dxpy 0.378.0__tar.gz → 0.380.0__tar.gz

{dxpy-0.378.0 → dxpy-0.380.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.378.0
+Version: 0.380.0
 Summary: DNAnexus Platform API bindings for Python
 Home-page: https://github.com/dnanexus/dx-toolkit
 Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung
@@ -21,8 +21,9 @@ Provides-Extra: xattr
 
 dxpy: DNAnexus Python API
 =========================
+[DNAnexus Documentation](https://documentation.dnanexus.com/)
 
-[API Documentation](http://autodoc.dnanexus.com/bindings/python/current/)
+[dxpy API Documentation](http://autodoc.dnanexus.com/bindings/python/current/)
 
 Building
 --------

{dxpy-0.378.0 → dxpy-0.380.0}/Readme.md

@@ -1,7 +1,8 @@
 dxpy: DNAnexus Python API
 =========================
+[DNAnexus Documentation](https://documentation.dnanexus.com/)
 
-[API Documentation](http://autodoc.dnanexus.com/bindings/python/current/)
+[dxpy API Documentation](http://autodoc.dnanexus.com/bindings/python/current/)
 
 Building
 --------

{dxpy-0.378.0 → dxpy-0.380.0}/dxpy/scripts/dx_build_app.py

@@ -1033,7 +1033,7 @@ def get_project_to_check(destination, extra_args):
 
 def verify_nf_license(destination, extra_args):
     dest_project_to_check = get_project_to_check(destination, extra_args)
-    features = dxpy.DXHTTPRequest("/" + dest_project_to_check + "/checkFeatureAccess", {"features": ["dxNextflow"]}).get("features", {})
+    features = dxpy.DXHTTPRequest("/" + dest_project_to_check + "/checkFeatureAccess", {"features": ["dxNextflow"]}, always_retry=True).get("features", {})
     dx_nextflow_lic = features.get("dxNextflow", False)
     if not dx_nextflow_lic:
         raise dxpy.app_builder.AppBuilderException("PermissionDenied: billTo of the applet's destination project must have the dxNextflow feature enabled. For inquiries, please contact support@dnanexus.com")

{dxpy-0.378.0 → dxpy-0.380.0}/dxpy/templating/templates/nextflow/src/nextflow.sh

@@ -35,9 +35,7 @@ main() {
     set -x
   fi
 
-  # If cache is used, it will be stored in the project at
-  DX_CACHEDIR=$DX_PROJECT_CONTEXT_ID:/.nextflow_cache_db
-  get_nextaur_version
+  detect_nextaur_plugin_version
 
   # unset properties
   cloned_job_properties=$(dx describe "$DX_JOB_ID" --json | jq -r '.properties | to_entries[] | select(.key | startswith("nextflow")) | .key')
@@ -46,11 +44,6 @@ main() {
   # check if all run opts provided by user are supported
   validate_run_opts
 
-  # Check if limit reached for Nextflow sessions preserved in this project's cache
-  if [[ $preserve_cache == true ]]; then
-    check_cache_db_storage
-  fi
-
   # set default NXF env constants
 
   # Disable use of newer flag --cpus when running Docker
@@ -88,36 +81,6 @@ main() {
   # get current executable name
   EXECUTABLE_NAME=$(jq -r .executableName /home/dnanexus/dnanexus-job.json)
 
-  # If resuming session, use resume id; otherwise create id for this session
-  if [[ -n $resume ]]; then
-    get_resume_session_id
-  else
-    NXF_UUID=$(uuidgen)
-  fi
-  export NXF_UUID
-
-  # Using the lenient mode to caching makes it possible to reuse working files for resume on the platform
-  export NXF_CACHE_MODE=LENIENT
-
-  if [[ $preserve_cache == true ]]; then
-    dx set_properties "$DX_JOB_ID" \
-      nextflow_executable="$EXECUTABLE_NAME" \
-      nextflow_session_id="$NXF_UUID" \
-      nextflow_preserve_cache="$preserve_cache"
-  fi
-
-  # check if there are any ongoing jobs resuming
-  # and generating new cache for the session to resume
-  if [[ $preserve_cache == true && -n $resume ]]; then
-    check_running_jobs
-  fi
-
-  # restore previous cache and create resume argument to nextflow run
-  RESUME_CMD=""
-  if [[ -n $resume ]]; then
-    restore_cache
-  fi
-
   # download default applet file type inputs
   dx-download-all-inputs --parallel @@EXCLUDE_INPUT_DOWNLOAD@@ 2>/dev/null 1>&2
   RUNTIME_CONFIG_CMD=''
@@ -140,7 +103,6 @@ main() {
     run @@RESOURCES_SUBPATH@@ \
     $profile_arg \
     -name ${DX_JOB_ID}${env_job_suffix} \
-    $RESUME_CMD \
     $nextflow_run_opts \
     $RUNTIME_PARAMS_FILE \
     $nextflow_pipeline_params)"
@@ -156,9 +118,23 @@ main() {
   aws_login
   aws_relogin_loop & AWS_RELOGIN_PID=$!
 
+  set_vars_session_and_cache
+  
+  if [[ $preserve_cache == true ]]; then
+    set_job_properties_cache
+    check_cache_db_storage_limit
+    if [[ -n $resume ]]; then
+      check_no_concurrent_job_same_cache
+    fi
+  fi
+
+  RESUME_CMD=""
+  if [[ -n $resume ]]; then
+    restore_cache_and_set_resume_cmd
+  fi
+
   # Set Nextflow workdir based on S3 workdir / preserve_cache options
   setup_workdir
-  export NXF_WORK
 
   # set beginning timestamp
   BEGIN_TIME="$(date +"%Y-%m-%d %H:%M:%S")"
@@ -230,24 +206,9 @@ on_exit() {
     set -xe
   fi
 
-  # backup cache
   if [[ $preserve_cache == true ]]; then
     echo "=== Execution completed — caching current session to $DX_CACHEDIR/$NXF_UUID"
-
-    # wrap cache folder and upload cache.tar
-    if [[ -n "$(ls -A .nextflow)" ]]; then
-      tar -cf cache.tar .nextflow
-
-      CACHE_ID=$(dx upload "cache.tar" --path "$DX_CACHEDIR/$NXF_UUID/cache.tar" --no-progress --brief --wait -p -r) &&
-        echo "Upload cache of current session as file: $CACHE_ID" &&
-        rm -f cache.tar ||
-        echo "Failed to upload cache of current session $NXF_UUID"
-    else
-      echo "No cache is generated from this execution. Skip uploading cache."
-    fi
-
-  # preserve_cache is false
-  # clean up files of this session
+    upload_session_cache_file
   else
     echo "=== Execution completed — cache and working files will not be resumable"
   fi
@@ -378,7 +339,7 @@ docker_registry_login() {
 aws_login() {
   if [ -f "$AWS_ENV" ]; then
     source $AWS_ENV
-    detect_using_s3_workdir
+    detect_if_using_s3_workdir
   
     # aws env file example values:
     # "iamRoleArnToAssume", "jobTokenAudience", "jobTokenSubjectClaims", "awsRegion"
@@ -414,7 +375,7 @@ aws_relogin_loop() {
 # Helpers: workdir configuration
 # =========================================================
 
-detect_using_s3_workdir() {
+detect_if_using_s3_workdir() {
   if [[ -f "$AWS_ENV" ]]; then
     source $AWS_ENV
   fi
@@ -441,6 +402,8 @@ setup_workdir() {
     # Work dir on platform and not using cache, use workspace
     NXF_WORK="dx://$DX_WORKSPACE_ID:/work/"
   fi
+
+  export NXF_WORK
 }
 
 # =========================================================
@@ -454,7 +417,7 @@ validate_run_opts() {
   for opt in "${opts[@]}"; do
     case $opt in
     -w=* | -work-dir=* | -w | -work-dir)
-      dx-jobutil-report-error "Nextflow workDir is set as $DX_CACHEDIR/<session_id>/work/ if preserve_cache=true, or $DX_WORKSPACE_ID:/work/ if preserve_cache=false. Please remove workDir specification (-w|-work-dir path) in nextflow_run_opts and run again."
+      dx-jobutil-report-error "Please remove workDir specification (-w|-work-dir path) in nextflow_run_opts. For Nextflow runs on DNAnexus, the workdir will be located at 1) In the workspace container-xxx 2) In project-yyy:/.nextflow_cache_db if preserve_cache=true, or 3) on S3, if specified."
       ;;
     -profile | -profile=*)
       if [ -n "$profile_arg" ]; then
@@ -467,26 +430,7 @@ validate_run_opts() {
   done
 }
 
-dx_path() {
-  local str=${1#"dx://"}
-  local tmp=$(mktemp -t nf-XXXXXXXXXX)
-  case $str in
-    project-*)
-      dx download $str -o $tmp --no-progress --recursive -f
-      echo file://$tmp
-      ;;
-    container-*)
-      dx download $str -o $tmp --no-progress --recursive -f
-      echo file://$tmp
-      ;;
-    *)
-      echo "Invalid $2 path: $1"
-      return 1
-      ;;
-  esac
-}
-
-get_nextaur_version() {
+detect_nextaur_plugin_version() {
   executable=$(cat dnanexus-executable.json | jq -r .id )
   bundled_dependency=$(dx describe ${executable} --json | jq -r '.runSpec.bundledDepends[] | select(.name=="nextaur.tar.gz") | .id."$dnanexus_link"')
   asset_dependency=$(dx describe ${bundled_dependency} --json | jq -r .properties.AssetBundle)
@@ -513,6 +457,7 @@ log_context_info() {
   echo "=== NF projectDir   : @@RESOURCES_SUBPATH@@"
   echo "=== NF session ID   : ${NXF_UUID}"
   echo "=== NF log file     : dx://${DX_JOB_OUTDIR%/}/${LOG_NAME}"
+  echo "=== NF workdir      : ${NXF_WORK}"
   if [[ $preserve_cache == true ]]; then
     echo "=== NF cache folder : dx://${DX_CACHEDIR}/${NXF_UUID}/"
   fi
@@ -569,6 +514,22 @@ download_cmd_launcher_file() {
 # Helpers: run with preserve cache, resume
 # =========================================================
 
+set_vars_session_and_cache() {
+  # Path in project to store cached sessions
+  export DX_CACHEDIR="${DX_PROJECT_CONTEXT_ID}:/.nextflow_cache_db"
+
+  # Using the lenient mode to caching makes it possible to reuse working files for resume on the platform
+  export NXF_CACHE_MODE=LENIENT
+
+  # If resuming session, use resume id; otherwise create id for this session
+  if [[ -n $resume ]]; then
+    get_resume_session_id
+  else
+    NXF_UUID=$(uuidgen)
+  fi
+  export NXF_UUID
+}
+
 get_resume_session_id() {
   if [[ $resume == 'true' || $resume == 'last' ]]; then
     # find the latest job run by applet with the same name
@@ -603,7 +564,48 @@ get_resume_session_id() {
   NXF_UUID=$PREV_JOB_SESSION_ID
 }
 
-restore_cache() {
+set_job_properties_cache() {
+  # Set properties on job, which can be used to look up cached job later
+  dx set_properties "$DX_JOB_ID" \
+    nextflow_executable="$EXECUTABLE_NAME" \
+    nextflow_session_id="$NXF_UUID" \
+    nextflow_preserve_cache="$preserve_cache"
+}
+
+check_cache_db_storage_limit() {
+  # Enforce a limit on cached session workdirs stored in the DNAnexus project
+  # Removal must be manual, because applet can only upload, not delete project files
+  # Limit does not apply when the workdir is external (e.g. S3)
+
+  MAX_CACHE_STORAGE=20
+  existing_cache=$(dx ls $DX_CACHEDIR --folders 2>/dev/null | wc -l)
+  [[ $existing_cache -lt $MAX_CACHE_STORAGE || $USING_S3_WORKDIR == true ]] ||
+    dx-jobutil-report-error "The limit for preserved sessions in the project is $MAX_CACHE_STORAGE. Please remove folders from $DX_CACHEDIR to be under the limit, run without preserve_cache=true, or use S3 as workdir."
+}
+
+check_no_concurrent_job_same_cache() {
+  # Do not allow more than 1 concurrent run with the same session id,
+  # to prevent conflicting workdir contents
+
+  FIRST_RESUMED_JOB=$(
+    dx api system findExecutions \
+      '{"state":["idle", "waiting_on_input", "runnable", "running", "debug_hold", "waiting_on_output", "restartable", "terminating"],
+        "project":"'$DX_PROJECT_CONTEXT_ID'",
+        "includeSubjobs":false,
+        "properties":{
+          "nextflow_session_id":"'$NXF_UUID'",
+          "nextflow_preserve_cache":"true",
+          "nextflow_executable":"'$EXECUTABLE_NAME'"}}' 2>/dev/null |
+      jq -r '.results[-1].id // empty'
+  )
+
+  [[ -n $FIRST_RESUMED_JOB && $DX_JOB_ID == $FIRST_RESUMED_JOB ]] ||
+    dx-jobutil-report-error "There is at least one other non-terminal state job with the same sessionID $NXF_UUID. 
+    Please wait until all other jobs sharing the same sessionID to enter their terminal state and rerun, 
+    or run without preserve_cache set to true."
+}
+
+restore_cache_and_set_resume_cmd() {
   # download latest cache.tar from $DX_CACHEDIR/$PREV_JOB_SESSION_ID/
   PREV_JOB_CACHE_FILE=$(
     dx api system findDataObjects \
@@ -643,30 +645,16 @@ restore_cache() {
   dx tag "$DX_JOB_ID" "resumed"
 }
 
-# Have to ask user to empty the cache if limit exceeded because Nextflow only
-# has UPLOAD access to project
-check_cache_db_storage() {
-  MAX_CACHE_STORAGE=20
-  existing_cache=$(dx ls $DX_CACHEDIR --folders 2>/dev/null | wc -l)
-  [[ $existing_cache -le MAX_CACHE_STORAGE ]] ||
-    dx-jobutil-report-error "The number of preserved sessions is already at the limit ($MAX_CACHE_STORAGE) and preserve_cache is true. Please remove the folders in $DX_CACHEDIR to be under the limit, or run without preserve_cache set to true."
-}
-
-check_running_jobs() {
-  FIRST_RESUMED_JOB=$(
-    dx api system findExecutions \
-      '{"state":["idle", "waiting_on_input", "runnable", "running", "debug_hold", "waiting_on_output", "restartable", "terminating"],
-        "project":"'$DX_PROJECT_CONTEXT_ID'",
-        "includeSubjobs":false,
-        "properties":{
-          "nextflow_session_id":"'$NXF_UUID'",
-          "nextflow_preserve_cache":"true",
-          "nextflow_executable":"'$EXECUTABLE_NAME'"}}' 2>/dev/null |
-      jq -r '.results[-1].id // empty'
-  )
+upload_session_cache_file() {
+  # wrap cache folder and upload cache.tar
+  if [[ -n "$(ls -A .nextflow)" ]]; then
+    tar -cf cache.tar .nextflow
 
-  [[ -n $FIRST_RESUMED_JOB && $DX_JOB_ID == $FIRST_RESUMED_JOB ]] ||
-    dx-jobutil-report-error "There is at least one other non-terminal state job with the same sessionID $NXF_UUID. 
-    Please wait until all other jobs sharing the same sessionID to enter their terminal state and rerun, 
-    or run without preserve_cache set to true."
+    CACHE_ID=$(dx upload "cache.tar" --path "$DX_CACHEDIR/$NXF_UUID/cache.tar" --no-progress --brief --wait -p -r) &&
+      echo "Upload cache of current session as file: $CACHE_ID" &&
+      rm -f cache.tar ||
+      echo "Failed to upload cache of current session $NXF_UUID"
+  else
+    echo "No cache is generated from this execution. Skip uploading cache."
+  fi
 }

dxpy-0.380.0/dxpy/toolkit_version.py

@@ -0,0 +1 @@
+version = '0.380.0'

{dxpy-0.378.0 → dxpy-0.380.0}/dxpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.378.0
+Version: 0.380.0
 Summary: DNAnexus Platform API bindings for Python
 Home-page: https://github.com/dnanexus/dx-toolkit
 Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung
@@ -21,8 +21,9 @@ Provides-Extra: xattr
 
 dxpy: DNAnexus Python API
 =========================
+[DNAnexus Documentation](https://documentation.dnanexus.com/)
 
-[API Documentation](http://autodoc.dnanexus.com/bindings/python/current/)
+[dxpy API Documentation](http://autodoc.dnanexus.com/bindings/python/current/)
 
 Building
 --------

{dxpy-0.378.0 → dxpy-0.380.0}/dxpy.egg-info/requires.txt

@@ -16,6 +16,7 @@ colorama<=0.4.6,>=0.4.4
 
 [pandas]
 pandas==1.3.5
+numpy<2.0.0
 
 [xattr]
 

{dxpy-0.378.0 → dxpy-0.380.0}/requirements_test.txt

@@ -6,4 +6,5 @@ pytest-timeout==2.1.0
 parameterized==0.8.1
 pandas==1.3.5; python_version>='3.7'
 pandas>=0.23.3,<=0.25.3; python_version>='3.5.3' and python_version<'3.7'
+numpy<2.0.0
 requests

{dxpy-0.378.0 → dxpy-0.380.0}/setup.py

@@ -100,7 +100,7 @@ setup(
     python_requires = '>=3.8',
     install_requires = dependencies,
     extras_require={
-        'pandas': ["pandas==1.3.5"],
+        'pandas': ["pandas==1.3.5", "numpy<2.0.0"],
         'xattr': ["xattr==0.10.1; sys_platform == 'linux2' or sys_platform == 'linux'"]
     },
     tests_require = test_dependencies,

{dxpy-0.378.0 → dxpy-0.380.0}/test/test_dxclient.py

@@ -320,7 +320,7 @@ class TestDXClient(DXTestCase):
             fd.close()
             run("dx api {p} describe --input {fn}".format(p=self.project, fn=fd.name))
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_PROJ_INVITE_USER"])
     @unittest.skipUnless(testutil.TEST_NO_RATE_LIMITS,
                          'skipping tests that need rate limits to be disabled')
@@ -332,7 +332,7 @@ class TestDXClient(DXTestCase):
         with self.assertSubprocessFailure(stderr_regexp="invalid choice", exit_code=2):
             run(("dx invite alice.nonexistent : ПРОСМОТР").format(p=self.project))
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_PROJ_REVOKE_USER_PERMISSIONS"])
     @unittest.skipUnless(testutil.TEST_NO_RATE_LIMITS,
                          'skipping tests that need rate limits to be disabled')
@@ -656,7 +656,7 @@ class TestDXClient(DXTestCase):
         self.assertEqual(run("dx find projects --brief --name {name}".format(name=project_name)), "")
 
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV, 'skipping test that requires presence of test user')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_API_PROJ_VIEW_SHAREES","DNA_API_PROJ_ADD_USERS"])
     def test_dx_project_invite_without_email(self):
         user_id = 'user-bob'
@@ -2273,7 +2273,7 @@ class TestDXClientDescribe(DXTestCaseBuildWorkflows):
 
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that would create apps')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_API_APP_DELETE"])
     def test_describe_deleted_app(self):
         applet_id = dxpy.api.applet_new({"project": self.project,
@@ -5017,7 +5017,7 @@ class TestDXClientFind(DXTestCase):
 
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that creates apps')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_API_APP_PUBLISH"])
     def test_dx_find_apps(self):
         test_applet_id = dxpy.api.applet_new({"name": "my_find_applet",
@@ -5100,7 +5100,7 @@ class TestDXClientFind(DXTestCase):
 
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that creates global workflows')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_WORKFLOW_LIST_AVAILABLE_WORKFLOWS_GLOBALWF"])
     def test_dx_find_globalworkflows(self):
         test_applet_id = dxpy.api.applet_new({"name": "my_find_applet",
@@ -5464,7 +5464,7 @@ class TestDXClientFind(DXTestCase):
 
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that depends on a public project only defined in the nucleus integration tests')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_API_PROJ_VIEW_PUBLIC_PROJECTS"])
     def test_dx_find_public_projects(self):
         unique_project_name = 'dx find public projects test ' + str(time.time())
@@ -5917,7 +5917,7 @@ class TestDXClientFind(DXTestCase):
             self.assertEqual(get_ids(run("dx find jobs " + options3)), set([job_id, subjob_id]))
             self.assertEqual(get_ids(run("dx find analyses " + options3)), set([analysis_id]))
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_ORG_LIST_ORGS"])
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that requires presence of test org')
@@ -6007,7 +6007,7 @@ class TestDXClientFindInOrg(DXTestCaseBuildApps):
         with self.assertSubprocessFailure(stderr_regexp='error: argument --level: expected one argument', exit_code=2):
             run("dx find org members org-piratelabs --level")
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_ORG_LIST_MEMBERS",
                                           "DNA_API_ORG_FIND_MEMBERS"])
     def test_dx_find_org_members(self):
@@ -6083,7 +6083,7 @@ class TestDXClientFindInOrg(DXTestCaseBuildApps):
         with self.assertSubprocessFailure(stderr_regexp='expected one argument', exit_code=2):
             run(cmd.format(opts="--phi"))
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_ORG_LIST_PROJECTS",
                                           "DNA_API_ORG_FIND_PROJECTS"])
     def test_dx_find_org_projects(self):
@@ -6245,7 +6245,7 @@ class TestDXClientFindInOrg(DXTestCaseBuildApps):
             self.assertTrue(len(res) == 1, "Expected to find one project")
             self.assertEqual(res[0], project1_id)
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_APP_LIST_APPS_ORG",
                                           "DNA_API_ORG_FIND_APPS"])
     def test_dx_find_org_apps(self):
@@ -6311,7 +6311,7 @@ class TestDXClientOrg(DXTestCase):
                                      "error: argument --member-list-visibility: invalid choice"):
             run('dx new org --member-list-visibility NONE')
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_ORG_CREATE",
                                           "DNA_API_ORG_CREATE",
                                           "DNA_API_ORG_DESCRIBE"])
@@ -6481,7 +6481,7 @@ class TestDXClientOrg(DXTestCase):
         with self.assertSubprocessFailure(stderr_regexp="--project-transfer-ability.*invalid", exit_code=2):
             run("dx update org {o} --project-transfer-ability PUBLIC".format(o=self.org_id))
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_ORG_UPDATE_INFORMATION"])
     def test_org_update(self):
         def get_name_and_policies(org_id=None):
@@ -6586,7 +6586,7 @@ class TestDXClientNewProject(DXTestCase):
         with self.assertRaisesRegex(subprocess.CalledProcessError, "InvalidInput"):
             run("dx new project --brief --region aws:not-a-region InvalidRegionProject")
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_PROJ_CREATE_NEW_PROJECT",
                                           "DNA_API_USR_MGMT_SET_BILLING_ACCOUNT",
                                           "DNA_API_ORG_ALLOW_BILLABLE_ACTIVITIES"])
@@ -6664,7 +6664,7 @@ class TestDXClientNewUser(DXTestCase):
     def tearDown(self):
         super(TestDXClientNewUser, self).tearDown()
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_USR_MGMT_NEW_USER"])
     def test_create_user_account_and_set_bill_to_negative(self):
         username, email = generate_unique_username_email()
@@ -6783,7 +6783,7 @@ class TestDXClientNewUser(DXTestCase):
                                          "last": last,
                                          "middle": middle})
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_API_ORG_ADD_USER"])
     def test_create_user_account_and_invite_to_org(self):
         # TODO: Test --no-email flag.
@@ -6954,7 +6954,7 @@ class TestDXClientMembership(DXTestCase):
         self._remove_user(self.user_id)
         super(TestDXClientMembership, self).tearDown()
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_ORG_ADD_MEMBER"])
     def test_add_membership_default(self):
         cmd = "dx add member {o} {u} --level {l}"
@@ -7023,7 +7023,7 @@ class TestDXClientMembership(DXTestCase):
         with self.assertRaisesRegex(subprocess.CalledProcessError, "DXCLIError"):
             run(" ".join([cmd, self.org_id, self.username, "--level ADMIN"]))
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_ORG_REMOVE_MEMBER",
                                           "DNA_API_ORG_REMOVE_USER"])
     def test_remove_membership_default(self):
@@ -7146,7 +7146,7 @@ class TestDXClientMembership(DXTestCase):
             with self.assertRaises(subprocess.CalledProcessError):
                 run(" ".join([cmd, invalid_opts]))
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_ORG_UPDATE_USER_MEMBERSHIP",
                                           "DNA_API_ORG_CHANGE_USER_PERMISSIONS"])
     def test_update_membership_positive(self):
@@ -7663,7 +7663,7 @@ class TestDXBuildWorkflow(DXTestCaseBuildWorkflows):
         
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that would create global workflows')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_WORKFLOW_REMOVE_AUTHORIZED_USERS_GLOBALWF",
                                           "DNA_CLI_WORKFLOW_LIST_AUTHORIZED_USERS_GLOBALWF",
                                           "DNA_CLI_WORKFLOW_ADD_AUTHORIZED_USERS_GLOBALWF"])
@@ -7716,7 +7716,7 @@ class TestDXBuildWorkflow(DXTestCaseBuildWorkflows):
         run('dx remove users wf_test_dx_users nonexistentuser')
         run('dx remove users wf_test_dx_users piratelabs')
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_WORKFLOW_ADD_DEVELOPERS_GLOBALWF",
                                           "DNA_CLI_WORKFLOW_LIST_DEVELOPERS_GLOBALWF",
                                           "DNA_CLI_WORKFLOW_REMOVE_DEVELOPERS_GLOBALWF"])
@@ -7779,7 +7779,7 @@ class TestDXBuildWorkflow(DXTestCaseBuildWorkflows):
         run('dx remove developers wf_test_dx_developers piratelabs')
 
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_WORKFLOW_PUBLISH_GLOBALWF"])
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that would create global workflows')
@@ -8296,7 +8296,7 @@ class TestDXBuildApp(DXTestCaseBuildApps):
 
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that would create apps')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_API_APP_DESCRIBE"])
     def test_build_single_region_app_without_regional_options(self):
         # Backwards-compatible.
@@ -8817,7 +8817,7 @@ class TestDXBuildApp(DXTestCaseBuildApps):
 
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that would create apps')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_API_APP_CREATE"])
     def test_build_app_with_bill_to(self):
         alice_id = "user-alice"
@@ -8969,7 +8969,7 @@ class TestDXBuildApp(DXTestCaseBuildApps):
         self.assertEqual(json.loads(run("dx api " + app_id + " listCategories"))["categories"], ['B'])
 
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV, 'skipping test that would create apps')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_API_APP_LIST_AUTHORIZED_USERS","DNA_API_APP_ADD_AUTHORIZED_USER"])
     def test_update_app_authorized_users(self):
         app0_spec = dict(self.base_app_spec, name="update_app_authorized_users")
@@ -8991,7 +8991,7 @@ class TestDXBuildApp(DXTestCaseBuildApps):
         self.assertEqual(json.loads(run("dx api " + app_id +
                                          " listAuthorizedUsers"))["authorizedUsers"], ["user-eve"])
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_APP_ADD_AUTHORIZED_USERS_APP",
                                           "DNA_CLI_APP_LIST_AUTHORIZED_USERS_APP",
                                           "DNA_CLI_APP_REMOVE_AUTHORIZED_USERS_APP"])
@@ -9044,7 +9044,7 @@ class TestDXBuildApp(DXTestCaseBuildApps):
         run('dx remove users test_dx_users nonexistentuser')
         run('dx remove users test_dx_users piratelabs')
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_APP_ADD_DEVELOPERS_APP",
                                           "DNA_CLI_APP_LIST_DEVELOPERS_APP",
                                           "DNA_CLI_APP_REMOVE_DEVELOPERS_APP",
@@ -9980,7 +9980,7 @@ def main(in1):
 
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that would create app')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_APP_PUBLISH"])
     def test_dx_publish_app(self):
         app_name = "dx_publish_app"
@@ -10102,7 +10102,7 @@ class TestDXGetWorkflows(DXTestCaseBuildWorkflows):
             with self.assertSubprocessFailure(stderr_regexp='already exists', exit_code=3):
                 run("dx get -o destdir_withfile get_workflow")
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_DATA_OBJ_DOWNLOAD_EXECUTABLE"])
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV, 'skipping test that would create global workflows')
     def test_get_global_workflow(self):
@@ -10699,7 +10699,7 @@ class TestDXGetAppsAndApplets(DXTestCaseBuildApps):
                     break
             self.assertTrue(seenResources)
 
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_CLI_APP_LIST_AVAILABLE_APPS",
                                           "DNA_CLI_APP_INSTALL_APP",
                                           "DNA_CLI_APP_UNINSTALL_APP",
@@ -11213,7 +11213,7 @@ class TestDXRun(DXTestCase):
 class TestDXUpdateApp(DXTestCaseBuildApps):
     @unittest.skipUnless(testutil.TEST_ISOLATED_ENV,
                          'skipping test that creates apps')
-    @pytest.mark.TRACEABILITY_MATRIX
+    @pytest.mark.TRACEABILITY_ISOLATED_ENV
     @testutil.update_traceability_matrix(["DNA_API_APP_UPDATE"])
     def test_update_app(self):
         # Build and publish app with initial version

dxpy-0.378.0/dxpy/toolkit_version.py

@@ -1 +0,0 @@
-version = '0.378.0'