pvanheus

diff -ur nose.old/case.py nose/case.py
--- nose.old/case.py	2022-08-27 19:21:19.686914283 +0000
+++ nose/case.py	2022-08-27 19:22:16.688908658 +0000
@@ -9,7 +9,7 @@
 from nose.config import Config
 from nose.failure import Failure # for backwards compatibility
 from nose.util import resolve_name, test_address, try_run
-import collections
+from collections.abc import Callable
 

pvanheus

#!/usr/bin/env python

import argparse
import json
from typing import TextIO
import urllib3


def submit_project(project_name: str, csv_file: TextIO, newick_file: TextIO,
                   access_token: str = None):

pvanheus

run-parts: executing /app/scripts/0_init_container.sh 
Apply database migrations from /app/cloudman 
/app/venv/lib/python3.6/site-packages/urllib3/connectionpool.py:986: InsecureRequestWarning: Unverified HTTPS request is being made to host '192.168.10.54'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings 
  InsecureRequestWarning, 
System check identified some issues: 
 
WARNINGS: 
?: (urls.W005) URL namespace 'admin' isn't unique. You may not be able to reverse all URLs in this namespace 
?: (urls.W005) URL namespace 'djcloudbridge' isn't unique. You may not be able to reverse all URLs in this namespace 
?: (urls.W005) URL namespace 'pubapp' isn't unique. You may not be able to reverse all URLs in this namespace 

pvanheus

{
    "a_galaxy_workflow": "true",
    "annotation": "Workflow for generating SARS-Cov2 consensus ",
    "format-version": "0.1",
    "name": "SARS-Cov2-Amplicon-Artic (imported from uploaded file)",
    "steps": {
        "0": {
            "annotation": "",
            "content_id": null,
            "errors": null,

pvanheus

{
    "a_galaxy_workflow": "true",
    "annotation": "",
    "format-version": "0.1",
    "name": "SARS-CoV-2 ARTIC amplicon analysis (v. 2)",
    "steps": {
        "0": {
            "annotation": "",
            "content_id": null,
            "errors": null,

pvanheus

{
    "a_galaxy_workflow": "true",
    "annotation": "",
    "format-version": "0.1",
    "name": "Copy of COVID-19: variation analysis (imported from uploaded file)",
    "steps": {
        "0": {
            "annotation": "",
            "content_id": null,
            "errors": null,

pvanheus

19:11:27.943318 IP 192.168.66.107.48212 > 129.114.17.223.443: Flags [.], ack 3096, win 487, options [nop,nop,TS val 2519331564 ecr 1801106980,nop,nop,sack 1 {11994:17466}], length 0


19:12:27.947113 IP 192.168.66.107.48212 > 129.114.17.223.443: Flags [.], ack 3096, win 487, options [nop,nop,TS val 2519391566 ecr 1801106980,nop,nop,sack 1 {11994:17466}], length 0
19:12:28.136522 IP 129.114.17.223.443 > 192.168.66.107.48212: Flags [.], ack 779, win 114, options [nop,nop,TS val 1801167234 ecr 2519331564], length 0
19:12:32.946732 IP 129.114.17.223.443 > 192.168.66.107.48212: Flags [FP.], seq 17466:17497, ack 779, win 114, options [nop,nop,TS val 1801172045 ecr 2519331564], length 31
19:12:32.946767 IP 192.168.66.107.48212 > 129.114.17.223.443: Flags [.], ack 3096, win 535, options [nop,nop,TS val 2519396565 ecr 1801106980,nop,nop,sack 1 {11994:17498}], length 0
19:13:33.099106 IP 192.168.66.107.48212 > 129.114.17.223.443: Flags [.], ack 3096, win 535, options [nop,nop,TS val 2519456715 ecr 1801106980,nop,nop,sa

pvanheus

$ curl -verbose https://testtoolshed.g2.bx.psu.edu/
*   Trying 129.114.17.223...
* TCP_NODELAY set
* Connected to testtoolshed.g2.bx.psu.edu (129.114.17.223) port 443 (#0)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
*   CAfile: /etc/ssl/certs/ca-certificates.crt
  CApath: /etc/ssl/certs
* TLSv1.3 (OUT), TLS handshake, Client hello (1):

pvanheus

13:33:18.790460 IP galaxy-masters2.sanbi.ac.za.44220 > js-129-114-17-223.jetstream-cloud.org.https: Flags [S], seq 711925144, win 28200, options [mss 1410,sackOK,TS val 1513391783 ecr 0,nop,wscale 7], length 0
13:33:18.980677 IP js-129-114-17-223.jetstream-cloud.org.https > galaxy-masters2.sanbi.ac.za.44220: Flags [S.], seq 3622071767, ack 711925145, win 26844, options [mss 8960,sackOK,TS val 1168817789 ecr 1513391783,nop,wscale 8], length 0
13:33:18.980773 IP galaxy-masters2.sanbi.ac.za.44220 > js-129-114-17-223.jetstream-cloud.org.https: Flags [.], ack 1, win 221, options [nop,nop,TS val 1513391973 ecr 1168817789], length 0
13:33:18.981872 IP galaxy-masters2.sanbi.ac.za.44220 > js-129-114-17-223.jetstream-cloud.org.https: Flags [P.], seq 1:518, ack 1, win 221, options [nop,nop,TS val 1513391974 ecr 1168817789], length 517
13:33:19.171876 IP js-129-114-17-223.jetstream-cloud.org.https > galaxy-masters2.sanbi.ac.za.44220: Flags [.], ack 518, win 110, options [nop,nop,TS val 1168817980 ecr 1513391974], length 

pvanheus

git --git-dir /home/pvh/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*'
git --git-dir /home/pvh/.planemo/gx_repo config remote.origin.mirror true
git --git-dir /home/pvh/.planemo/gx_repo remote update >/dev/null 2>&1
git clone --branch master /home/pvh/.planemo/gx_repo /tmp/tmp4bznxpwc/galaxy-dev && cd /tmp/tmp4bznxpwc/galaxy-dev && if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/pvh/.planemo/gx_venv; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/pvh/anaconda3/envs/planemo/bin/virtualenv -p /usr/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; fi && COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}
Cloning into '/tmp/tmp4bznxpwc/galaxy-dev'...
done.
Set COMMON