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Add fusionV2 and wave for Azure CE #340

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merged 4 commits into from
Oct 13, 2023
Merged

Add fusionV2 and wave for Azure CE #340

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42f6f26
add fusionV2 and wave for azure CE, forge and manual
JaimeSeqLabs Sep 22, 2023
b0244b1
update reflection files
JaimeSeqLabs Sep 22, 2023
95d3136
Update src/main/java/io/seqera/tower/cli/commands/computeenvs/platfor…
JaimeSeqLabs Sep 29, 2023
d93d5c7
Update src/main/java/io/seqera/tower/cli/commands/computeenvs/platfor…
JaimeSeqLabs Sep 29, 2023
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9 changes: 6 additions & 3 deletions conf/reflect-config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2150,19 +2150,22 @@
"name":"io.seqera.tower.model.AzBatchConfig",
"allDeclaredFields":true,
"allDeclaredMethods":true,
"allDeclaredConstructors":true
"allDeclaredConstructors":true,
"methods":[{"name":"getAutoPoolMode","parameterTypes":[] }, {"name":"getDeleteJobsOnCompletion","parameterTypes":[] }, {"name":"getDeletePoolsOnCompletion","parameterTypes":[] }, {"name":"getDiscriminator","parameterTypes":[] }, {"name":"getEnvironment","parameterTypes":[] }, {"name":"getForge","parameterTypes":[] }, {"name":"getFusion2Enabled","parameterTypes":[] }, {"name":"getHeadPool","parameterTypes":[] }, {"name":"getPostRunScript","parameterTypes":[] }, {"name":"getPreRunScript","parameterTypes":[] }, {"name":"getRegion","parameterTypes":[] }, {"name":"getTokenDuration","parameterTypes":[] }, {"name":"getWaveEnabled","parameterTypes":[] }, {"name":"getWorkDir","parameterTypes":[] }]
},
{
"name":"io.seqera.tower.model.AzBatchForgeConfig",
"allDeclaredFields":true,
"allDeclaredMethods":true,
"allDeclaredConstructors":true
"allDeclaredConstructors":true,
"methods":[{"name":"getAutoScale","parameterTypes":[] }, {"name":"getContainerRegIds","parameterTypes":[] }, {"name":"getDisposeOnDeletion","parameterTypes":[] }, {"name":"getVmCount","parameterTypes":[] }, {"name":"getVmType","parameterTypes":[] }]
},
{
"name":"io.seqera.tower.model.AzureSecurityKeys",
"allDeclaredFields":true,
"allDeclaredMethods":true,
"allDeclaredConstructors":true
"allDeclaredConstructors":true,
"methods":[{"name":"<init>","parameterTypes":[] }, {"name":"setBatchKey","parameterTypes":["java.lang.String"] }, {"name":"setBatchName","parameterTypes":["java.lang.String"] }, {"name":"setStorageKey","parameterTypes":["java.lang.String"] }, {"name":"setStorageName","parameterTypes":["java.lang.String"] }]
},
{
"name":"io.seqera.tower.model.BitBucketSecurityKeys",
Expand Down
7 changes: 7 additions & 0 deletions src/main/java/io/seqera/tower/cli/commands/computeenvs/platforms/AzBatchForgePlatform.java
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Expand Up @@ -48,6 +48,11 @@ public class AzBatchForgePlatform extends AbstractPlatform<AzBatchConfig> {
@Option(names = {"--registry-credentials"}, split = ",", paramLabel = "<credential_name>", description = "Comma-separated list of container registry credentials name.")
public List<String> registryCredentials;

@Option(names = {"--fusion-v2"}, description = "With Fusion v2 enabled, S3 buckets specified in the Pipeline work directory and Allowed S3 Buckets fields will be accessible in the compute nodes storage (requires Wave containers service).")
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public boolean fusionV2;

@Option(names = {"--wave"}, description = "Allow access to private container repositories and the provisioning of containers in your Nextflow pipelines via the Wave containers service.")
public boolean wave;

@ArgGroup(heading = "%nAdvanced options:%n", validate = false)
public AdvancedOptions adv;
Expand All @@ -66,6 +71,8 @@ public AzBatchConfig computeConfig(Long workspaceId, DefaultApi api) throws ApiE
.preRunScript(preRunScriptString())
.postRunScript(postRunScriptString())
.environment(environmentVariables())
.fusion2Enabled(fusionV2)
.waveEnabled(wave)
.region(location);

if (adv != null) {
Expand Down
8 changes: 8 additions & 0 deletions src/main/java/io/seqera/tower/cli/commands/computeenvs/platforms/AzBatchManualPlatform.java
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Expand Up @@ -28,6 +28,12 @@ public class AzBatchManualPlatform extends AbstractPlatform<AzBatchConfig> {
@Option(names = {"--compute-pool-name"}, description = "The Azure Batch compute pool to be used to run the Nextflow jobs. This needs to be a pre-configured Batch compute pool which includes the azcopy command line (see the Tower documentation for details).", required = true)
public String computePoolName;

@Option(names = {"--fusion-v2"}, description = "With Fusion v2 enabled, S3 buckets specified in the Pipeline work directory and Allowed S3 Buckets fields will be accessible in the compute nodes storage (requires Wave containers service).")
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public boolean fusionV2;

@Option(names = {"--wave"}, description = "Allow access to private container repositories and the provisioning of containers in your Nextflow pipelines via the Wave containers service.")
public boolean wave;

@ArgGroup(heading = "%nAdvanced options:%n", validate = false)
public AdvancedOptions adv;

Expand All @@ -45,6 +51,8 @@ public AzBatchConfig computeConfig() throws ApiException, IOException {
.preRunScript(preRunScriptString())
.postRunScript(postRunScriptString())
.environment(environmentVariables())
.fusion2Enabled(fusionV2)
.waveEnabled(wave)
.region(location)
.headPool(computePoolName);

Expand Down
11 changes: 8 additions & 3 deletions src/test/java/io/seqera/tower/cli/computeenvs/platforms/AzBatchForgePlatformTest.java
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Expand Up @@ -18,6 +18,7 @@
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.EnumSource;
import org.mockserver.client.MockServerClient;
import org.mockserver.model.JsonBody;
import org.mockserver.model.MediaType;

import static io.seqera.tower.cli.commands.AbstractApiCmd.USER_WORKSPACE_NAME;
Expand All @@ -33,14 +34,16 @@ class AzBatchForgePlatformTest extends BaseCmdTest {
@EnumSource(OutputType.class)
void testAdd(OutputType format, MockServerClient mock) {

mock.reset();

mock.when(
request().withMethod("GET").withPath("/credentials").withQueryStringParameter("platformId", "azure-batch"), exactly(1)
).respond(
response().withStatusCode(200).withBody("{\"credentials\":[{\"id\":\"57Ic6reczFn78H1DTaaXkp\",\"name\":\"azure\",\"description\":null,\"discriminator\":\"azure\",\"baseUrl\":null,\"category\":null,\"deleted\":null,\"lastUsed\":null,\"dateCreated\":\"2021-09-07T13:50:21Z\",\"lastUpdated\":\"2021-09-07T13:50:21Z\"}]}").withContentType(MediaType.APPLICATION_JSON)
);

mock.when(
request().withMethod("POST").withPath("/compute-envs").withBody("{\"computeEnv\":{\"name\":\"azure\",\"platform\":\"azure-batch\",\"config\":{\"workDir\":\"az://nextflow-ci/jordeu\",\"region\":\"europe\",\"forge\":{\"vmCount\":10,\"autoScale\":true,\"disposeOnDeletion\":true}},\"credentialsId\":\"57Ic6reczFn78H1DTaaXkp\"}}"), exactly(1)
request().withMethod("POST").withPath("/compute-envs").withBody(JsonBody.json("{\"computeEnv\":{\"name\":\"azure\",\"platform\":\"azure-batch\",\"config\":{\"workDir\":\"az://nextflow-ci/jordeu\",\"region\":\"europe\",\"forge\":{\"vmCount\":10,\"autoScale\":true,\"disposeOnDeletion\":true}},\"credentialsId\":\"57Ic6reczFn78H1DTaaXkp\"}}")), exactly(1)
).respond(
response().withStatusCode(200).withBody("{\"computeEnvId\":\"isnEDBLvHDAIteOEF44ow\"}").withContentType(MediaType.APPLICATION_JSON)
);
Expand All @@ -52,19 +55,21 @@ void testAdd(OutputType format, MockServerClient mock) {
@Test
void testAddWithAdvancedOptions(MockServerClient mock) {

mock.reset();

mock.when(
request().withMethod("GET").withPath("/credentials").withQueryStringParameter("platformId", "azure-batch"), exactly(1)
).respond(
response().withStatusCode(200).withBody("{\"credentials\":[{\"id\":\"57Ic6reczFn78H1DTaaXkp\",\"name\":\"azure\",\"description\":null,\"discriminator\":\"azure\",\"baseUrl\":null,\"category\":null,\"deleted\":null,\"lastUsed\":null,\"dateCreated\":\"2021-09-07T13:50:21Z\",\"lastUpdated\":\"2021-09-07T13:50:21Z\"}]}").withContentType(MediaType.APPLICATION_JSON)
);

mock.when(
request().withMethod("POST").withPath("/compute-envs").withBody("{\"computeEnv\":{\"name\":\"azure\",\"platform\":\"azure-batch\",\"config\":{\"workDir\":\"az://nextflow-ci/jordeu\",\"region\":\"europe\",\"forge\":{\"vmCount\":10,\"autoScale\":true,\"disposeOnDeletion\":true},\"tokenDuration\":\"24\"},\"credentialsId\":\"57Ic6reczFn78H1DTaaXkp\"}}"), exactly(1)
request().withMethod("POST").withPath("/compute-envs").withBody(JsonBody.json("{\"computeEnv\":{\"name\":\"azure\",\"platform\":\"azure-batch\",\"config\":{\"workDir\":\"az://nextflow-ci/jordeu\",\"region\":\"europe\",\"fusion2Enabled\":true,\"waveEnabled\":true,\"forge\":{\"vmCount\":10,\"autoScale\":true,\"disposeOnDeletion\":true},\"tokenDuration\":\"24\"},\"credentialsId\":\"57Ic6reczFn78H1DTaaXkp\"}}")), exactly(1)
).respond(
response().withStatusCode(200).withBody("{\"computeEnvId\":\"isnEDBLvHDAIteOEF44ow\"}").withContentType(MediaType.APPLICATION_JSON)
);

ExecOut out = exec(mock, "compute-envs", "add", "azure-batch", "forge", "-n", "azure", "-l", "europe", "--work-dir", "az://nextflow-ci/jordeu", "--token-duration=24", "--vm-count", "10");
ExecOut out = exec(mock, "compute-envs", "add", "azure-batch", "forge", "-n", "azure", "-l", "europe", "--work-dir", "az://nextflow-ci/jordeu", "--fusion-v2", "--wave", "--token-duration=24", "--vm-count", "10");

assertEquals("", out.stdErr);
assertEquals(new ComputeEnvAdded("azure-batch", "isnEDBLvHDAIteOEF44ow", "azure", null, USER_WORKSPACE_NAME).toString(), out.stdOut);
Expand Down
13 changes: 9 additions & 4 deletions src/test/java/io/seqera/tower/cli/computeenvs/platforms/AzBatchManualPlatformTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.EnumSource;
import org.mockserver.client.MockServerClient;
import org.mockserver.model.JsonBody;
import org.mockserver.model.MediaType;

import static io.seqera.tower.cli.commands.AbstractApiCmd.USER_WORKSPACE_NAME;
Expand All @@ -33,14 +34,16 @@ class AzBatchManualPlatformTest extends BaseCmdTest {
@EnumSource(OutputType.class)
void testAdd(OutputType format, MockServerClient mock) {

mock.reset();

mock.when(
request().withMethod("GET").withPath("/credentials").withQueryStringParameter("platformId", "azure-batch"), exactly(1)
).respond(
response().withStatusCode(200).withBody("{\"credentials\":[{\"id\":\"57Ic6reczFn78H1DTaaXkp\",\"name\":\"azure\",\"description\":null,\"discriminator\":\"azure\",\"baseUrl\":null,\"category\":null,\"deleted\":null,\"lastUsed\":null,\"dateCreated\":\"2021-09-07T13:50:21Z\",\"lastUpdated\":\"2021-09-07T13:50:21Z\"}]}").withContentType(MediaType.APPLICATION_JSON)
response().withStatusCode(200).withBody(JsonBody.json("{\"credentials\":[{\"id\":\"57Ic6reczFn78H1DTaaXkp\",\"name\":\"azure\",\"description\":null,\"discriminator\":\"azure\",\"baseUrl\":null,\"category\":null,\"deleted\":null,\"lastUsed\":null,\"dateCreated\":\"2021-09-07T13:50:21Z\",\"lastUpdated\":\"2021-09-07T13:50:21Z\"}]}")).withContentType(MediaType.APPLICATION_JSON)
);

mock.when(
request().withMethod("POST").withPath("/compute-envs").withBody("{\"computeEnv\":{\"name\":\"azure-manual\",\"platform\":\"azure-batch\",\"config\":{\"workDir\":\"az://nextflow-ci/jordeu\",\"region\":\"europe\",\"headPool\":\"tower_pool\"},\"credentialsId\":\"57Ic6reczFn78H1DTaaXkp\"}}"), exactly(1)
request().withMethod("POST").withPath("/compute-envs").withBody(JsonBody.json("{\"computeEnv\":{\"name\":\"azure-manual\",\"platform\":\"azure-batch\",\"config\":{\"workDir\":\"az://nextflow-ci/jordeu\",\"region\":\"europe\",\"fusion2Enabled\":false,\"waveEnabled\":false,\"headPool\":\"tower_pool\"},\"credentialsId\":\"57Ic6reczFn78H1DTaaXkp\"}}")), exactly(1)
).respond(
response().withStatusCode(200).withBody("{\"computeEnvId\":\"isnEDBLvHDAIteOEF44ow\"}").withContentType(MediaType.APPLICATION_JSON)
);
Expand All @@ -52,19 +55,21 @@ void testAdd(OutputType format, MockServerClient mock) {
@Test
void testAddWithAdvancedOptions(MockServerClient mock) {

mock.reset();

mock.when(
request().withMethod("GET").withPath("/credentials").withQueryStringParameter("platformId", "azure-batch"), exactly(1)
).respond(
response().withStatusCode(200).withBody("{\"credentials\":[{\"id\":\"57Ic6reczFn78H1DTaaXkp\",\"name\":\"azure\",\"description\":null,\"discriminator\":\"azure\",\"baseUrl\":null,\"category\":null,\"deleted\":null,\"lastUsed\":null,\"dateCreated\":\"2021-09-07T13:50:21Z\",\"lastUpdated\":\"2021-09-07T13:50:21Z\"}]}").withContentType(MediaType.APPLICATION_JSON)
);

mock.when(
request().withMethod("POST").withPath("/compute-envs").withBody("{\"computeEnv\":{\"name\":\"azure-manual\",\"platform\":\"azure-batch\",\"config\":{\"workDir\":\"az://nextflow-ci/jordeu\",\"region\":\"europe\",\"headPool\":\"tower_pool\",\"tokenDuration\":\"24\"},\"credentialsId\":\"57Ic6reczFn78H1DTaaXkp\"}}"), exactly(1)
request().withMethod("POST").withPath("/compute-envs").withBody(JsonBody.json("{\"computeEnv\":{\"name\":\"azure-manual\",\"platform\":\"azure-batch\",\"config\":{\"workDir\":\"az://nextflow-ci/jordeu\",\"region\":\"europe\",\"fusion2Enabled\":true,\"waveEnabled\":true,\"headPool\":\"tower_pool\",\"tokenDuration\":\"24\"},\"credentialsId\":\"57Ic6reczFn78H1DTaaXkp\"}}")), exactly(1)
).respond(
response().withStatusCode(200).withBody("{\"computeEnvId\":\"isnEDBLvHDAIteOEF44ow\"}").withContentType(MediaType.APPLICATION_JSON)
);

ExecOut out = exec(mock, "compute-envs", "add", "azure-batch", "manual", "-n", "azure-manual", "-l", "europe", "--work-dir", "az://nextflow-ci/jordeu", "--compute-pool-name=tower_pool", "--token-duration=24");
ExecOut out = exec(mock, "compute-envs", "add", "azure-batch", "manual", "-n", "azure-manual", "-l", "europe", "--work-dir", "az://nextflow-ci/jordeu", "--fusion-v2", "--wave", "--compute-pool-name=tower_pool", "--token-duration=24");

assertEquals("", out.stdErr);
assertEquals(new ComputeEnvAdded("azure-batch", "isnEDBLvHDAIteOEF44ow", "azure-manual", null, USER_WORKSPACE_NAME).toString(), out.stdOut);
Expand Down
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