@stencila/dockter - npm Package Compare versions

Comparing version 0.11.0 to 0.11.1

dist/DockerBuilder.js

@@ -13,2 +13,3 @@ "use strict";
 const zlib_1 = __importDefault(require("zlib"));
+const ndjson = require('ndjson');
 /**
@@ -108,4 +109,3 @@ * Builds Docker images from Dockerfiles
             let id;
-            stream.on('data', data => {
-                data = JSON.parse(data);
+            stream.pipe(ndjson.parse()).on('data', (data) => {
                 if (data.error) {
@@ -181,3 +181,2 @@ messages.push({
                     const copy = instruction.args;
-                    console.error(step, instruction.name, copy.join(' '));
                     const to = copy.pop();
@@ -201,3 +200,2 @@ const pack = tar_fs_1.default.pack(dir, {
                     const script = instruction.args;
-                    console.error(step, 'RUN', script);
                     const exec = await container.exec({
@@ -204,0 +202,0 @@ Cmd: ['bash', '-c', `${script}`],

dist/Doer.js

@@ -58,3 +58,3 @@ "use strict";
         try {
-            value = await node_persist_1.default.getItem(url);
+            value = false; // await persist.getItem(url)
         }
@@ -61,0 +61,0 @@ catch (error) {

dist/JavascriptParser.js

@@ -64,3 +64,2 @@ "use strict";
         const pkg = new schema_1.SoftwarePackage();
-        // TODO: populate properties based on CodeMeta crosswalk (see note above)
         // schema:Thing
@@ -72,2 +71,27 @@ pkg.name = data.name;
         pkg.runtimePlatform = 'Node.js';
+        pkg.license = data.license;
+        pkg.description = data.description;
+        if (data.author) {
+            if (typeof data.author === 'string') {
+                pkg.authors = [schema_1.Person.fromText(data.author)];
+            }
+            else {
+                let authorStr = '';
+                if (data.author.name)
+                    authorStr = data.author.name;
+                if (data.author.email)
+                    authorStr += ` <${data.author.email}>`;
+                if (data.author.url)
+                    authorStr += ` (${data.author.url})`;
+                pkg.authors = [schema_1.Person.fromText(authorStr)];
+            }
+        }
+        if (data.repository) {
+            if (typeof data.repository === 'string') {
+                pkg.codeRepository = data.repository;
+            }
+            else {
+                pkg.codeRepository = data.repository.url;
+            }
+        }
         // stencila:SoftwarePackage
@@ -74,0 +98,0 @@ if (data.dependencies) {

package.json

 {
   "name": "@stencila/dockter",
-  "version": "0.11.0",
+  "version": "0.11.1",
   "description": "A Docker image builder for researchers",
@@ -85,2 +85,3 @@ "main": "dist/index.js",
     "js-yaml": "^3.12.0",
+    "ndjson": "^1.5.0",
     "node-persist": "^3.0.1",
@@ -87,0 +88,0 @@ "rimraf": "^2.6.2",

src/DockerBuilder.ts

@@ -9,2 +9,14 @@ import crypto from 'crypto'
 
+const ndjson = require('ndjson')
+
+interface DockerMessageAux {
+  ID?: string
+}
+
+interface DockerMessage {
+  error?: string
+  stream?: string
+  aux?: DockerMessageAux
+}
+
 /**
@@ -112,4 +124,3 @@ * Builds Docker images from Dockerfiles
       let id: string
-      stream.on('data', data => {
-        data = JSON.parse(data)
+      stream.pipe(ndjson.parse()).on('data', (data: DockerMessage) => {
         if (data.error) {
@@ -184,3 +195,2 @@ messages.push({
           const copy = instruction.args as Array<string>
-          console.error(step, instruction.name, copy.join(' '))
           const to = copy.pop() as string
@@ -205,3 +215,2 @@ const pack = tarFs.pack(dir, {
           const script = instruction.args as string
-          console.error(step, 'RUN', script)
           const exec = await container.exec({
@@ -208,0 +217,0 @@ Cmd: ['bash', '-c', `${script}`],

src/Doer.ts

@@ -66,3 +66,3 @@ import fs from 'fs'
     try {
-      value = await persist.getItem(url)
+      value = false // await persist.getItem(url)
     } catch (error) {
@@ -69,0 +69,0 @@ if (error.message.includes('does not look like a valid storage file')) {

src/JavascriptParser.ts

@@ -63,4 +63,2 @@ // @ts-ignore
 
-    // TODO: populate properties based on CodeMeta crosswalk (see note above)
-
     // schema:Thing
@@ -75,37 +73,61 @@ pkg.name = data.name
 
+    pkg.license = data.license
+    pkg.description = data.description
+
+    if (data.author) {
+      if (typeof data.author === 'string') {
+        pkg.authors = [Person.fromText(data.author)]
+      } else {
+        let authorStr = ''
+        if (data.author.name) authorStr = data.author.name
+        if (data.author.email) authorStr += ` <${data.author.email}>`
+        if (data.author.url) authorStr += ` (${data.author.url})`
+
+        pkg.authors = [Person.fromText(authorStr)]
+      }
+    }
+
+    if (data.repository) {
+      if (typeof data.repository === 'string') {
+        pkg.codeRepository = data.repository
+      } else {
+        pkg.codeRepository = data.repository.url
+      }
+    }
+
     // stencila:SoftwarePackage
     if (data.dependencies) {
       pkg.softwareRequirements = await Promise.all(
-        Object.entries(data.dependencies).map(async ([name, versionRange]) => {
-          // Determine the minimum version that satisfies the range specified in the
-          // If we can't determine a minimum version from the versionRange
-          // (e.g. because it's a github url) then try to get latest
-          let version = 'latest'
-          if (versionRange !== 'latest' || versionRange !== '*') {
-            const range = semver.validRange(versionRange as string)
-            if (range) {
-              const match = range.match(/(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)/)
-              if (match) version = match[0]
+          Object.entries(data.dependencies).map(async ([name, versionRange]) => {
+            // Determine the minimum version that satisfies the range specified in the
+            // If we can't determine a minimum version from the versionRange
+            // (e.g. because it's a github url) then try to get latest
+            let version = 'latest'
+            if (versionRange !== 'latest' || versionRange !== '*') {
+              const range = semver.validRange(versionRange as string)
+              if (range) {
+                const match = range.match(/(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)/)
+                if (match) version = match[0]
+              }
             }
-          }
 
-          // Fetch meta-data from NPM
-          const data = await this.fetch(`https://registry.npmjs.org/${name}/${version}`, {
-            json: true,
-            headers: {
-              'Accept': 'application/vnd.npm.install-v1+json; q=1.0, application/json; q=0.8, */*'
+            // Fetch meta-data from NPM
+            const data = await this.fetch(`https://registry.npmjs.org/${name}/${version}`, {
+              json: true,
+              headers: {
+                'Accept': 'application/vnd.npm.install-v1+json; q=1.0, application/json; q=0.8, */*'
+              }
+            })
+
+            if (data) {
+              return this.createPackage(data)
+            } else {
+              // All we know is name and version, so return that
+              const dependency = new SoftwarePackage()
+              dependency.name = name
+              dependency.version = versionRange as string
+              dependency.runtimePlatform = 'Node.js'
+              return dependency
             }
           })
-
-          if (data) {
-            return this.createPackage(data)
-          } else {
-            // All we know is name and version, so return that
-            const dependency = new SoftwarePackage()
-            dependency.name = name
-            dependency.version = versionRange as string
-            dependency.runtimePlatform = 'Node.js'
-            return dependency
-          }
-        })
       )
@@ -112,0 +134,0 @@ }

tests/fixtures/js-package/package.json

@@ -7,3 +7,7 @@ {
   "scripts": {},
-  "author": "",
+  "author": {
+    "name": "Jason Bloggs",
+    "email": "[e-mail]",
+    "url": "https://jbloggs.example.com"
+  },
   "license": "ISC",
@@ -16,3 +20,7 @@ "dependencies": {
     "a-package-that-is-not-on-npm": "org/repo"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/stencila/dockter/"
   }
 }

tests/JavascriptParser.test.ts

 import fixture from './fixture'
 import JavascriptParser from '../src/JavascriptParser'
-import { SoftwarePackage } from '@stencila/schema'
+import { Person, SoftwarePackage } from '@stencila/schema'
+import fs from 'fs'
+import { REQUEST_CACHE_DIR } from '../src/Doer'
 
@@ -8,58 +10,73 @@ // Increase timeout (in milliseconds) to allow for HTTP requests
 jest.setTimeout(30 * 60 * 1000)
+describe('JavascriptParser', () => {
+  beforeEach(() => {
+    if (fs.existsSync(REQUEST_CACHE_DIR)) {
+      for (let item of fs.readdirSync(REQUEST_CACHE_DIR)) {
+        try {
+          fs.unlinkSync(REQUEST_CACHE_DIR + '/' + item)
+        } catch (e) {
+          // Cleanups might execute in parallel in multiple test runs so don't worry if remove fails
+        }
+      }
+    }
+  })
 
-/**
- * When applied to an empty folder, parse should return null.
- */
-test('parse:empty', async () => {
-  const parser = new JavascriptParser(fixture('empty'))
-  expect(await parser.parse()).toBeNull()
-})
+  /**
+   * When applied to an empty folder, parse should return null.
+   */
+  test('parse:empty', async () => {
+    const parser = new JavascriptParser(fixture('empty'))
+    expect(await parser.parse()).toBeNull()
+  })
 
-/**
- * When applied to a folder with no JS code, parse should return null.
- */
-test('parse:r-date', async () => {
-  const parser = new JavascriptParser(fixture('empty'))
-  expect(await parser.parse()).toBeNull()
-})
+  /**
+   * When applied to a folder with no JS code, parse should return null.
+   */
+  test('parse:r-date', async () => {
+    const parser = new JavascriptParser(fixture('empty'))
+    expect(await parser.parse()).toBeNull()
+  })
 
-/**
- * When applied to a folder with a `package.json` file, parse should return
- * a `SoftwarePackage` with `name`, `softwareRequirements` etc
- * populated correctly.
- */
-test('parse:js-package', async () => {
-  const parser = new JavascriptParser(fixture('js-package'))
-  const pkg = await parser.parse() as SoftwarePackage
-  
-  expect(pkg.name).toEqual('js-package')
-  expect(pkg.softwareRequirements.length).toEqual(5)
-  const expecteds = [
-    ['is-array', '1.0.1'],
-    ['mkdirp', '0.5.1'],
-    ['rimraf', '2.6.2'],
-    ['array-swap', '0.0.2'],
-    ['a-package-that-is-not-on-npm', 'org/repo']
-  ]
-  for (let index in expecteds) {
-    let {name, version} = pkg.softwareRequirements[index]
-    expect(name).toEqual(expecteds[index][0])
-    expect(version).toEqual(expecteds[index][1])
-  }
-})
+  /**
+   * When applied to a folder with a `package.json` file, parse should return
+   * a `SoftwarePackage` with `name`, `softwareRequirements` etc
+   * populated correctly.
+   */
+  test('parse:js-package', async () => {
+    const parser = new JavascriptParser(fixture('js-package'))
+    const pkg = await parser.parse() as SoftwarePackage
 
+    expect(pkg.name).toEqual('js-package')
+    expect(pkg.license).toEqual('ISC')
+    expect(pkg.authors).toEqual([Person.fromText('Jason Bloggs <[e-mail]> (https://jbloggs.example.com)')])
+    expect(pkg.codeRepository).toEqual('https://github.com/stencila/dockter/')
+    expect(pkg.softwareRequirements.length).toEqual(5)
+    const expecteds = [
+      ['is-array', '1.0.1'],
+      ['mkdirp', '0.5.1'],
+      ['rimraf', '2.6.2'],
+      ['array-swap', '0.0.2'],
+      ['a-package-that-is-not-on-npm', 'org/repo']
+    ]
+    for (let index in expecteds) {
+      let { name, version } = pkg.softwareRequirements[index]
+      expect(name).toEqual(expecteds[index][0])
+      expect(version).toEqual(expecteds[index][1])
+    }
+  })
 
-/**
- * When applied to a folder with a `*.js` files, parse should return
- * a `SoftwarePackage` with `name`, `softwareRequirements` etc
- * populated correctly.
- */
-test('parse:js-sources', async () => {
-  const parser = new JavascriptParser(fixture('js-sources'))
-  const pkg = await parser.parse() as SoftwarePackage
-  
-  expect(pkg.name).toEqual('js-sources')
-  expect(pkg.softwareRequirements.length).toEqual(2)
-  expect(pkg.softwareRequirements[1].name).toEqual('array-swap')
-  expect(pkg.softwareRequirements[0].name).toEqual('is-sorted')
+  /**
+   * When applied to a folder with a `*.js` files, parse should return
+   * a `SoftwarePackage` with `name`, `softwareRequirements` etc
+   * populated correctly.
+   */
+  test('parse:js-sources', async () => {
+    const parser = new JavascriptParser(fixture('js-sources'))
+    const pkg = await parser.parse() as SoftwarePackage
+
+    expect(pkg.name).toEqual('js-sources')
+    expect(pkg.softwareRequirements.length).toEqual(2)
+    expect(pkg.softwareRequirements[1].name).toEqual('array-swap')
+    expect(pkg.softwareRequirements[0].name).toEqual('is-sorted')
+  })
 })

tests/PythonParser.test.ts

@@ -12,3 +12,7 @@ import fixture from './fixture'
       for (let item of fs.readdirSync(REQUEST_CACHE_DIR)) {
-        fs.unlinkSync(REQUEST_CACHE_DIR + '/' + item)
+        try {
+          fs.unlinkSync(REQUEST_CACHE_DIR + '/' + item)
+        } catch (e) {
+          // Cleanups might execute in parallel in multiple test runs so don't worry if remove fails
+        }
       }
@@ -15,0 +19,0 @@ }

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

1356318

increased by0.46%

Number of package files

149

increased by1.36%

Lines of code

5975

increased by1.43%

Worsened metrics

Dependency count

16

increased by6.67%

Dependency changes

• + Addedndjson@^1.5.0

• + Addedjson-stringify-safe@5.0.1(transitive)

• + Addedndjson@1.5.0(transitive)

• + Addedsplit2@2.2.0(transitive)

• + Addedthrough2@2.0.5(transitive)