter.ts
similarity index 100%
rename from src/apps/cif2bcif/converter.ts
rename to src/cli/cif2bcif/converter.ts
diff --git a/src/apps/cif2bcif/index.ts b/src/cli/cif2bcif/index.ts
similarity index 98%
rename from src/apps/cif2bcif/index.ts
rename to src/cli/cif2bcif/index.ts
index c3b278d6f..c862695ec 100644
--- a/src/apps/cif2bcif/index.ts
+++ b/src/cli/cif2bcif/index.ts
@@ -1,3 +1,4 @@
+#!/usr/bin/env node
/**
* Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
diff --git a/src/apps/cifschema/index.ts b/src/cli/cifschema/index.ts
similarity index 99%
rename from src/apps/cifschema/index.ts
rename to src/cli/cifschema/index.ts
index b20754ce8..41032a038 100644
--- a/src/apps/cifschema/index.ts
+++ b/src/cli/cifschema/index.ts
@@ -1,3 +1,4 @@
+#!/usr/bin/env node
/**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
diff --git a/src/apps/cifschema/util/cif-dic.ts b/src/cli/cifschema/util/cif-dic.ts
similarity index 100%
rename from src/apps/cifschema/util/cif-dic.ts
rename to src/cli/cifschema/util/cif-dic.ts
diff --git a/src/apps/cifschema/util/generate.ts b/src/cli/cifschema/util/generate.ts
similarity index 100%
rename from src/apps/cifschema/util/generate.ts
rename to src/cli/cifschema/util/generate.ts
diff --git a/src/apps/cifschema/util/helper.ts b/src/cli/cifschema/util/helper.ts
similarity index 100%
rename from src/apps/cifschema/util/helper.ts
rename to src/cli/cifschema/util/helper.ts
diff --git a/src/apps/cifschema/util/schema.ts b/src/cli/cifschema/util/schema.ts
similarity index 100%
rename from src/apps/cifschema/util/schema.ts
rename to src/cli/cifschema/util/schema.ts
diff --git a/src/cli/lipid-params/index.ts b/src/cli/lipid-params/index.ts
new file mode 100644
index 000000000..1aec421c4
--- /dev/null
+++ b/src/cli/lipid-params/index.ts
@@ -0,0 +1,59 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse';
+import * as fs from 'fs';
+import * as path from 'path';
+import fetch from 'node-fetch';
+
+const BUILD_DIR = path.resolve(__dirname, '../build/');
+const LIPIDS_DIR = path.resolve(BUILD_DIR, 'lipids/');
+
+const MARTINI_LIPIDS_PATH = path.resolve(LIPIDS_DIR, 'martini_lipids.itp');
+const MARTINI_LIPIDS_URL = 'http://www.cgmartini.nl/images/parameters/lipids/Collections/martini_v2.0_lipids_all_201506.itp';
+
+async function ensureAvailable(path: string, url: string) {
+ if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
+ const name = url.substr(url.lastIndexOf('/') + 1);
+ console.log(`downloading ${name}...`);
+ const data = await fetch(url);
+ if (!fs.existsSync(LIPIDS_DIR)) {
+ fs.mkdirSync(LIPIDS_DIR);
+ }
+ fs.writeFileSync(path, await data.text());
+ console.log(`done downloading ${name}`);
+ }
+}
+
+async function ensureLipidsAvailable() { await ensureAvailable(MARTINI_LIPIDS_PATH, MARTINI_LIPIDS_URL); }
+
+async function run() {
+ await ensureLipidsAvailable();
+ const lipidsItpStr = fs.readFileSync(MARTINI_LIPIDS_PATH, 'utf8');
+
+ const m = lipidsItpStr.match(/\[moleculetype\]\n; molname nrexcl\n(DGPC)/g);
+ console.log(m);
+}
+
+const parser = new argparse.ArgumentParser({
+ addHelp: true,
+ description: 'Create lipid params (from martini lipids itp)'
+});
+parser.addArgument([ '--forceDownload', '-f' ], {
+ action: 'storeTrue',
+ help: 'Force download of martini lipids itp'
+});
+interface Args {
+ forceDownload: boolean
+}
+const args: Args = parser.parseArgs();
+
+const FORCE_DOWNLOAD = args.forceDownload;
+
+run().catch(e => {
+ console.error(e);
+});
\ No newline at end of file
diff --git a/src/apps/state-docs/index.ts b/src/cli/state-docs/index.ts
similarity index 99%
rename from src/apps/state-docs/index.ts
rename to src/cli/state-docs/index.ts
index bdc50e654..36ed9a903 100644
--- a/src/apps/state-docs/index.ts
+++ b/src/cli/state-docs/index.ts
@@ -1,3 +1,4 @@
+#!/usr/bin/env node
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
diff --git a/src/apps/state-docs/pd-to-md.ts b/src/cli/state-docs/pd-to-md.ts
similarity index 100%
rename from src/apps/state-docs/pd-to-md.ts
rename to src/cli/state-docs/pd-to-md.ts
diff --git a/src/apps/structure-info/helpers.ts b/src/cli/structure-info/helpers.ts
similarity index 100%
rename from src/apps/structure-info/helpers.ts
rename to src/cli/structure-info/helpers.ts
diff --git a/src/apps/structure-info/model.ts b/src/cli/structure-info/model.ts
similarity index 99%
rename from src/apps/structure-info/model.ts
rename to src/cli/structure-info/model.ts
index f50df0dab..39c9f73ed 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/cli/structure-info/model.ts
@@ -1,3 +1,4 @@
+#!/usr/bin/env node
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
diff --git a/src/apps/structure-info/volume.ts b/src/cli/structure-info/volume.ts
similarity index 99%
rename from src/apps/structure-info/volume.ts
rename to src/cli/structure-info/volume.ts
index cfedb46e9..27b13ba0e 100644
--- a/src/apps/structure-info/volume.ts
+++ b/src/cli/structure-info/volume.ts
@@ -1,3 +1,4 @@
+#!/usr/bin/env node
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index 3b4fc5030..8e4481de2 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -1,7 +1,7 @@
import { MolScriptBuilder } from '../mol-script/language/builder';
import { compile, QuerySymbolRuntime, DefaultQueryRuntimeTable } from '../mol-script/runtime/query/compiler';
import { QueryContext, Structure, StructureQuery } from '../mol-model/structure';
-import { readCifFile, getModelsAndStructure } from '../apps/structure-info/model';
+import { readCifFile, getModelsAndStructure } from '../cli/structure-info/model';
import { CustomPropSymbol } from '../mol-script/language/symbol';
import Type from '../mol-script/language/type';
import { parseMolScript } from '../mol-script/language/parser';
diff --git a/tsconfig.json b/tsconfig.json
index df2e30317..8f10a37be 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -20,5 +20,5 @@
"outDir": "lib"
},
"include": [ "src/**/*" ],
- "exclude": [ "src/servers/**/*" ]
+ "exclude": [ "src/servers/**/*", "src/perf-tests/*", "src/cli/**/*" ]
}
\ No newline at end of file
diff --git a/tsconfig.servers.json b/tsconfig.servers.json
index 023a1cec3..0a29bd69b 100644
--- a/tsconfig.servers.json
+++ b/tsconfig.servers.json
@@ -17,7 +17,7 @@
"jsx": "react",
"lib": [ "es6", "dom", "esnext.asynciterable", "es2016" ],
"rootDir": "src",
- "outDir": "lib/servers"
+ "outDir": "lib"
},
- "include": [ "src/servers/**/*", "src/perf-tests/*" ]
+ "include": [ "src/servers/**/*", "src/perf-tests/*", "src/cli/**/*" ]
}
\ No newline at end of file
--
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