[ARVADOS] updated: a84be631958ac0bb45b5e06efdb2782f02fdb2af
git at public.curoverse.com
git at public.curoverse.com
Tue May 20 09:58:40 EDT 2014
Summary of changes:
apps/workbench/.gitignore | 4 +
apps/workbench/Gemfile | 18 +-
apps/workbench/Gemfile.lock | 147 ++--
.../api_client_authorizations.js.coffee | 3 -
.../assets/javascripts/authorized_keys.js.coffee | 3 -
.../app/assets/javascripts/collections.js | 1 -
.../app/assets/javascripts/folders.js.coffee | 3 -
.../app/assets/javascripts/groups.js.coffee | 3 -
.../app/assets/javascripts/humans.js.coffee | 3 -
.../app/assets/javascripts/job_tasks.js.coffee | 3 -
.../app/assets/javascripts/jobs.js.coffee | 3 -
.../app/assets/javascripts/keep_disks.js.coffee | 31 +-
.../app/assets/javascripts/links.js.coffee | 3 -
.../app/assets/javascripts/logs.js.coffee | 3 -
.../app/assets/javascripts/nodes.js.coffee | 3 -
.../app/assets/javascripts/pipeline_instances.js | 1 -
.../javascripts/pipeline_templates.js.coffee | 3 -
.../app/assets/javascripts/repositories.js.coffee | 3 -
.../app/assets/javascripts/sessions.js.coffee | 3 -
apps/workbench/app/assets/javascripts/sizing.js | 2 +-
.../app/assets/javascripts/specimens.js.coffee | 3 -
.../app/assets/javascripts/traits.js.coffee | 3 -
.../assets/javascripts/user_agreements.js.coffee | 3 -
.../app/assets/javascripts/users.js.coffee | 3 -
.../assets/javascripts/virtual_machines.js.coffee | 3 -
.../app/assets/stylesheets/keep_disks.css.scss | 8 +
.../app/controllers/actions_controller.rb | 2 +-
.../api_client_authorizations_controller.rb | 13 -
.../app/controllers/application_controller.rb | 21 +-
.../app/controllers/collections_controller.rb | 3 +-
apps/workbench/app/controllers/jobs_controller.rb | 7 +-
.../app/controllers/keep_disks_controller.rb | 47 ++
.../controllers/pipeline_instances_controller.rb | 2 +-
.../app/controllers/sessions_controller.rb | 2 +-
apps/workbench/app/controllers/users_controller.rb | 10 +-
.../app/helpers/arvados_api_client_helper.rb | 13 +
apps/workbench/app/models/arvados_api_client.rb | 43 +-
apps/workbench/app/models/arvados_base.rb | 60 +-
apps/workbench/app/models/arvados_resource_list.rb | 7 +-
apps/workbench/app/models/collection.rb | 4 +-
apps/workbench/app/models/group.rb | 4 +-
apps/workbench/app/models/job.rb | 4 +
apps/workbench/app/models/pipeline_instance.rb | 3 +-
apps/workbench/app/models/user.rb | 26 +-
apps/workbench/app/models/user_agreement.rb | 8 +-
.../application/_pipeline_status_label.html.erb | 6 +-
.../app/views/application/_show_metadata.html.erb | 4 +-
.../workbench/app/views/jobs/_show_recent.html.erb | 6 +-
.../app/views/keep_disks/_content_layout.html.erb | 21 +
.../app/views/layouts/application.html.erb | 7 +-
apps/workbench/app/views/links/_recent.html.erb | 2 +-
.../pipeline_instances/_show_components.html.erb | 27 +-
.../views/pipeline_instances/_show_recent.html.erb | 8 +-
.../app/views/pipeline_instances/show.js.erb | 6 +-
.../workbench/app/views/users/_show_admin.html.erb | 2 +-
apps/workbench/app/views/users/welcome.html.erb | 2 +-
apps/workbench/app/views/websocket/index.html.erb | 2 +-
apps/workbench/config/application.default.yml | 14 +-
apps/workbench/config/application.rb | 15 +-
.../config/environments/development.rb.example | 12 +-
.../config/environments/production.rb.example | 6 +-
apps/workbench/config/environments/test.rb.example | 6 -
.../config/initializers/zzz_arvados_api_client.rb | 8 -
.../zza_load_config.rb => load_config.rb} | 0
apps/workbench/config/routes.rb | 8 +-
.../workbench/test/integration/collections_test.rb | 9 +
apps/workbench/test/integration/users_test.rb | 7 +-
apps/workbench/test/test_helper.rb | 78 +-
.../install-workbench-app.html.textile.liquid | 11 +
doc/sdk/python/sdk-python.html.textile.liquid | 3 +-
sdk/cli/arvados-cli.gemspec | 1 +
sdk/cli/bin/arv | 11 +-
sdk/cli/bin/arv-run-pipeline-instance | 62 +-
sdk/cli/bin/crunch-job | 13 +-
.../main/java/org/arvados/sdk/java/Arvados.java | 86 +-
.../java/org/arvados/sdk/java/ArvadosTest.java | 72 +-
sdk/perl/lib/Arvados.pm | 2 +-
sdk/perl/lib/Arvados/Request.pm | 9 +-
sdk/python/arvados/api.py | 7 +-
sdk/python/requirements.txt | 14 +-
sdk/python/run_test_server.py | 196 ++++-
sdk/python/setup.py | 3 +-
sdk/python/setup.py.src | 23 -
sdk/python/setup_header.py | 11 -
sdk/python/test_keep_client.py | 23 +-
sdk/python/test_pipeline_template.py | 18 +-
sdk/python/test_websockets.py | 6 +-
sdk/ruby/arvados.gemspec | 1 +
sdk/ruby/lib/arvados.rb | 7 +-
services/api/.gitignore | 4 +
services/api/Gemfile.lock | 10 +-
services/api/app/models/api_client.rb | 2 +-
services/api/app/models/arvados_model.rb | 10 +-
services/api/app/models/authorized_key.rb | 2 +-
services/api/app/models/collection.rb | 2 +-
services/api/app/models/group.rb | 5 +-
services/api/app/models/human.rb | 2 +-
services/api/app/models/job.rb | 2 +-
services/api/app/models/job_task.rb | 2 +-
services/api/app/models/keep_disk.rb | 2 +-
services/api/app/models/link.rb | 2 +-
services/api/app/models/log.rb | 2 +-
services/api/app/models/node.rb | 2 +-
services/api/app/models/pipeline_instance.rb | 38 +-
services/api/app/models/pipeline_template.rb | 2 +-
services/api/app/models/repository.rb | 2 +-
services/api/app/models/specimen.rb | 2 +-
services/api/app/models/trait.rb | 2 +-
services/api/app/models/user.rb | 6 +-
services/api/app/models/virtual_machine.rb | 2 +-
services/api/config/application.default.yml | 10 +
services/api/config/application.yml.example | 7 -
services/api/config/initializers/assign_uuid.rb | 1 -
services/api/config/initializers/eventbus.rb | 6 +-
.../20140422011506_pipeline_instance_state.rb | 2 +
services/api/lib/assign_uuid.rb | 31 -
services/api/lib/can_be_an_owner.rb | 47 ++
services/api/lib/has_uuid.rb | 42 +
services/api/lib/record_filters.rb | 4 +
services/api/script/crunch-dispatch.rb | 20 +-
services/api/test/fixtures/links.yml | 16 +
services/api/test/fixtures/pipeline_instances.yml | 3 +
.../api/test/functional/arvados/v1/filters_test.rb | 16 +
services/api/test/unit/arvados_model_test.rb | 34 +
services/api/test/unit/link_test.rb | 14 +-
services/api/test/unit/owner_test.rb | 126 +++
services/api/test/unit/pipeline_instance_test.rb | 26 +-
services/datamanager/experimental/datamanager.py | 887 +++++++++++++++++++++
.../datamanager/experimental/datamanager_test.py | 41 +
services/fuse/.gitignore | 1 +
.../fuse/arvados_fuse}/__init__.py | 27 +-
{sdk/python => services/fuse}/bin/arv-mount | 6 +-
{sdk/python => services/fuse}/readme.llfuse | 0
services/fuse/requirements.txt | 3 +
services/fuse/run_test_server.py | 1 +
sdk/python/setup_fuse.py => services/fuse/setup.py | 13 +-
{sdk/python => services/fuse}/test_mount.py | 21 +-
services/keep/src/keep/handler_test.go | 438 ++++++++++
services/keep/src/keep/keep.go | 274 ++++++-
services/keep/src/keep/keep_test.go | 5 +-
services/keep/src/keep/perms.go | 11 +-
141 files changed, 2924 insertions(+), 692 deletions(-)
delete mode 100644 apps/workbench/app/assets/javascripts/api_client_authorizations.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/authorized_keys.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/folders.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/groups.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/humans.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/job_tasks.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/jobs.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/links.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/logs.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/nodes.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/pipeline_templates.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/repositories.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/sessions.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/specimens.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/traits.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/user_agreements.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/users.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/virtual_machines.js.coffee
create mode 100644 apps/workbench/app/helpers/arvados_api_client_helper.rb
create mode 100644 apps/workbench/app/views/keep_disks/_content_layout.html.erb
delete mode 100644 apps/workbench/config/initializers/zzz_arvados_api_client.rb
rename apps/workbench/config/{initializers/zza_load_config.rb => load_config.rb} (100%)
delete mode 100644 sdk/python/setup.py.src
delete mode 100644 sdk/python/setup_header.py
delete mode 100644 services/api/config/initializers/assign_uuid.rb
delete mode 100644 services/api/lib/assign_uuid.rb
create mode 100644 services/api/lib/can_be_an_owner.rb
create mode 100644 services/api/lib/has_uuid.rb
create mode 100644 services/api/test/functional/arvados/v1/filters_test.rb
create mode 100644 services/api/test/unit/arvados_model_test.rb
create mode 100644 services/api/test/unit/owner_test.rb
create mode 100755 services/datamanager/experimental/datamanager.py
create mode 100755 services/datamanager/experimental/datamanager_test.py
create mode 120000 services/fuse/.gitignore
rename {sdk/python/arvados/fuse => services/fuse/arvados_fuse}/__init__.py (95%)
rename {sdk/python => services/fuse}/bin/arv-mount (96%)
rename {sdk/python => services/fuse}/readme.llfuse (100%)
create mode 100644 services/fuse/requirements.txt
create mode 120000 services/fuse/run_test_server.py
rename sdk/python/setup_fuse.py => services/fuse/setup.py (68%)
rename {sdk/python => services/fuse}/test_mount.py (95%)
create mode 100644 services/keep/src/keep/handler_test.go
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commit a84be631958ac0bb45b5e06efdb2782f02fdb2af
Author: radhika <radhika at curoverse.com>
Date: Tue May 20 09:57:20 2014 -0400
2525: handling of array objects was not quite correct. it would not have worked if a pure array object that is not filters is passed in.
diff --git a/sdk/java/src/main/java/org/arvados/sdk/java/Arvados.java b/sdk/java/src/main/java/org/arvados/sdk/java/Arvados.java
index acaaf52..b9b7a8f 100644
--- a/sdk/java/src/main/java/org/arvados/sdk/java/Arvados.java
+++ b/sdk/java/src/main/java/org/arvados/sdk/java/Arvados.java
@@ -189,28 +189,49 @@ public class Arvados {
* @return Set
* @throws Exception
*/
- public Set<String> getAvailableParametersForMethod(String resourceName, String methodName)
+ public Map<String,List<String>> getAvailableParametersForMethod(String resourceName, String methodName)
throws Exception {
RestMethod method = getMatchingMethod(resourceName, methodName);
- Set<String> parameters = method.getParameters().keySet();
- Request request = method.getRequest();
- if (request != null) {
- Object requestProperties = request.get("properties");
- if (requestProperties != null) {
- if (requestProperties instanceof Map) {
- Map properties = (Map)requestProperties;
- Set<String> propertyKeys = properties.keySet();
- if (propertyKeys.size()>0) {
- try {
- propertyKeys.addAll(parameters);
- return propertyKeys;
- } catch (Exception e){
- logger.error(e);
+ Map<String, List<String>> parameters = new HashMap<String, List<String>>();
+ List<String> requiredParameters = new ArrayList<String>();
+ List<String> optionalParameters = new ArrayList<String>();
+ parameters.put ("required", requiredParameters);
+ parameters.put("optional", optionalParameters);
+
+ try {
+ // get any request parameters
+ Request request = method.getRequest();
+ if (request != null) {
+ Object required = request.get("required");
+ Object requestProperties = request.get("properties");
+ if (requestProperties != null) {
+ if (requestProperties instanceof Map) {
+ Map properties = (Map)requestProperties;
+ Set<String> propertyKeys = properties.keySet();
+ for (String property : propertyKeys) {
+ if (Boolean.TRUE.equals(required)) {
+ requiredParameters.add(property);
+ } else {
+ optionalParameters.add(property);
+ }
}
}
}
}
+
+ // get other listed parameters
+ Map<String,JsonSchema> methodParameters = method.getParameters();
+ for (Map.Entry<String, JsonSchema> entry : methodParameters.entrySet()) {
+ if (Boolean.TRUE.equals(entry.getValue().getRequired())) {
+ requiredParameters.add(entry.getKey());
+ } else {
+ optionalParameters.add(entry.getKey());
+ }
+ }
+ } catch (Exception e){
+ logger.error(e);
}
+
return parameters;
}
@@ -329,6 +350,8 @@ public class Arvados {
value = new BigInteger(parameterValue.toString());
} else if ("float".equals(parameter.getType())) {
value = new BigDecimal(parameterValue.toString());
+ } else if ("Java.util.Calendar".equals(parameter.getType())) {
+ value = new BigDecimal(parameterValue.toString());
} else if (("array".equals(parameter.getType())) ||
("Array".equals(parameter.getType()))) {
if (parameterValue.getClass().isArray()){
@@ -355,32 +378,35 @@ public class Arvados {
private String getJsonValueFromArrayType (Object parameterValue) {
String arrayStr = Arrays.deepToString((Object[])parameterValue);
- arrayStr = arrayStr.substring(1, arrayStr.length()-1);
+
+ // we can expect either an array of array objects or an array of objects
+ if (arrayStr.startsWith("[[")) {
+ Object[][] array = new Object[1][];
+ arrayStr = arrayStr.substring(2, arrayStr.length()-2);
+ String jsonStr = getJsonStringForArray(arrayStr);
+ String value = "[" + jsonStr + "]";
+ return value;
+ } else {
+ arrayStr = arrayStr.substring(1, arrayStr.length()-1);
+ return (getJsonStringForArray(arrayStr));
+ }
+ }
+
+ private String getJsonStringForArray(String arrayStr) {
Object[] array = arrayStr.split(",");
Object[] trimmedArray = new Object[array.length];
for (int i=0; i<array.length; i++){
trimmedArray[i] = array[i].toString().trim();
}
- String jsonString = JSONArray.toJSONString(Arrays.asList(trimmedArray));
- String value = "["+ jsonString +"]";
-
+ String value = JSONArray.toJSONString(Arrays.asList(trimmedArray));
return value;
}
private String getJsonValueFromListType (Object parameterValue) {
List paramList = (List)parameterValue;
Object[] array = new Object[paramList.size()];
- String arrayStr = Arrays.deepToString(paramList.toArray(array));
- arrayStr = arrayStr.substring(1, arrayStr.length()-1);
- array = arrayStr.split(",");
- Object[] trimmedArray = new Object[array.length];
- for (int i=0; i<array.length; i++){
- trimmedArray[i] = array[i].toString().trim();
- }
- String jsonString = JSONArray.toJSONString(Arrays.asList(trimmedArray));
- String value = "["+ jsonString +"]";
-
- return value;
+ Arrays.deepToString(paramList.toArray(array));
+ return (getJsonValueFromArrayType(array));
}
private String getJsonValueFromMapType (Object parameterValue) {
diff --git a/sdk/java/src/test/java/org/arvados/sdk/java/ArvadosTest.java b/sdk/java/src/test/java/org/arvados/sdk/java/ArvadosTest.java
index bb1cf64..5176e8c 100644
--- a/sdk/java/src/test/java/org/arvados/sdk/java/ArvadosTest.java
+++ b/sdk/java/src/test/java/org/arvados/sdk/java/ArvadosTest.java
@@ -2,7 +2,11 @@ package org.arvados.sdk.java;
import java.io.File;
import java.io.FileInputStream;
+import java.math.BigDecimal;
import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -334,11 +338,12 @@ public class ArvadosTest {
Map response = arv.call("links", "list", params);
assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
- String[] filters = new String[3];
- filters[0] = "name";
- filters[1] = "=";
- filters[2] = "can_manage";
-
+ String[][] filters = new String[1][];
+ String[] condition = new String[3];
+ condition[0] = "name";
+ condition[1] = "=";
+ condition[2] = "can_manage";
+ filters[0] = condition;
params.put("filters", filters);
response = arv.call("links", "list", params);
@@ -356,11 +361,12 @@ public class ArvadosTest {
Map response = arv.call("links", "list", params);
assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
- List<String> filters = new ArrayList<String>();
- filters.add("name");
- filters.add("is_a");
- filters.add("can_manage");
-
+ List<List> filters = new ArrayList<List>();
+ List<String> condition = new ArrayList<String>();
+ condition.add("name");
+ condition.add("is_a");
+ condition.add("can_manage");
+ filters.add(condition);
params.put("filters", filters);
response = arv.call("links", "list", params);
@@ -370,6 +376,35 @@ public class ArvadosTest {
}
@Test
+ public void testGetLinksWithTimestampFilters() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map response = arv.call("links", "list", params);
+ assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
+
+ // get links created "tomorrow". Expect none in response
+ Calendar calendar = new GregorianCalendar();
+ calendar.setTime(new Date());
+ calendar.add(Calendar.DAY_OF_MONTH, 1);
+
+ Object[][] filters = new Object[1][];
+ Object[] condition = new Object[3];
+ condition[0] = "created_at";
+ condition[1] = ">";
+ condition[2] = calendar.get(Calendar.YEAR) + "-" + (calendar.get(Calendar.MONTH)+1) + "-" + calendar.get(Calendar.DAY_OF_MONTH);
+ filters[0] = condition;
+ params.put("filters", filters);
+
+ response = arv.call("links", "list", params);
+
+ assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
+ int items_avail = ((BigDecimal)response.get("items_available")).intValue();
+ assertEquals("Expected zero links", items_avail, 0);
+ }
+
+ @Test
public void testGetLinksWithWhereClause() throws Exception {
Arvados arv = new Arvados("arvados", "v1");
@@ -404,17 +439,26 @@ public class ArvadosTest {
@Test
public void testGetAvailableParametersForUsersGetMethod() throws Exception {
Arvados arv = new Arvados("arvados", "v1");
- Set<String> parameters = arv.getAvailableParametersForMethod("users", "get");
+ Map<String,List<String>> parameters = arv.getAvailableParametersForMethod("users", "get");
assertNotNull("Expected parameters", parameters);
- assertTrue("Excected uuid parameter for get method for users", parameters.contains("uuid"));
+ assertTrue("Excected uuid parameter for get method for users", parameters.get("required").contains("uuid"));
}
@Test
public void testGetAvailableParametersForUsersCreateMethod() throws Exception {
Arvados arv = new Arvados("arvados", "v1");
- Set<String> parameters = arv.getAvailableParametersForMethod("users", "create");
+ Map<String,List<String>> parameters = arv.getAvailableParametersForMethod("users", "create");
+ assertNotNull("Expected parameters", parameters);
+ assertTrue("Excected user parameter for get method for users", parameters.get("required").contains("user"));
+ }
+
+ @Test
+ public void testGetAvailableParametersForUsersListMethod() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+ Map<String,List<String>> parameters = arv.getAvailableParametersForMethod("users", "list");
assertNotNull("Expected parameters", parameters);
- assertTrue("Excected user parameter for create method for users", parameters.contains("user"));
+ assertTrue("Excected no required parameter for list method for users", parameters.get("required").size() == 0);
+ assertTrue("Excected some optional parameters for list method for users", parameters.get("optional").contains("filters"));
}
}
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