Merge pull request #13 from umccr/feat/git-force

fix: remote git fetch logic

docs/CONFIG.md

@@ -6,26 +6,26 @@
 
 ## CorsConifg
 
-Defined in: [lib/config.ts:134](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L134)
+Defined in: [lib/config.ts:134](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L134)
 
 CORS configuration for the htsget-rs server.
 
 ### Properties
 
 | Property | Type | Default value | Description | Defined in |
 | ------ | ------ | ------ | ------ | ------ |
-| <a id="allowcredentials"></a> `allowCredentials?` | `boolean` | `false` | CORS allow credentials. | [lib/config.ts:140](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L140) |
-| <a id="allowheaders"></a> `allowHeaders?` | `string`[] | `["*"]` | CORS allow headers. | [lib/config.ts:147](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L147) |
-| <a id="allowmethods"></a> `allowMethods?` | `CorsHttpMethod`[] | `[CorsHttpMethod.ANY]` | CORS allow methods. | [lib/config.ts:154](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L154) |
-| <a id="alloworigins"></a> `allowOrigins?` | `string`[] | `["*"]` | CORS allow origins. | [lib/config.ts:161](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L161) |
-| <a id="exposeheaders"></a> `exposeHeaders?` | `string`[] | `["*"]` | CORS expose headers. | [lib/config.ts:168](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L168) |
-| <a id="maxage"></a> `maxAge?` | `Duration` | `Duration.days(30)` | CORS max age. | [lib/config.ts:175](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L175) |
+| <a id="allowcredentials"></a> `allowCredentials?` | `boolean` | `false` | CORS allow credentials. | [lib/config.ts:140](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L140) |
+| <a id="allowheaders"></a> `allowHeaders?` | `string`[] | `["*"]` | CORS allow headers. | [lib/config.ts:147](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L147) |
+| <a id="allowmethods"></a> `allowMethods?` | `CorsHttpMethod`[] | `[CorsHttpMethod.ANY]` | CORS allow methods. | [lib/config.ts:154](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L154) |
+| <a id="alloworigins"></a> `allowOrigins?` | `string`[] | `["*"]` | CORS allow origins. | [lib/config.ts:161](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L161) |
+| <a id="exposeheaders"></a> `exposeHeaders?` | `string`[] | `["*"]` | CORS expose headers. | [lib/config.ts:168](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L168) |
+| <a id="maxage"></a> `maxAge?` | `Duration` | `Duration.days(30)` | CORS max age. | [lib/config.ts:175](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L175) |
 
 ***
 
 ## HtsgetConfig
 
-Defined in: [lib/config.ts:182](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L182)
+Defined in: [lib/config.ts:182](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L182)
 
 Configuration for the htsget-rs server. This allows specifying the options
 available in the htsget-rs config: https://github.com/umccr/htsget-rs/tree/main/htsget-config
@@ -34,63 +34,63 @@ available in the htsget-rs config: https://github.com/umccr/htsget-rs/tree/main/
 
 | Property | Type | Default value | Description | Defined in |
 | ------ | ------ | ------ | ------ | ------ |
-| <a id="environment_override"></a> `environment_override?` | `Record`\<`string`, `unknown`\> | `undefined` | Any additional htsget-rs options can be specified here as environment variables. These will override any options set in this construct, and allows using advanced configuration. Options here should contain the `HTSGET_` prefix. | [lib/config.ts:208](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L208) |
-| <a id="locations"></a> `locations?` | [`HtsgetLocation`](CONFIG.md#htsgetlocation)[] | `[]` | The locations for the htsget-rs server. This is the same as the htsget-rs config locations: https://github.com/umccr/htsget-rs/tree/main/htsget-config#quickstart Any `s3://...` locations will automatically be added to the bucket access policy. | [lib/config.ts:191](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L191) |
-| <a id="service_info"></a> `service_info?` | `Record`\<`string`, `unknown`\> | `undefined` | Service info fields to configure for the server. This is the same as the htsget-rs config service_info: https://github.com/umccr/htsget-rs/tree/main/htsget-config#service-info-config | [lib/config.ts:199](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L199) |
+| <a id="environment_override"></a> `environment_override?` | `Record`\<`string`, `unknown`\> | `undefined` | Any additional htsget-rs options can be specified here as environment variables. These will override any options set in this construct, and allows using advanced configuration. Options here should contain the `HTSGET_` prefix. | [lib/config.ts:208](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L208) |
+| <a id="locations"></a> `locations?` | [`HtsgetLocation`](CONFIG.md#htsgetlocation)[] | `[]` | The locations for the htsget-rs server. This is the same as the htsget-rs config locations: https://github.com/umccr/htsget-rs/tree/main/htsget-config#quickstart Any `s3://...` locations will automatically be added to the bucket access policy. | [lib/config.ts:191](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L191) |
+| <a id="service_info"></a> `service_info?` | `Record`\<`string`, `unknown`\> | `undefined` | Service info fields to configure for the server. This is the same as the htsget-rs config service_info: https://github.com/umccr/htsget-rs/tree/main/htsget-config#service-info-config | [lib/config.ts:199](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L199) |
 
 ***
 
 ## HtsgetLambdaProps
 
-Defined in: [lib/config.ts:10](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L10)
+Defined in: [lib/config.ts:10](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L10)
 
 Settings related to the htsget lambda construct props.
 
 ### Properties
 
 | Property | Type | Default value | Description | Defined in |
 | ------ | ------ | ------ | ------ | ------ |
-| <a id="cargolambdaflags"></a> `cargoLambdaFlags?` | `string`[] | `undefined` | Override any cargo lambda flags for the build. By default, features are resolved automatically based on the config and `HtsgetLocation[]`. This option overrides that and any automatically added flags. | [lib/config.ts:68](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L68) |
-| <a id="copytestdata"></a> `copyTestData?` | `boolean` | `false` | Copy the test data directory to a new bucket: https://github.com/umccr/htsget-rs/tree/main/data Also copies the Crypt4GH keys to Secrets Manager. Automatically the htsget-rs server access to the bucket and secrets using the locations config. | [lib/config.ts:79](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L79) |
-| <a id="cors"></a> `cors?` | [`CorsConifg`](CONFIG.md#corsconifg) | same as the `CorsConfig` defaults | CORS configuration for the htsget-rs server. Values here are propagated to CORS options in htsget-rs. | [lib/config.ts:45](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L45) |
-| <a id="domain"></a> `domain?` | `string` | `undefined` | The domain name for the htsget server. This must be specified if `httpApi` is not set. This assumes that a `HostedZone` exists for this domain. | [lib/config.ts:24](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L24) |
-| <a id="gitforceclone"></a> `gitForceClone?` | `boolean` | `false` | Whether to force a git clone for every build. If this is false, then the git repo is only cloned once for every git reference in a temporary directory. Otherwise, the repo is cloned every time. | [lib/config.ts:60](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L60) |
-| <a id="gitreference"></a> `gitReference?` | `string` | `"main"` | The git reference to fetch from the htsget-rs repo. | [lib/config.ts:52](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L52) |
-| <a id="hostedzone"></a> `hostedZone?` | `HostedZone` | `undefined` | Use the provided hosted zone instead of looking it up from the domain name. | [lib/config.ts:101](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L101) |
-| <a id="htsgetconfig-1"></a> `htsgetConfig?` | [`HtsgetConfig`](CONFIG.md#htsgetconfig) | `undefined` | The htsget-rs config options. Use this to specify any locations and htsget-rs options. | [lib/config.ts:16](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L16) |
-| <a id="httpapi"></a> `httpApi?` | `HttpApi` | `undefined` | Manually specify an `HttpApi`. This will not create a `HostedZone`, any Route53 records, certificates, or authorizers, and will instead rely on the existing `HttpApi`. | [lib/config.ts:94](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L94) |
-| <a id="jwt"></a> `jwt?` | [`JwtConfig`](CONFIG.md#jwtconfig) | `undefined`, defaults to a public deployment | Whether this deployment is gated behind a JWT authorizer, or if its public. | [lib/config.ts:38](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L38) |
-| <a id="role"></a> `role?` | `Role` | `undefined` | Use the provided role instead of creating one. This will ignore any configuration related to permissions for buckets and secrets, and rely on the existing role. | [lib/config.ts:109](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L109) |
-| <a id="subdomain"></a> `subDomain?` | `string` | `"htsget"` | The domain name prefix to use for the htsget-rs server. | [lib/config.ts:31](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L31) |
-| <a id="vpc"></a> `vpc?` | `IVpc` | `undefined` | Optionally specify a VPC for the Lambda function. | [lib/config.ts:86](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L86) |
+| <a id="cargolambdaflags"></a> `cargoLambdaFlags?` | `string`[] | `undefined` | Override any cargo lambda flags for the build. By default, features are resolved automatically based on the config and `HtsgetLocation[]`. This option overrides that and any automatically added flags. | [lib/config.ts:68](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L68) |
+| <a id="copytestdata"></a> `copyTestData?` | `boolean` | `false` | Copy the test data directory to a new bucket: https://github.com/umccr/htsget-rs/tree/main/data Also copies the Crypt4GH keys to Secrets Manager. Automatically the htsget-rs server access to the bucket and secrets using the locations config. | [lib/config.ts:79](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L79) |
+| <a id="cors"></a> `cors?` | [`CorsConifg`](CONFIG.md#corsconifg) | same as the `CorsConfig` defaults | CORS configuration for the htsget-rs server. Values here are propagated to CORS options in htsget-rs. | [lib/config.ts:45](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L45) |
+| <a id="domain"></a> `domain?` | `string` | `undefined` | The domain name for the htsget server. This must be specified if `httpApi` is not set. This assumes that a `HostedZone` exists for this domain. | [lib/config.ts:24](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L24) |
+| <a id="gitforceclone"></a> `gitForceClone?` | `boolean` | `false` | Whether to force a git clone for every build. If this is false, then the git repo is only cloned once for every git reference in a temporary directory. Otherwise, the repo is cloned every time. | [lib/config.ts:60](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L60) |
+| <a id="gitreference"></a> `gitReference?` | `string` | `"main"` | The git reference to fetch from the htsget-rs repo. | [lib/config.ts:52](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L52) |
+| <a id="hostedzone"></a> `hostedZone?` | `HostedZone` | `undefined` | Use the provided hosted zone instead of looking it up from the domain name. | [lib/config.ts:101](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L101) |
+| <a id="htsgetconfig-1"></a> `htsgetConfig?` | [`HtsgetConfig`](CONFIG.md#htsgetconfig) | `undefined` | The htsget-rs config options. Use this to specify any locations and htsget-rs options. | [lib/config.ts:16](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L16) |
+| <a id="httpapi"></a> `httpApi?` | `HttpApi` | `undefined` | Manually specify an `HttpApi`. This will not create a `HostedZone`, any Route53 records, certificates, or authorizers, and will instead rely on the existing `HttpApi`. | [lib/config.ts:94](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L94) |
+| <a id="jwt"></a> `jwt?` | [`JwtConfig`](CONFIG.md#jwtconfig) | `undefined`, defaults to a public deployment | Whether this deployment is gated behind a JWT authorizer, or if its public. | [lib/config.ts:38](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L38) |
+| <a id="role"></a> `role?` | `Role` | `undefined` | Use the provided role instead of creating one. This will ignore any configuration related to permissions for buckets and secrets, and rely on the existing role. | [lib/config.ts:109](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L109) |
+| <a id="subdomain"></a> `subDomain?` | `string` | `"htsget"` | The domain name prefix to use for the htsget-rs server. | [lib/config.ts:31](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L31) |
+| <a id="vpc"></a> `vpc?` | `IVpc` | `undefined` | Optionally specify a VPC for the Lambda function. | [lib/config.ts:86](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L86) |
 
 ***
 
 ## HtsgetLocation
 
-Defined in: [lib/config.ts:214](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L214)
+Defined in: [lib/config.ts:214](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L214)
 
 Config for locations.
 
 ### Properties
 
 | Property | Type | Default value | Description | Defined in |
 | ------ | ------ | ------ | ------ | ------ |
-| <a id="location"></a> `location` | `string` | `undefined` | The location string. | [lib/config.ts:218](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L218) |
-| <a id="private_key"></a> `private_key?` | `string` | `undefined` | Optional Crypt4GH private key secret ARN or name. | [lib/config.ts:224](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L224) |
-| <a id="public_key"></a> `public_key?` | `string` | `undefined` | Optional Crypt4GH public key secret ARN or name. | [lib/config.ts:230](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L230) |
+| <a id="location"></a> `location` | `string` | `undefined` | The location string. | [lib/config.ts:218](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L218) |
+| <a id="private_key"></a> `private_key?` | `string` | `undefined` | Optional Crypt4GH private key secret ARN or name. | [lib/config.ts:224](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L224) |
+| <a id="public_key"></a> `public_key?` | `string` | `undefined` | Optional Crypt4GH public key secret ARN or name. | [lib/config.ts:230](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L230) |
 
 ***
 
 ## JwtConfig
 
-Defined in: [lib/config.ts:115](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L115)
+Defined in: [lib/config.ts:115](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L115)
 
 JWT authorization settings.
 
 ### Properties
 
 | Property | Type | Default value | Description | Defined in |
 | ------ | ------ | ------ | ------ | ------ |
-| <a id="audience"></a> `audience?` | `string`[] | `[]` | The JWT audience. | [lib/config.ts:121](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L121) |
-| <a id="coguserpoolid"></a> `cogUserPoolId?` | `string` | `undefined`, creates a new user pool | The cognito user pool id for the authorizer. If this is not set, then a new user pool is created. | [lib/config.ts:128](https://github.com/umccr/htsget-deploy/blob/20bfd80f92b571f73f944590d9c849c556e847d2/lib/config.ts#L128) |
+| <a id="audience"></a> `audience?` | `string`[] | `[]` | The JWT audience. | [lib/config.ts:121](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L121) |
+| <a id="coguserpoolid"></a> `cogUserPoolId?` | `string` | `undefined`, creates a new user pool | The cognito user pool id for the authorizer. If this is not set, then a new user pool is created. | [lib/config.ts:128](https://github.com/umccr/htsget-deploy/blob/1be5957352d45a343fefae9ba0cf727132d9bd58/lib/config.ts#L128) |

lib/htsget-lambda.ts

@@ -1,4 +1,4 @@
-import { readFileSync } from "fs";
+import { readFileSync, mkdirSync } from "fs";
 import { join } from "node:path";
 import { tmpdir } from "os";
 
@@ -72,17 +72,27 @@ export class HtsgetLambda extends Construct {
     }
 
     const gitRemote = "https://github.com/umccr/htsget-rs";
-    const gitReference = props.gitReference;
-    const latestCommit = exec("git", [
-      "ls-remote",
-      gitRemote,
-      gitReference || "HEAD",
-    ])
+    const gitReference = props.gitReference || "HEAD";
+    const latestCommit = exec("git", ["ls-remote", gitRemote, gitReference])
       .stdout.toString()
       .split(/(\s+)/)[0];
 
     const localPath = join(tmpdir(), latestCommit);
 
+    mkdirSync(localPath, { recursive: true });
+
+    const args = ["clone"];
+    if (gitReference === "HEAD") {
+      args.push("--depth", "1");
+    }
+
+    args.push(gitRemote, localPath);
+    exec("git", args);
+
+    if (gitReference !== "HEAD") {
+      exec("git", ["checkout", gitReference], { cwd: localPath });
+    }
+
     const manifestPath = getManifestPath({
       manifestPath: join(localPath, "Cargo.toml"),
       gitRemote,

package.json

@@ -36,5 +36,5 @@
     "watch": "tsc -w",
     "typedoc": "typedoc"
   },
-  "version": "0.8.4"
+  "version": "0.8.5"
 }