anton-khodak

2019-10-04 14:15:13 INFO: Checking MISO storage paths...
2019-10-04 14:15:13 INFO: Directory (/storage/miso) exists.
2019-10-04 14:15:13 INFO: Directory (/storage/miso/log) exists.
2019-10-04 14:15:13 INFO: Directory (/storage/miso/temp) exists.
2019-10-04 14:15:13 INFO: Directory (/storage/miso/files) exists.
2019-10-04 14:15:13 INFO: Directory (/storage/miso/files/submission) exists.
2019-10-04 14:15:13 INFO: All storage directories OK
2019-10-04 14:15:13 INFO: Replacing default namingScheme with OicrNamingScheme
2019-10-04 14:15:13 INFO: FrameworkServlet 'miso': initialization started
2019-10-04 14:15:13 INFO: Refreshing WebApplicationContext for namespace 'miso-servlet': startup date

anton-khodak

install.packages("rentrez")
if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("iSEE", version = "3.8")
BiocManager::install("org.Hs.eg.db") # required for the PBMC4k demo
BiocManager::install("HDF5Array") # required for HDF5-backed assays

anton-khodak

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0

inputs: []
outputs: []

steps:
  step1:
    in: []

anton-khodak

from tests.util import get_data
import cwltool.factory

import cwltool

f = cwltool.factory.Factory(on_error="continue")
# fail = f.make(get_data("tests/wf/scatterfail.cwl"))
fail = f.make(get_data("tests/wf/wffail.cwl"))
try:
    fail()

anton-khodak

--- Running conformance test v1.0 on /Users/anton/.virtualenvs/reana-py3/bin/reana-cwl-runner ---
[INFO] REANA Server URL ($REANA_SERVER_URL) is: http://192.168.99.100:31628
/Users/anton/.virtualenvs/reana-py3/bin/reana-cwl-runner 1.0.20171219150536
[INFO] /Users/anton/.virtualenvs/reana-py3/bin/reana-cwl-runner 1.0.20171219150536
[DEBUG] Running find_module: rdflib.plugins.memory...
[DEBUG] Running load_module for rdflib.plugins.memory...
[DEBUG] Excluded rdflib.plugins.memory from translation
Search path is ['/Users/anton/Programming/CWL/common-workflow-language/v1.0/v1.0/search.cwl#main', '/Users/anton/.local/share/commonwl/v1.0/search.cwl#main', '/usr/local/share/commonwl/v1.0/search.cwl#main', '/usr/share/commonwl/v1.0/search.cwl#main']
[DEBUG] Search path is ['/Users/anton/Programming/CWL/common-workflow-language/v1.0/v1.0/search.cwl#main', '/Users/anton/.local/share/commonwl/v1.0/search.cwl#main', '/usr/local/share/commonwl/v1.0/search.cwl#main', '/usr/share/commonwl/v1.0/search.cwl#main']
[DEBUG] Runn

anton-khodak

#!/bin/bash

read -rd "\000" helpmessage <<EOF
$(basename $0): Run common workflow tool description language conformance tests.

Syntax:
        $(basename $0) [RUNNER=/path/to/cwl-runner] [DRAFT=cwl-draft-version]

Options:
  -nT   Run a specific test.

anton-khodak

---
apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: cwl-default-worker
spec:
  replicas:
  template:
    metadata:
      labels:

anton-khodak

---
apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: cwl-default-worker
spec:
  replicas: 1
  template:
    metadata:
      labels:

anton-khodak

DISCLAIMER: CWL conformance testing on REANA is in progress, please ask for clarifications if things go wrong.

Instructions

To run CWL conformance tests on REANA follow the next steps:

1. Install and launch REANA according to instructions

2. Replace the following REANA components with latest images that support CWL execution:

anton-khodak

package org.rabix.backend.local.slurm;


import org.apache.commons.io.FileUtils;
import org.rabix.bindings.BindingException;
import org.rabix.bindings.Bindings;
import org.rabix.bindings.BindingsFactory;
import org.rabix.bindings.model.Job;
import org.rabix.bindings.model.requirement.ResourceRequirement;
import org.rabix.common.helper.JSONHelper;