def main():
argparser = argparse.ArgumentParser(
description="Run WDL compiler tests on the platform")
argparser.add_argument("--compile-only",
help="Only compile the workflows, don't run them",
action="store_true",
default=False)
args = argparser.parse_args()
version_id = util.get_version_id(top_dir)
wdl_source_file = os.path.join(test_dir, "multi_region/trivial.wdl")
dx_objects = []
test_exec_objs = []
# build version of the applet on all regions
for proj_name in projects:
dx_proj = util.get_project(proj_name)
if dx_proj is None:
raise RuntimeError("Could not find project {}".format(proj_name))
oid = build_test(wdl_source_file, dx_proj, target_folder, version_id)
if args.compile_only:
continue
anl = run_workflow(dx_proj, target_folder, oid)
print("Running {}".format(oid))
test_exec_objs.append(anl)
# Wait for completion
print("executables: " + ", ".join([a.get_id() for a in test_exec_objs]))
wait_for_completion(test_exec_objs)
def main():
global test_locked
argparser = argparse.ArgumentParser(description="Run WDL proxy tests")
argparser.add_argument("--do-not-build",
help="Do not assemble the dxWDL jar file",
action="store_true",
default=False)
argparser.add_argument("--project",
help="DNAnexus project ID",
default="dxWDL_playground")
argparser.add_argument("--verbose",
help="Verbose compilation",
action="store_true",
default=False)
args = argparser.parse_args()
print("top_dir={} test_dir={}".format(top_dir, test_dir))
version_id = util.get_version_id(top_dir)
project = util.get_project(args.project)
if project is None:
raise RuntimeError("Could not find project {}".format(args.project))
folder = build_dirs(project, version_id)
print("project: {} ({})".format(project.name, project.get_id()))
print("folder: {}".format(folder))
test_dict = {"aws:us-east-1": project.name + ":" + folder}
# build the dxWDL jar file, only on us-east-1
if not args.do_not_build:
util.build(project, folder, version_id, top_dir, test_dict)
try:
# make sure that squid is installed and running
setup()
# test_deny(project, folder, version_id)
test_allow(project, folder, version_id)
# test_allow_auth(project, folder, version_id)
test_ntlm_auth(project, folder, version_id)
# test_network_blocking(project, folder, version_id)
# test_squid_allows_bypassing_firewall(project, folder, version_id)
finally:
print("Test complete")
shutdown()
def copy_wf_test(tname, src_proj, src_folder, debug_flag):
alt_proj_name = "dxWDL_playground_2"
trg_proj = util.get_project(alt_proj_name)
if trg_proj is None:
raise RuntimeError("Could not find project {}".format(alt_proj_name))
test_folder = "/test"
# clean up target
print("cleaning up target")
trg_proj.remove_folder(test_folder, recurse=True)
trg_proj.new_folder(test_folder, parents=True)
# copy to alternate project
src_wf_id = lookup_dataobj(tname, src_proj, src_folder)
print("copy {} to alternate project".format(src_wf_id))
wf = dxpy.DXWorkflow(dxid=src_wf_id)
wf2 = wf.clone(trg_proj.get_id(), folder=test_folder)
# Run the workflow, and wait for completion
runnable = {tname: wf2.get_id()}
run_test_subset(trg_proj, runnable, test_folder, debug_flag)
def main():
global test_locked
argparser = argparse.ArgumentParser(description="Run WDL proxy tests")
argparser.add_argument("--do-not-build",
help="Do not assemble the dxWDL jar file",
action="store_true",
default=False)
argparser.add_argument("--project",
help="DNAnexus project ID",
default="dxWDL_playground")
argparser.add_argument("--verbose",
help="Verbose compilation",
action="store_true",
default=False)
args = argparser.parse_args()
print("top_dir={} test_dir={}".format(top_dir, test_dir))
version_id = util.get_version_id(top_dir)
project = util.get_project(args.project)
if project is None:
raise RuntimeError("Could not find project {}".format(args.project))
folder = util.build_dirs(project, version_id)
print("project: {} ({})".format(project.name, project.get_id()))
print("folder: {}".format(folder))
test_dict = {"aws:us-east-1": project.name + ":" + folder}
# build the dxWDL jar file, only on us-east-1
#if not args.do_not_build:
# util.build(project, folder, version_id, top_dir, test_dict)
# For some reason, the ip-tables state is not completely
# cleared. Therefore, we need to run those tests first.
test_networking(project, folder, version_id)
test_authorization(project, folder, version_id)
def main():
global test_locked
argparser = argparse.ArgumentParser(
description="Run WDL compiler tests on the platform")
argparser.add_argument("--archive",
help="Archive old applets",
action="store_true",
default=False)
argparser.add_argument("--compile-only",
help="Only compile the workflows, don't run them",
action="store_true",
default=False)
argparser.add_argument("--compile-mode", help="Compilation mode")
argparser.add_argument("--delay-workspace-destruction",
help="Flag passed to workflow run",
action="store_true",
default=False)
argparser.add_argument("--do-not-build",
help="Do not assemble the dxWDL jar file",
action="store_true",
default=False)
argparser.add_argument("--force",
help="Remove old versions of applets and workflows",
action="store_true",
default=False)
argparser.add_argument(
"--folder", help="Use an existing folder, instead of building dxWDL")
argparser.add_argument("--lazy",
help="Only compile workflows that are unbuilt",
action="store_true",
default=False)
argparser.add_argument("--locked",
help="Generate locked-down workflows",
action="store_true",
default=False)
argparser.add_argument("--regular",
help="Generate only regular workflows",
action="store_true",
default=False)
argparser.add_argument("--no-wait",
help="Exit immediately after launching tests",
action="store_true",
default=False)
argparser.add_argument("--project",
help="DNAnexus project ID",
default="dxWDL_playground")
argparser.add_argument(
"--runtime-debug-level",
help="printing verbosity of task/workflow runner, {0,1,2}")
argparser.add_argument("--test",
help="Run a test, or a subgroup of tests",
action="append",
default=[])
argparser.add_argument("--test-list",
help="Print a list of available tests",
action="store_true",
default=False)
argparser.add_argument("--verbose",
help="Verbose compilation",
action="store_true",
default=False)
args = argparser.parse_args()
register_all_tests()
if args.test_list:
print_test_list()
exit(0)
test_names = []
if len(args.test) == 0:
args.test = 'M'
for t in args.test:
test_names += choose_tests(t)
print("Running tests {}".format(test_names))
version_id = util.get_version_id(top_dir)
project = util.get_project(args.project)
if project is None:
raise RuntimeError("Could not find project {}".format(args.project))
if args.folder is None:
base_folder = build_dirs(project, version_id)
else:
# Use existing prebuilt folder
base_folder = args.folder
applet_folder = base_folder + "/applets"
test_folder = base_folder + "/test"
print("project: {} ({})".format(project.name, project.get_id()))
print("folder: {}".format(base_folder))
test_dict = {"aws:us-east-1": project.name + ":" + base_folder}
# build the dxWDL jar file, only on us-east-1
if not args.do_not_build:
util.build(project, base_folder, version_id, top_dir)
util.build_compiler_jar(version_id, top_dir, test_dict)
if args.regular:
# Disable all locked workflows
args.locked = False
test_locked = []
compiler_flags = []
if args.locked:
compiler_flags.append("-locked")
test_locked += test_names
if args.archive:
compiler_flags.append("-archive")
if args.compile_mode:
compiler_flags += ["-compileMode", args.compile_mode]
if args.force:
compiler_flags.append("-force")
if args.verbose:
compiler_flags.append("-verbose")
if args.runtime_debug_level:
compiler_flags += ["-runtimeDebugLevel", args.runtime_debug_level]
compiler_flags += ["--extras", os.path.join(top_dir, "test/extras.json")]
if "call_native" in test_names:
native_call_setup(project, applet_folder, version_id)
if "call_native_app" in test_names:
native_call_app_setup(version_id)
try:
# Compile the WDL files to dx:workflows and dx:applets
runnable = {}
for tname in test_names:
oid = None
if args.lazy:
oid = lookup_dataobj(tname, project, applet_folder)
if oid is None:
c_flags = compiler_flags[:] + compiler_per_test_flags(tname)
oid = build_test(tname, project, applet_folder, version_id,
c_flags)
runnable[tname] = oid
print("runnable({}) = {}".format(tname, oid))
if not args.compile_only:
run_test_subset(project, runnable, test_folder,
args.delay_workspace_destruction, args.no_wait)
finally:
print("Test complete")
def main():
argparser = argparse.ArgumentParser(
description="Build a dxCompiler release")
argparser.add_argument("--force",
help="Build even if there is an existing version",
action='store_true',
default=False)
argparser.add_argument("--multi-region",
help="Copy to all supported regions",
action='store_true',
default=False)
argparser.add_argument("--dry-run",
help="Don't build any artifacts",
action='store_true',
default=False)
args = argparser.parse_args()
# build multi-region jar for releases, or
# if explicitly specified
multi_region = args.multi_region
# Choose which dictionary to use
if multi_region:
project_dict = RELEASE_DICT
else:
project_dict = TEST_DICT
project = util.get_project(project_dict[HOME_REGION])
print("project: {} ({})".format(project.name, project.get_id()))
# Figure out what the current version is
version_id = util.get_version_id(top_dir)
print("version: {}".format(version_id))
# Set the folder
folder = "/releases/{}".format(version_id)
print("folder: {}".format(folder))
if args.dry_run:
args.force = False
# remove the existing directory paths
if args.force:
for proj_name in project_dict.values():
print("removing path {}:{}".format(proj_name, folder))
dx_proj = util.get_project(proj_name)
try:
dx_proj.remove_folder(folder, recurse=True)
except dxpy.DXError:
pass
# Make sure the target directory exists
project.new_folder(folder, parents=True)
# Build the asset, and the compiler jar file.
path_dict = dict(
map(lambda kv: (kv[0], kv[1] + ":" + folder), project_dict.items()))
if args.dry_run:
return
home_ad = util.build(project, folder, version_id, top_dir, path_dict)
if multi_region:
for lang, asset_desc in home_ad.asset_ids.items():
home_rec = dxpy.DXRecord(asset_desc)
all_regions = project_dict.keys()
# Leave only regions where the asset is missing
target_regions = []
for dest_region in all_regions:
dest_proj = util.get_project(project_dict[dest_region])
dest_asset = util.find_asset(dest_proj, folder, lang)
if dest_asset == None:
target_regions.append(dest_region)
_clone_asset(home_rec, folder, target_regions, project_dict)
def _clone_asset(record, folder, regions, project_dict):
"""
This function will attempt to clone the given record into all of the given regions.
It will return a dictionary with the regions as keys and the record-ids of the
corresponding asset as the values. If an asset is not able to be created in a given
region, the value will be set to None.
"""
# Get the asset record
fid = record.get_details()['archiveFileId']['$dnanexus_link']
curr_region = dxpy.describe(record.project)['region']
# Only run once per region
regions = set(regions) - set([curr_region])
if len(regions) == 0:
# there is nothing to do
return
app_supported_regions = set(
COPY_FILE_APP.describe()['regionalOptions'].keys())
if len(regions - app_supported_regions) > 0:
print('Currently no support for the following region(s): [{regions}]'.
format(regions=', '.join(regions - app_supported_regions)),
file=sys.stderr)
sys.exit(1)
# Get information about the asset
asset_properties = record.get_properties()
asset_properties['cloned_from'] = record.get_id()
asset_file_name = dxpy.describe(fid)['name']
url = dxpy.DXFile(fid).get_download_url(
preauthenticated=True,
project=dxpy.DXFile.NO_PROJECT_HINT,
duration=URL_DURATION)[0]
# setup target folders
region2projid = {}
for region in regions:
dest_proj = util.get_project(project_dict[region])
dest_proj.new_folder(folder, parents=True)
region2projid[region] = dest_proj.get_id()
print(region2projid)
# Fire off a clone process for each region
# Wait for the cloning to complete
for i in [1, 2, 3]:
jobs = _clone_to_all_regions(region2projid, regions, asset_file_name,
folder, url)
retval = _wait_for_completion(jobs)
if retval:
break
# make records for each file
for region in regions:
dest_proj_id = region2projid[region]
results = list(
dxpy.find_data_objects(classname="file",
visibility="hidden",
name=asset_file_name,
project=dest_proj_id,
folder=folder))
file_ids = [p["id"] for p in results]
if len(file_ids) == 0:
raise RuntimeError("Found no files {}:{}/{}".format(
dest_proj_id, folder, asset_file_name))
if len(file_ids) > 1:
raise RuntimeError(
"Found {} files {}:{}/{}, instead of just one".format(
len(dxfiles), dest_proj_id, folder, asset_file_name))
dest_asset = dxpy.new_dxrecord(
name=record.name,
types=['AssetBundle'],
details={'archiveFileId': dxpy.dxlink(file_ids[0])},
properties=record.get_properties(),
project=dest_proj_id,
folder=folder,
close=True)
def main():
global test_unlocked
argparser = argparse.ArgumentParser(
description="Run WDL compiler tests on the platform")
argparser.add_argument("--archive",
help="Archive old applets",
action="store_true",
default=False)
argparser.add_argument("--compile-only",
help="Only compile the workflows, don't run them",
action="store_true",
default=False)
argparser.add_argument("--compile-mode", help="Compilation mode")
argparser.add_argument("--debug",
help="Run applets with debug-hold, and allow ssh",
action="store_true",
default=False)
argparser.add_argument("--do-not-build",
help="Do not assemble the dxWDL jar file",
action="store_true",
default=False)
argparser.add_argument("--extras",
help="run extra tests",
action="store_true",
default=False)
argparser.add_argument("--force",
help="Remove old versions of applets and workflows",
action="store_true",
default=False)
argparser.add_argument(
"--folder", help="Use an existing folder, instead of building dxWDL")
argparser.add_argument("--lazy",
help="Only compile workflows that are unbuilt",
action="store_true",
default=False)
argparser.add_argument("--list",
"--test-list",
help="Print a list of available tests",
action="store_true",
dest="test_list",
default=False)
argparser.add_argument("--locked",
help="Generate locked-down workflows",
action="store_true",
default=False)
argparser.add_argument("--project",
help="DNAnexus project ID",
default="dxWDL_playground")
argparser.add_argument(
"--runtime-debug-level",
help="printing verbosity of task/workflow runner, {0,1,2}")
argparser.add_argument("--test",
help="Run a test, or a subgroup of tests",
action="append",
default=[])
argparser.add_argument("--unlocked",
help="Generate only unlocked workflows",
action="store_true",
default=False)
argparser.add_argument("--verbose",
help="Verbose compilation",
action="store_true",
default=False)
argparser.add_argument("--verbose-key",
help="Verbose compilation",
action="append",
default=[])
args = argparser.parse_args()
print("top_dir={} test_dir={}".format(top_dir, test_dir))
register_all_tests()
if args.test_list:
print_test_list()
exit(0)
test_names = []
if len(args.test) == 0:
args.test = 'M'
for t in args.test:
test_names += choose_tests(t)
print("Running tests {}".format(test_names))
version_id = util.get_version_id(top_dir)
project = util.get_project(args.project)
if project is None:
raise RuntimeError("Could not find project {}".format(args.project))
if args.folder is None:
base_folder = build_dirs(project, version_id)
else:
# Use existing prebuilt folder
base_folder = args.folder
applet_folder = base_folder + "/applets"
test_folder = base_folder + "/test"
print("project: {} ({})".format(project.name, project.get_id()))
print("folder: {}".format(base_folder))
test_dict = {"aws:us-east-1": project.name + ":" + base_folder}
# build the dxWDL jar file, only on us-east-1
if not args.do_not_build:
util.build(project, base_folder, version_id, top_dir, test_dict)
if args.unlocked:
# Disable all locked workflows
args.locked = False
test_unlocked = test_names
compiler_flags = []
if args.locked:
compiler_flags.append("-locked")
test_unlocked = []
if args.archive:
compiler_flags.append("-archive")
if args.compile_mode:
compiler_flags += ["-compileMode", args.compile_mode]
if args.force:
compiler_flags.append("-force")
if args.verbose:
compiler_flags.append("-verbose")
if args.verbose_key:
for key in args.verbose_key:
compiler_flags += ["-verboseKey", key]
if args.runtime_debug_level:
compiler_flags += ["-runtimeDebugLevel", args.runtime_debug_level]
# is "native" included in one of the test names?
if ("call_native" in test_names or "call_native_v1" in test_names):
native_call_setup(project, applet_folder, version_id)
if "call_native_app" in test_names:
native_call_app_setup(version_id)
try:
# Compile the WDL files to dx:workflows and dx:applets
runnable = compile_tests_to_project(project, test_names, applet_folder,
compiler_flags, version_id,
args.lazy)
if not args.compile_only:
run_test_subset(project, runnable, test_folder, args.debug)
finally:
print("Completed running tasks in {}".format(args.project))
if args.extras:
print("Copy workflow and run in alternate project ")
copy_wf_test("linear", project, applet_folder, args.debug)
def main():
argparser = argparse.ArgumentParser(description="Build the dxWDL jar file")
argparser.add_argument("--folder", help="Destination folder")
argparser.add_argument("--multi-region",
help="Copy to all supported regions",
action='store_true',
default=False)
argparser.add_argument("--release",
help="Create a dxWDL release, implies multi-region",
action='store_true',
default=False)
args = argparser.parse_args()
# resolve project
project_dict = None
if args.release:
project_dict = RELEASE_DICT
else:
project_dict = TEST_DICT
project = util.get_project(project_dict[HOME_REGION])
print("project: {} ({})".format(project.name, project.get_id()))
# Set the folder, build one if necessary
if args.folder is not None:
folder = args.folder
elif args.release:
folder = time.strftime("/releases/%Y-%m-%d/%H%M%S")
project.new_folder(folder, parents=True)
else:
folder = time.strftime("/builds/%Y-%m-%d/%H%M%S")
project.new_folder(folder, parents=True)
print("folder: {}".format(folder))
# build multi-region jar for releases, or
# if explicitly specified
multi_region = args.multi_region
if args.release:
multi_region = True
# Figure out what the current version is
version_id = util.get_version_id(top_dir)
print("version: {}".format(version_id))
# build the asset
home_ad = util.build(project, folder, version_id, top_dir)
ad_all = [home_ad]
if multi_region:
# download dxWDL runtime library
home_rec = dxpy.DXRecord(home_ad.asset_id)
fid = home_rec.get_details()['archiveFileId']['$dnanexus_link']
fn = dxpy.describe(fid)['name']
rtlib_path = "/tmp/{}".format(fn)
print("Download asset file {}".format(fn))
dxpy.download_dxfile(fid, rtlib_path, show_progress=True)
# copy to all other regions
for region in project_dict.keys():
if region != home_ad.region:
proj = project_dict[region]
if proj is None:
raise Exception(
"No project configured for region {}".format(region))
dest_proj = util.get_project(proj)
dest_ad = util.copy_across_regions(rtlib_path, home_rec,
region, dest_proj, folder)
ad_all.append(dest_ad)
# build the final jar file, containing a list of the per-region
# assets
jar_path = util.build_final_jar(version_id, top_dir, ad_all)
# Upload compiler jar file
if args.release:
util.upload_local_file(jar_path, project, folder)
def main():
global test_unlocked
argparser = argparse.ArgumentParser(description="Run WDL compiler tests on the platform")
argparser.add_argument("--archive", help="Archive old applets",
action="store_true", default=False)
argparser.add_argument("--compile-only", help="Only compile the workflows, don't run them",
action="store_true", default=False)
argparser.add_argument("--compile-mode", help="Compilation mode")
argparser.add_argument("--debug", help="Run applets with debug-hold, and allow ssh",
action="store_true", default=False)
argparser.add_argument("--delay-workspace-destruction", help="Run applets with delayWorkspaceDestruction",
action="store_true", default=False)
argparser.add_argument("--force", help="Remove old versions of applets and workflows",
action="store_true", default=False)
argparser.add_argument("--folder", help="Use an existing folder, instead of building dxCompiler")
argparser.add_argument("--lazy", help="Only compile workflows that are unbuilt",
action="store_true", default=False)
argparser.add_argument("--list", "--test-list", help="Print a list of available tests",
action="store_true",
dest="test_list",
default=False)
argparser.add_argument("--clean", help="Remove build directory in the project after running tests",
action="store_true", default=False)
argparser.add_argument("--locked", help="Generate locked-down workflows",
action="store_true", default=False)
argparser.add_argument("--project", help="DNAnexus project ID",
default="dxCompiler_playground")
argparser.add_argument("--project-wide-reuse", help="look for existing applets in the entire project",
action="store_true", default=False)
argparser.add_argument("--stream-all-files", help="Stream all input files with dxfs2",
action="store_true", default=False)
argparser.add_argument("--runtime-debug-level",
help="printing verbosity of task/workflow runner, {0,1,2}")
argparser.add_argument("--test", help="Run a test, or a subgroup of tests",
action="append", default=[])
argparser.add_argument("--unlocked", help="Generate only unlocked workflows",
action="store_true", default=False)
argparser.add_argument("--verbose", help="Verbose compilation",
action="store_true", default=False)
argparser.add_argument("--verbose-key", help="Verbose compilation",
action="append", default=[])
args = argparser.parse_args()
print("top_dir={} test_dir={}".format(top_dir, test_dir))
register_all_tests(args.verbose)
if args.test_list:
print_test_list()
exit(0)
test_names = []
if len(args.test) == 0:
args.test = 'M'
for t in args.test:
test_names += choose_tests(t)
print("Running tests {}".format(test_names))
version_id = util.get_version_id(top_dir)
project = util.get_project(args.project)
if project is None:
raise RuntimeError("Could not find project {}".format(args.project))
if args.folder is None:
base_folder = util.create_build_dirs(project, version_id)
else:
# Use existing prebuilt base folder
base_folder = args.folder
util.create_build_subdirs(project, base_folder)
applet_folder = base_folder + "/applets"
test_folder = base_folder + "/test"
print("project: {} ({})".format(project.name, project.get_id()))
print("folder: {}".format(base_folder))
test_dict = {
"aws:us-east-1" : project.name + ":" + base_folder
}
# build the dxCompiler jar file, only on us-east-1
assets = util.build(project, base_folder, version_id, top_dir, test_dict)
print("assets: {}".format(assets))
if args.unlocked:
# Disable all locked workflows
args.locked = False
test_unlocked = test_names
compiler_flags = []
if args.locked:
compiler_flags.append("-locked")
test_unlocked = []
if args.archive:
compiler_flags.append("-archive")
if args.compile_mode:
compiler_flags += ["-compileMode", args.compile_mode]
if args.force:
compiler_flags.append("-force")
if args.verbose:
compiler_flags.append("-verbose")
if args.stream_all_files:
compiler_flags.append("-streamAllFiles")
if args.verbose_key:
for key in args.verbose_key:
compiler_flags += ["-verboseKey", key]
if args.runtime_debug_level:
compiler_flags += ["-runtimeDebugLevel", args.runtime_debug_level]
if args.project_wide_reuse:
compiler_flags.append("-projectWideReuse")
# is "native" included in one of the test names?
if ("call_native" in test_names or
"call_native_v1" in test_names):
native_call_setup(project, applet_folder, version_id, args.verbose)
if "call_native_app" in test_names:
native_call_app_setup(project, version_id, args.verbose)
try:
# Compile the WDL files to dx:workflows and dx:applets
runnable = compile_tests_to_project(project,
test_names,
applet_folder,
compiler_flags,
version_id,
args.lazy)
if not args.compile_only:
run_test_subset(project, runnable, test_folder, args.debug, args.delay_workspace_destruction)
finally:
if args.clean:
project.remove_folder(base_folder, recurse=True, force=True)
print("Completed running tasks in {}".format(args.project))
def main():
argparser = argparse.ArgumentParser(description="Build a dxWDL release")
argparser.add_argument(
"--force",
help="Build even if the there is an existing version",
action='store_true',
default=False)
argparser.add_argument("--multi-region",
help="Copy to all supported regions",
action='store_true',
default=False)
args = argparser.parse_args()
# build multi-region jar for releases, or
# if explicitly specified
multi_region = args.multi_region
# Choose which dictionary to use
if multi_region:
project_dict = RELEASE_DICT
else:
project_dict = TEST_DICT
project = util.get_project(project_dict[HOME_REGION])
print("project: {} ({})".format(project.name, project.get_id()))
# Figure out what the current version is
version_id = util.get_version_id(top_dir)
print("version: {}".format(version_id))
# Set the folder
folder = "/releases/{}".format(version_id)
print("folder: {}".format(folder))
# remove the existing directory paths
if args.force:
for proj_name in project_dict.values():
print("removing path {}:{}".format(proj_name, folder))
dx_proj = util.get_project(proj_name)
try:
dx_proj.remove_folder(folder, recurse=True)
except dxpy.DXError:
pass
# Make sure the target directory exists
project.new_folder(folder, parents=True)
# Build the asset, and the compiler jar file.
path_dict = dict(
map(lambda kv: (kv[0], kv[1] + ":" + folder), project_dict.items()))
(jar_path, home_ad) = util.build(project, folder, version_id, top_dir,
path_dict)
if multi_region:
# download dxWDL runtime library
home_rec = dxpy.DXRecord(home_ad.asset_id)
fid = home_rec.get_details()['archiveFileId']['$dnanexus_link']
fn = dxpy.describe(fid)['name']
rtlib_path = "/tmp/{}".format(fn)
print("Download asset file {}".format(fn))
dxpy.download_dxfile(fid, rtlib_path, show_progress=True)
# copy to all other regions
for region in project_dict.keys():
if region != home_ad.region:
proj = project_dict[region]
if proj is None:
raise Exception(
"No project configured for region {}".format(region))
dest_proj = util.get_project(proj)
if dest_proj is not None:
dest_ad = util.copy_across_regions(rtlib_path, home_rec,
region, dest_proj,
folder)
else:
print("No project named {}".format(proj))
# Upload compiler jar file
util.upload_local_file(jar_path, project, folder)
def get(self, eId):
projectList = findTopKProjectsPerUser(eId)
result = get_project(projectList)
#result = {'projectsRecommended': projectList}
return jsonify(result)
