Running tests in temporary directory: '/tmp/viash_test_logistic_regression_288619653788075328'
====================================================================
+/tmp/viash_test_logistic_regression_288619653788075328/build_engine_environment/logistic_regression ---verbosity 6 ---setup cachedbuild ---engine docker
[notice] Building container 'ghcr.io/openproblems-bio/task_template/methods/logistic_regression:test' with Dockerfile
[info] docker build -t 'ghcr.io/openproblems-bio/task_template/methods/logistic_regression:test' '/tmp/viash_test_logistic_regression_288619653788075328/build_engine_environment' -f '/tmp/viash_test_logistic_regression_288619653788075328/build_engine_environment/tmp/dockerbuild-logistic_regression-V2mJGM/Dockerfile'
#0 building with "default" instance using docker driver
#1 [internal] load build definition from Dockerfile
#1 transferring dockerfile: 571B done
#1 DONE 0.0s
#2 [internal] load metadata for docker.io/openproblems/base_python:1.0.0
#2 ...
#3 [auth] openproblems/base_python:pull token for registry-1.docker.io
#3 DONE 0.0s
#2 [internal] load metadata for docker.io/openproblems/base_python:1.0.0
#2 DONE 0.8s
#4 [internal] load .dockerignore
#4 transferring context: 2B done
#4 DONE 0.0s
#5 [1/2] FROM docker.io/openproblems/base_python:1.0.0@sha256:bbb0a093e275498bf905237c8cd26124d436f5d35d0f8dd1749c06d0a0a2e88c
#5 resolve docker.io/openproblems/base_python:1.0.0@sha256:bbb0a093e275498bf905237c8cd26124d436f5d35d0f8dd1749c06d0a0a2e88c done
#5 sha256:f3113a160ebb790d7b7e5c9a2148c422ca3f71d30ab661b05c922da5923e4672 9.52kB / 9.52kB done
#5 sha256:2e6afa3f266c11e8960349e7866203a9df478a50362bb5488c45fe39d99b2707 0B / 24.05MB 0.1s
#5 sha256:2e66a70da0bec13fb3d492fcdef60fd8a5ef0a1a65c4e8a4909e26742852f0f2 0B / 64.15MB 0.1s
#5 sha256:bbb0a093e275498bf905237c8cd26124d436f5d35d0f8dd1749c06d0a0a2e88c 2.43kB / 2.43kB done
#5 sha256:8cd46d290033f265db57fd808ac81c444ec5a5b3f189c3d6d85043b647336913 0B / 49.56MB 0.1s
#5 sha256:2e6afa3f266c11e8960349e7866203a9df478a50362bb5488c45fe39d99b2707 24.05MB / 24.05MB 0.3s
#5 sha256:2e66a70da0bec13fb3d492fcdef60fd8a5ef0a1a65c4e8a4909e26742852f0f2 44.04MB / 64.15MB 0.3s
#5 sha256:2e6afa3f266c11e8960349e7866203a9df478a50362bb5488c45fe39d99b2707 24.05MB / 24.05MB 0.3s done
#5 sha256:2e66a70da0bec13fb3d492fcdef60fd8a5ef0a1a65c4e8a4909e26742852f0f2 60.82MB / 64.15MB 0.4s
#5 sha256:8cd46d290033f265db57fd808ac81c444ec5a5b3f189c3d6d85043b647336913 28.32MB / 49.56MB 0.4s
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 0B / 211.27MB 0.4s
#5 sha256:2e66a70da0bec13fb3d492fcdef60fd8a5ef0a1a65c4e8a4909e26742852f0f2 64.15MB / 64.15MB 0.5s done
#5 sha256:8cd46d290033f265db57fd808ac81c444ec5a5b3f189c3d6d85043b647336913 49.56MB / 49.56MB 0.5s
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 26.21MB / 211.27MB 0.5s
#5 extracting sha256:8cd46d290033f265db57fd808ac81c444ec5a5b3f189c3d6d85043b647336913
#5 sha256:8cd46d290033f265db57fd808ac81c444ec5a5b3f189c3d6d85043b647336913 49.56MB / 49.56MB 0.5s done
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 48.05MB / 211.27MB 0.6s
#5 sha256:a0ff605e08b8c97d64efd5de9004f7be648fe6181093227246142e70eda4d985 0B / 6.16MB 0.6s
#5 sha256:a040235ac426a0e27ffff8201c375bc2dea5e9b79fbe3de107e8640a3152cb3a 0B / 19.84MB 0.6s
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 77.59MB / 211.27MB 0.8s
#5 sha256:a0ff605e08b8c97d64efd5de9004f7be648fe6181093227246142e70eda4d985 6.16MB / 6.16MB 0.8s done
#5 sha256:a040235ac426a0e27ffff8201c375bc2dea5e9b79fbe3de107e8640a3152cb3a 19.84MB / 19.84MB 0.7s done
#5 sha256:608bb063c2b69dbab463e8ba089f65d9ca171add34cc5dc77434d44320dc4858 0B / 3.13MB 0.8s
#5 sha256:bf8c0a4030de5f4f6d52f2fd8d70281f7230aa557d51632f7fb27f5c7bca0720 0B / 232B 0.8s
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 94.37MB / 211.27MB 0.9s
#5 sha256:608bb063c2b69dbab463e8ba089f65d9ca171add34cc5dc77434d44320dc4858 3.13MB / 3.13MB 0.9s done
#5 sha256:bf8c0a4030de5f4f6d52f2fd8d70281f7230aa557d51632f7fb27f5c7bca0720 232B / 232B 0.8s done
#5 sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 0B / 32B 0.9s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 0B / 239.90MB 0.9s
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 109.05MB / 211.27MB 1.0s
#5 sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 32B / 32B 0.9s done
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 145.26MB / 211.27MB 1.2s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 44.42MB / 239.90MB 1.2s
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 164.03MB / 211.27MB 1.3s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 62.91MB / 239.90MB 1.3s
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 179.59MB / 211.27MB 1.4s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 84.93MB / 239.90MB 1.4s
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 202.38MB / 211.27MB 1.5s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 108.00MB / 239.90MB 1.5s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 133.17MB / 239.90MB 1.7s
#5 sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 211.27MB / 211.27MB 1.8s done
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 152.04MB / 239.90MB 1.8s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 166.72MB / 239.90MB 1.9s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 183.50MB / 239.90MB 2.0s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 197.32MB / 239.90MB 2.1s
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 231.74MB / 239.90MB 2.3s
#5 extracting sha256:8cd46d290033f265db57fd808ac81c444ec5a5b3f189c3d6d85043b647336913 2.0s done
#5 sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 239.90MB / 239.90MB 2.7s done
#5 extracting sha256:2e6afa3f266c11e8960349e7866203a9df478a50362bb5488c45fe39d99b2707 0.1s
#5 extracting sha256:2e6afa3f266c11e8960349e7866203a9df478a50362bb5488c45fe39d99b2707 0.5s done
#5 extracting sha256:2e66a70da0bec13fb3d492fcdef60fd8a5ef0a1a65c4e8a4909e26742852f0f2
#5 extracting sha256:2e66a70da0bec13fb3d492fcdef60fd8a5ef0a1a65c4e8a4909e26742852f0f2 2.0s done
#5 extracting sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81
#5 extracting sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 5.1s
#5 extracting sha256:1c8ff076d818ad6b8557e03e10c83657cc716ab287c8380054ff91571c8cae81 5.1s done
#5 extracting sha256:a0ff605e08b8c97d64efd5de9004f7be648fe6181093227246142e70eda4d985 0.1s
#5 extracting sha256:a0ff605e08b8c97d64efd5de9004f7be648fe6181093227246142e70eda4d985 0.3s done
#5 extracting sha256:a040235ac426a0e27ffff8201c375bc2dea5e9b79fbe3de107e8640a3152cb3a
#5 extracting sha256:a040235ac426a0e27ffff8201c375bc2dea5e9b79fbe3de107e8640a3152cb3a 0.4s done
#5 extracting sha256:bf8c0a4030de5f4f6d52f2fd8d70281f7230aa557d51632f7fb27f5c7bca0720
#5 extracting sha256:bf8c0a4030de5f4f6d52f2fd8d70281f7230aa557d51632f7fb27f5c7bca0720 done
#5 extracting sha256:608bb063c2b69dbab463e8ba089f65d9ca171add34cc5dc77434d44320dc4858 0.1s
#5 extracting sha256:608bb063c2b69dbab463e8ba089f65d9ca171add34cc5dc77434d44320dc4858 0.2s done
#5 extracting sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 done
#5 extracting sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 0.1s
#5 extracting sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 5.1s
#5 extracting sha256:2ab4a9a4417c3cba6da0695fbcb161acd24bd950f468b0c807bf365f4c09dfc2 7.6s done
#5 DONE 22.7s
#6 [2/2] RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "scikit-learn"
#6 0.506 Requirement already satisfied: pip in /usr/local/lib/python3.11/site-packages (24.2)
#6 0.671 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
#6 1.056 Requirement already satisfied: scikit-learn in /usr/local/lib/python3.11/site-packages (1.5.1)
#6 1.189 Requirement already satisfied: numpy>=1.19.5 in /usr/local/lib/python3.11/site-packages (from scikit-learn) (1.26.4)
#6 1.190 Requirement already satisfied: scipy>=1.6.0 in /usr/local/lib/python3.11/site-packages (from scikit-learn) (1.14.1)
#6 1.191 Requirement already satisfied: joblib>=1.2.0 in /usr/local/lib/python3.11/site-packages (from scikit-learn) (1.4.2)
#6 1.191 Requirement already satisfied: threadpoolctl>=3.1.0 in /usr/local/lib/python3.11/site-packages (from scikit-learn) (3.5.0)
#6 1.269 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
#6 DONE 1.5s
#7 exporting to image
#7 exporting layers
#7 exporting layers 2.0s done
#7 writing image sha256:4d7f0b6a9ec0517f535a33247c5e56e34f148897ac9f64b8b69c1fa5cbefb9c2 done
#7 naming to ghcr.io/openproblems-bio/task_template/methods/logistic_regression:test done
#7 DONE 2.0s
====================================================================
+/tmp/viash_test_logistic_regression_288619653788075328/test_run_and_check_output/test_executable
>> Running test 'run'
>> Checking whether input files exist
>> Running script as test
Reading input files
Preprocess data
Train model
Generate predictions
Write output AnnData to file
>> Checking whether output file exists
>> Reading h5ad files and checking formats
Reading and checking output
AnnData object with n_obs × n_vars = 213 × 0
obs: 'label_pred'
uns: 'dataset_id', 'method_id', 'normalization_id'
All checks succeeded!
====================================================================
+/tmp/viash_test_logistic_regression_288619653788075328/test_check_config/test_executable
Load config data
Check .namespace
Check .info.type
Check component metadata
Check references fields
Checking contents of .info.preferred_normalization
Check Nextflow runner
All checks succeeded!
====================================================================
SUCCESS! All 2 out of 2 test scripts succeeded!
Cleaning up temporary directoryRun tests
Run unit tests for a component
A component in OpenProblems will typically come with at least two unit tests out of the box:
- The first test will check if the config file has all the required fields.
- The second test will generally test if your component works and if the output has the expected dimensions and fields.
Use viash test to run all of the component’s unit tests.
Example
viash test src/tasks/label_projection/methods/knn/config.vsh.yamlOutput
Test multiple components
Use viash ns test to unit test all of the components of a given task.
viash ns test --parallelOutput
namespace name runner engine test_name exit_code duration result
control_methods true_labels executable docker start
metrics accuracy executable docker start
data_processors process_dataset executable docker start
methods logistic_regression executable docker start
data_processors process_dataset executable docker build_executable 0 2 SUCCESS
data_processors process_dataset executable docker run_and_check_output.py 0 4 SUCCESS
control_methods true_labels executable docker build_executable 0 2 SUCCESS
control_methods true_labels executable docker run_and_check_output.py 0 4 SUCCESS
control_methods true_labels executable docker check_config.py 0 3 SUCCESS
metrics accuracy executable docker build_executable 0 2 SUCCESS
metrics accuracy executable docker run_and_check_output.py 0 5 SUCCESS
metrics accuracy executable docker check_config.py 0 2 SUCCESS
methods logistic_regression executable docker build_executable 0 2 SUCCESS
methods logistic_regression executable docker run_and_check_output.py 0 5 SUCCESS
methods logistic_regression executable docker check_config.py 0 3 SUCCESSCommon errors
Below is a listing of common errors and how to solve them. If you come across any other problems, please take a look at our troubleshooting page, or reach out via GitHub issues.
Assertion error
An assertion error typically occurs when data format of input or output parameters is incorrect.
Component script errors:
Output file cannot be found: Check that your script writes to the correct output filename.
Some fields/objects cannot be found in the output file: Check whether the correct fields are written in the output file.
+/tmp/viash_test_knn12471306149427017048/test_generic_test/test_executable
>> Running script as test
>> Checking whether output file exists
>> Reading h5ad files
>> Checking whether predictions were added
Traceback (most recent call last):
File "/viash_automount/tmp/viash_test_knn12471306149427017048/test_generic_test/tmp//viash-run-knn-QTKmUM.py", line 57, in <module>
assert "label_predi" in output.obs
AssertionErrorComponent config errors:
When these AssertionErrors occur, check the spelling of the missing value if it is present in the file. If the field is irrelevant you can simply add an empty string "" to make sure it is included in the composed config file.
+/tmp/viash_test_knn12945373156205296243/test_check_method_config/test_executable
Load config data
check general fields
Traceback (most recent call last):
Check info fields
File "/viash_automount/tmp/viash_test_knn12945373156205296243/test_check_method_config/tmp//viash-run-knn-Xn2Vd7.py", line 42, in <module>
assert "summary" in info is not None, "summary not an info field or is empty"
AssertionError: summary not an info field or is emptyPython / R dependency does not exist
When a dependency for the unit test or the executed script is not added to the setup of the docker you will get a ModuleNotFoundError. Add the dependency to the setup.
ModuleNotFoundError: No module named 'yaml'Docker image not found
When this kind of error occurs make sure there are no spelling mistakes in the image name.
#3 ERROR: docker.io/library/python:3.1: not found
------
> [internal] load metadata for docker.io/library/python:3.1:
------
Dockerfile:1
--------------------
1 | >>> FROM python:3.1
2 |
3 | RUN pip install --upgrade pip && \
--------------------
ERROR: failed to solve: python:3.1: docker.io/library/python:3.1: not found
[error] Error occurred while building container 'ghcr.io/openproblems-bio/label_projection/methods/knn:test'
ERROR! Setup failed!Script error
When the executed script has an error it will be printed out like the example below. In most cases you can find the problem in the stack trace.
+/tmp/viash_test_knn14797416935521308344/test_generic_test/test_executable
>> Running script as test
Load input data
Traceback (most recent call last):
File "/tmp/viash-run-knn-p4pvkA.py", line 31, in <module>
input_test = ad.read_h5ad(par['input_test'])
File "/usr/local/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 224, in read_h5ad
with h5py.File(filename, "r") as f:
File "/usr/local/lib/python3.10/site-packages/h5py/_hl/files.py", line 542, in __init__
name = filename_encode(name)
File "/usr/local/lib/python3.10/site-packages/h5py/_hl/compat.py", line 19, in filename_encode
filename = fspath(filename)
TypeError: expected str, bytes or os.PathLike object, not NoneType
Method script with returncode ...