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Merge pull request #9529 from nsoranzo/update_dependencies

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Full Python dependencies update
This commit is contained in:
Dannon
2020-04-13 14:53:31 -04:00
committed by GitHub
parent 7855103d2c 9eae2c58cf
commit 267e7ebe56
25 changed files with 96 additions and 200 deletions
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.ci/jenkins/api-py3
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+1
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@@ -0,0 +1 @@
api
.ci/jenkins/api-py3/run_tests.sh
-3
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@@ -1,3 +0,0 @@
#!/bin/bash
./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails -api "$@"
.ci/jenkins/framework-py3
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+1
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@@ -0,0 +1 @@
framework
.ci/jenkins/framework-py3/run_tests.sh
-3
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@@ -1,3 +0,0 @@
#!/bin/bash
./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --framework "$@"
.ci/jenkins/integration-py3
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+1
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@@ -0,0 +1 @@
integration
.ci/jenkins/integration-py3/run_tests.sh
-3
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@@ -1,3 +0,0 @@
#!/bin/bash
DOCKER_RUN_EXTRA_ARGS="--privileged" ./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --integration "$@"
.ci/jenkins/main-tools-py3
Symlink
+1
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@@ -0,0 +1 @@
main-tools
.ci/jenkins/main-tools-py3/run_tests.sh
-3
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@@ -1,3 +0,0 @@
#!/bin/bash
./run_tests.sh --dockerize --python3 --db postgres --clean_pyc -main "$@"
.ci/jenkins/selenium-compose/run_galaxy.bash
+2 -3
View File
@@ -20,8 +20,7 @@ virtualenv "$GALAXY_VIRTUAL_ENV"
chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "$GALAXY_VIRTUAL_ENV"
cd /galaxy
HOME=/galaxy
sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
echo "Waiting for postgres to become available"
while ! nc -z postgres 5432;
@@ -34,7 +33,7 @@ echo "Creating postgres database for Galaxy"
createdb -w -U postgres -h postgres galaxy
echo "Starting and waiting for Galaxy daemon(s)"
sudo -E -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
sudo -E -H -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
echo "Galaxy daemon ready, monitoring Galaxy logs"
tail -f "$GALAXY_ROOT/main.log"
.ci/jenkins/selenium-py3
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+1
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@@ -0,0 +1 @@
selenium
.ci/jenkins/selenium-py3/run_tests.sh
-26
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@@ -1,26 +0,0 @@
#!/bin/bash
# Enable retries on tests to reduce chances of transient failures.
: ${GALAXY_TEST_SELENIUM_RETRIES:=1}
# If in Jenkins environment, use it for artifacts.
if [ -n "$BUILD_NUMBER" ];
then
: ${GALAXY_TEST_ERRORS_DIRECTORY:=${BUILD_NUMBER}-test-errors}
: ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=${BUILD_NUMBER}-test-screenshots}
else
: ${GALAXY_TEST_ERRORS_DIRECTORY:=database/test-errors}
: ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=database/test-screenshots}
fi
mkdir -p "$GALAXY_TEST_ERRORS_DIRECTORY"
mkdir -p "$GALAXY_TEST_SCREENSHOTS_DIRECTORY"
mkdir -p ~/.jenkins-yarn-cache
YARN_CACHE_FOLDER=~/.jenkins-yarn-cache
# Start Selenium server in the test Docker container.
DOCKER_RUN_EXTRA_ARGS="${DOCKER_RUN_EXTRA_ARGS} --shm-size=2g -v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY}"
export DOCKER_RUN_EXTRA_ARGS
./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails --selenium "$@"
lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+10 -8
View File
@@ -4,20 +4,20 @@ alabaster==0.7.12
atomicwrites==1.3.0
attrs==19.3.0
babel==2.8.0
certifi==2019.11.28
certifi==2020.4.5.1
chardet==3.0.4
commonmark==0.9.1
configparser==4.0.2 ; python_version < '3.2'
contextlib2==0.6.0.post1 ; python_version < '3.5'
coverage==5.0.3
deprecated==1.2.7
coverage==5.0.4
deprecated==1.2.9
docutils==0.15.2
funcsigs==1.0.2 ; python_version < '3.3'
future==0.18.2
gunicorn==19.10.0
idna==2.9
imagesize==1.2.0
importlib-metadata==1.5.0 ; python_version < '3.8'
importlib-metadata==1.6.0 ; python_version < '3.8'
jinja2==2.11.1
lxml==4.5.0
markdown==3.1.1
@@ -27,17 +27,18 @@ mock==3.0.5
more-itertools==5.0.0
nose==1.3.7
nosehtml==0.4.5
packaging==20.1
packaging==20.3
pathlib2==2.3.5 ; python_version < '3.6'
pathtools==0.1.2
pluggy==0.13.1
port-for==0.4
prettytable==0.7.2
psutil==5.7.0
py==1.8.1
pygithub==1.45
pygments==2.5.2
pyjwt==1.7.1
pyparsing==2.4.6
pyparsing==2.4.7
pytest-cov==2.8.1
pytest-html==1.22.1
pytest-metadata==1.8.0
@@ -61,6 +62,7 @@ twill==2.0
typing==3.7.4.1 ; python_version < '3.5'
urllib3==1.25.8
watchdog==0.10.2
wcwidth==0.1.8
wrapt==1.12.0
wcwidth==0.1.9
wrapt==1.12.1
xmlrunner==1.7.7
zipp==1.2.0
lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+29 -29
View File
@@ -23,8 +23,8 @@ bcrypt==3.1.7
bdbag==1.5.6
beaker==1.11.0
bioblend==0.13.0
bleach==3.1.1
boltons==20.0.0
bleach==3.1.4
boltons==20.1.0
boto3==1.9.114
boto==2.49.0
botocore==1.12.253
@@ -32,7 +32,7 @@ bx-python==0.8.8
bz2file==0.98 ; python_version < '3.3'
cachecontrol==0.11.7
cachetools==3.1.1
certifi==2019.11.28
certifi==2020.4.5.1
cffi==1.14.0
chardet==3.0.4
cheetah3==3.2.4
@@ -43,18 +43,18 @@ cmd2==0.8.9
coloredlogs==14.0
configparser==4.0.2 ; python_version < '3.2'
contextlib2==0.6.0.post1 ; python_version < '3.5'
cryptography==2.8
cryptography==2.9
cwltool==1.0.20191225192155
debtcollector==1.22.0
decorator==4.4.2
deprecated==1.2.7
deprecated==1.2.9
deprecation==2.0.7
dictobj==0.4
docopt==0.6.2
docutils==0.15.2
dogpile.cache==0.9.0
ecdsa==0.15
enum34==1.1.9 ; python_version < '3.4'
enum34==1.1.10 ; python_version < '3.4'
fabric3==1.14.post1
funcsigs==1.0.2 ; python_version < '3.3'
functools32==3.2.3.post2 ; python_version < '3.2'
@@ -63,13 +63,13 @@ futures==3.3.0 ; python_version == '2.6' or python_version == '2.7'
galaxy-sequence-utils==1.1.5
google-api-python-client==1.7.8
google-auth-httplib2==0.0.3
google-auth==1.11.2
gxformat2==0.10.1
google-auth==1.13.1
gxformat2==0.11.1
h5py==2.10.0
httplib2==0.17.0
humanfriendly==7.1.1
httplib2==0.17.2
humanfriendly==8.1
idna==2.9
importlib-metadata==1.5.0 ; python_version < '3.8'
importlib-metadata==1.6.0 ; python_version < '3.8'
ipaddress==1.0.23 ; python_version < '3.3'
isa-rwval==0.10.7
iso8601==0.1.12
@@ -78,14 +78,14 @@ jmespath==0.9.5
jsonpatch==1.25
jsonpointer==2.0
jsonschema==3.2.0
keystoneauth1==3.18.0
kombu==4.6.7
keystoneauth1==4.0.0
kombu==4.6.8
lockfile==0.12.2
lxml==4.5.0
mako==1.1.1
mako==1.1.2
markdown==3.1.1
markupsafe==1.1.1
mercurial==5.3
mercurial==5.3.2
mistune==0.8.4
monotonic==1.5
msgpack==1.0.0
@@ -102,7 +102,7 @@ numpy==1.16.6
oauth2client==4.1.3
oauthlib==3.1.0
openstacksdk==0.17.0
os-client-config==2.0.0
os-client-config==2.1.0
os-service-types==1.7.0
osc-lib==2.0.0
oslo.config==7.0.0
@@ -111,21 +111,21 @@ oslo.i18n==3.25.1
oslo.log==3.45.2
oslo.serialization==2.29.2
oslo.utils==3.42.1
packaging==20.1
packaging==20.3
paramiko==2.7.1
parsley==1.3
paste==3.4.0
pastedeploy==2.1.0
pastescript==3.2.0
pathlib2==2.3.5 ; python_version < '3.6'
pbr==5.4.4
pbr==5.4.5
prettytable==0.7.2
prov==1.5.1
psutil==5.7.0
pulsar-galaxy-lib==0.14.0.dev1
pyasn1-modules==0.2.8
pyasn1==0.4.8
pycparser==2.19
pycparser==2.20
pycryptodome==3.9.7
pyeventsystem==0.1.0
pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
@@ -133,9 +133,9 @@ pyjwt==1.7.1
pykwalify==1.7.0
pynacl==1.3.0
pyopenssl==19.1.0
pyparsing==2.4.6
pyperclip==1.7.0
pyrsistent==0.15.7
pyparsing==2.4.7
pyperclip==1.8.0
pyrsistent==0.16.0
pysam==0.15.2
pysftp==0.2.9
python-cinderclient==4.0.0
@@ -149,7 +149,7 @@ python-openid==2.2.5 ; python_version < '3.0'
python-swiftclient==3.6.0
pytz==2019.3
pyuwsgi==2.0.18.post0
pyyaml==5.3
pyyaml==5.3.1
rdflib-jsonld==0.4.0
rdflib==4.2.2
repoze.lru==0.7
@@ -157,7 +157,7 @@ requests-oauthlib==1.3.0
requests-toolbelt==0.9.1
requests==2.23.0
requestsexceptions==1.4.0
rfc3986==1.3.2
rfc3986==1.4.0
routes==2.4.1
rsa==4.0
ruamel.ordereddict==0.4.14 ; platform_python_implementation == 'CPython' and python_version <= '2.7'
@@ -172,15 +172,15 @@ simplejson==3.17.0
six==1.11.0
social-auth-core[openidconnect]==3.1.0+gx0
sqlalchemy-migrate==0.13.0
sqlalchemy-utils==0.36.1
sqlalchemy==1.3.13
sqlalchemy-utils==0.36.3
sqlalchemy==1.3.16
sqlparse==0.3.1
stevedore==1.32.0
subprocess32==3.5.4 ; python_version < '3.0'
svgwrite==1.3.1
tempita==0.5.2
tenacity==4.12.0
typing-extensions==3.7.4.1
typing-extensions==3.7.4.2
typing==3.7.4.1 ; python_version < '3.5'
tzlocal==2.0.0
unicodecsv==0.14.1 ; python_version < '3.0'
@@ -188,9 +188,9 @@ uritemplate==3.0.1
urllib3==1.25.8
vine==1.3.0
warlock==1.3.3
wcwidth==0.1.8
wcwidth==0.1.9
webencodings==0.5.1
webob==1.8.6
whoosh==2.7.4
wrapt==1.12.0
wrapt==1.12.1
zipp==1.2.0
lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
+1 -1
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@@ -1,7 +1,7 @@
-i https://pypi.python.org/simple
configparser==4.0.2 ; python_version < '3.2'
entrypoints==0.3
enum34==1.1.9 ; python_version < '3.4'
enum34==1.1.10 ; python_version < '3.4'
flake8-import-order==0.18.1
flake8==3.7.9
functools32==3.2.3.post2 ; python_version < '3.2'
lib/galaxy_test/api/embed_test_1.gxwf.yml
+2 -2
View File
@@ -14,7 +14,7 @@ steps:
- tool_id: cat1
state:
input1:
$link: first_cat#out_file1
$link: first_cat/out_file1
queries:
- input2:
$link: embed1#output1
$link: embed1/output1
lib/galaxy_test/api/test_workflow_extraction.py
+6 -6
View File
@@ -228,7 +228,7 @@ steps:
- tool_id: cat_collection
state:
input1:
$link: noop#out_file1
$link: noop/out_file1
test_data:
text_input1:
type: "list:paired"
@@ -274,11 +274,11 @@ steps:
tool_id: collection_split_on_column
state:
input1:
$link: cat_inputs#out_file1
$link: cat_inputs/out_file1
- tool_id: cat_list
state:
input1:
$link: split_up#split_output
$link: split_up/split_output
test_data:
text_input1: "samp1\t10.0\nsamp2\t20.0\n"
text_input2: "samp1\t30.0\nsamp2\t40.0\n"
@@ -316,16 +316,16 @@ steps:
tool_id: collection_creates_pair
state:
input1:
$link: cat_inputs#out_file1
$link: cat_inputs/out_file1
- label: cat_pairs
tool_id: cat_collection
state:
input1:
$link: pair_off#paired_output
$link: pair_off/paired_output
- tool_id: cat_list
state:
input1:
$link: cat_pairs#out_file1
$link: cat_pairs/out_file1
test_data:
text_input1:
type: list
lib/galaxy_test/api/test_workflows.py
+17 -59
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@@ -40,47 +40,6 @@ from galaxy_test.base.workflow_fixtures import (
from ._framework import ApiTestCase
NESTED_WORKFLOW_AUTO_LABELS_LEGACY_SYNTAX = """
class: GalaxyWorkflow
inputs:
outer_input: data
outputs:
outer_output:
outputSource: second_cat/out_file1
steps:
first_cat:
tool_id: cat1
in:
input1: outer_input
nested_workflow:
run:
class: GalaxyWorkflow
inputs:
- id: inner_input
outputs:
- source: 1#out_file1
steps:
random:
tool_id: random_lines1
state:
num_lines: 1
input:
$link: inner_input
seed_source:
seed_source_selector: set_seed
seed: asdf
in:
inner_input: first_cat/out_file1
second_cat:
tool_id: cat1
state:
input1:
$link: nested_workflow#1:out_file1
queries:
- input2:
$link: nested_workflow#1:out_file1
"""
NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX = """
class: GalaxyWorkflow
inputs:
@@ -487,10 +446,10 @@ steps:
- tool_id: cat1
state:
input1:
$link: first_cat#out_file1
$link: first_cat/out_file1
queries:
input2:
$link: embed1#output1
$link: embed1/output1
test_data:
input1: "hello world"
""")
@@ -832,12 +791,12 @@ steps:
inner_cond:
cond_param_inner: true
input1:
$link: 0#out_file1
$link: 0/out_file1
cat:
tool_id: cat1
in:
input1: identifier#output1
queries_0|input2: identifier#output1
input1: identifier/output1
queries_0|input2: identifier/output1
""")
with self.dataset_populator.test_history() as history_id:
invocation_id = self.__invoke_workflow(history_id, workflow_id)
@@ -873,11 +832,11 @@ steps:
list_in_list_out:
tool_id: collection_creates_list
in:
input1: job_props#list_output
input1: job_props/list_output
identifier:
tool_id: identifier_collection
in:
input1: list_in_list_out#list_output
input1: list_in_list_out/list_output
""")
with self.dataset_populator.test_history() as history_id:
invocation_id = self.__invoke_workflow(history_id, workflow_id)
@@ -1220,8 +1179,7 @@ test_data:
"chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n",
content)
for workflow_text in [NESTED_WORKFLOW_AUTO_LABELS_LEGACY_SYNTAX, NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX]:
run_test(workflow_text)
run_test(NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX)
@skip_without_tool("cat1")
@skip_without_tool("collection_paired_test")
@@ -1274,7 +1232,7 @@ steps:
tool_id: '__FLATTEN__'
state:
input:
$link: nested#list_output
$link: nested/list_output
join_identifier: '-'
""", test_data={}, history_id=history_id)
details = self.dataset_populator.get_history_collection_details(history_id, hid=14)
@@ -1400,7 +1358,7 @@ steps:
tool_id: "__FILTER_FAILED_DATASETS__"
state:
input:
$link: mixed_collection#out_file1
$link: mixed_collection/out_file1
cat:
tool_id: cat1
@@ -1870,7 +1828,7 @@ steps:
state:
num_lines: 2
input:
$link: empty_list#output
$link: empty_list/output
seed_source:
seed_source_selector: set_seed
seed: asdf
@@ -1953,7 +1911,7 @@ steps:
state:
num_lines: 2
input:
$link: empty_list#output
$link: empty_list/output
seed_source:
seed_source_selector: set_seed
seed: asdf
@@ -2388,7 +2346,7 @@ steps:
state:
floattest: 3.14
inttest:
$link: forty_two#out1
$link: forty_two/out1
test_data: {}
""", history_id=history_id)
@@ -2417,7 +2375,7 @@ steps:
- label: consume_expression_parameter
tool_id: validation_default
in:
input1: param_out#text_param
input1: param_out/text_param
outputs:
out_file1:
rename: "replaced_param_collection"
@@ -3272,7 +3230,7 @@ steps:
create_pair:
tool_id: collection_creates_pair
in:
input1: first_cat#out_file1
input1: first_cat/out_file1
outputs:
paired_output:
remove_tags:
@@ -4103,10 +4061,10 @@ steps:
- tool_id: cat1
state:
input1:
$link: first_cat#out_file1
$link: first_cat/out_file1
queries:
- input2:
$link: embed1#output1
$link: embed1/output1
test_data:
input1: "hello world"
""")
lib/galaxy_test/api/test_workflows_from_yaml.py
+2 -2
View File
@@ -296,10 +296,10 @@ steps:
- tool_id: cat1
state:
input1:
$link: first_cat#out_file1
$link: first_cat/out_file1
queries:
- input2:
$link: embed1#output1
$link: embed1/output1
test_data:
input1: "hello world"
""", history_id=history_id)
lib/galaxy_test/base/workflow_fixtures.py
+4 -4
View File
@@ -143,11 +143,11 @@ steps:
- tool_id: collection_paired_test
state:
f1:
$link: 1#paired_output
$link: 1/paired_output
- tool_id: cat_list
state:
input1:
$link: 2#out1
$link: 2/out1
"""
@@ -175,7 +175,7 @@ steps:
state:
num_lines: 1
input:
$link: apply#output
$link: apply/output
seed_source:
seed_source_selector: set_seed
seed: asdf
@@ -279,7 +279,7 @@ steps:
inner_input: data
outputs:
workflow_output:
outputSource: random_lines#out_file1
outputSource: random_lines/out_file1
steps:
- tool_id: random_lines1
label: random_lines
lib/tool_shed/test/base/twilltestcase.py
-3
View File
@@ -8,9 +8,6 @@ import tempfile
import time
from json import loads
# Be sure to use Galaxy's vanilla pyparsing instead of the older version
# imported by twill.
import pyparsing # noqa: F401
import requests
import twill.commands as tc
from mercurial import commands, hg, ui
run_tests.sh
+2 -2
View File
@@ -269,7 +269,7 @@ exists() {
type "$1" >/dev/null 2>/dev/null
}
DOCKER_DEFAULT_IMAGE='galaxy/testing-base:19.05.0'
DOCKER_DEFAULT_IMAGE='galaxy/testing-base:20.05.00'
test_script="./scripts/functional_tests.py"
report_file="run_functional_tests.html"
@@ -312,7 +312,7 @@ then
echo "Docker version:"
docker --version
echo "Launching docker container for testing with extra args ${DOCKER_RUN_EXTRA_ARGS}..."
name=$(python -c 'import re; import uuid; print re.sub("-", "", str(uuid.uuid4()))')
name=$(python -c 'import re; import uuid; print(re.sub("-", "", str(uuid.uuid4())))')
# Create a cache dir for pip, so it has the right owner
DOCKER_PIP_CACHE_DIR="$HOME"/.cache/docker_galaxy_pip
mkdir -p "$DOCKER_PIP_CACHE_DIR"
test/docker/base/Dockerfile
+4 -25
View File
@@ -1,4 +1,4 @@
FROM ubuntu:16.04
FROM ubuntu:18.04
LABEL maintainer="John Chilton <jmchilton@gmail.com>"
ARG CHROME_VERSION="google-chrome-beta"
@@ -11,8 +11,6 @@ ENV DEBIAN_FRONTEND=noninteractive \
POSTGRES_MAJOR=9.5 \
GALAXY_ROOT=/galaxy \
GALAXY_VIRTUAL_ENV=/galaxy_venv \
GALAXY_VIRTUAL_ENV_2=/galaxy_venv \
GALAXY_VIRTUAL_ENV_3=/galaxy_venv3 \
LC_ALL=C.UTF-8
# Pre-install a bunch of packages to speed up ansible steps.
@@ -20,13 +18,10 @@ RUN apt-get update -y && apt-get install -y software-properties-common apt-trans
apt-add-repository -y ppa:ansible/ansible && \
curl -s https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - && \
echo "deb http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google-chrome.list && \
curl -s http://neuro.debian.net/lists/xenial.us-ca.full > /etc/apt/sources.list.d/neurodebian.sources.list && \
apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \
apt-get update -y && \
apt-get install -y --no-install-recommends postgresql postgresql-client ansible wget \
python3-dev \
git-core \
python-prettytable python-virtualenv python-pip \
rsync swig sysstat unzip \
openssl \
bzip2 \
@@ -37,9 +32,6 @@ RUN apt-get update -y && apt-get install -y software-properties-common apt-trans
locales \
xvfb \
${CHROME_VERSION:-google-chrome-stable} \
ffmpeg \
bcftools \
singularity-container \
libnss3 libgconf-2-4 && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
@@ -69,24 +61,11 @@ RUN mkdir /etc/galaxy && cd /tmp/ansible && mkdir roles && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN cd $GALAXY_ROOT && \
virtualenv -p /usr/bin/python3 $GALAXY_VIRTUAL_ENV_3 && \
for VENV in $GALAXY_VIRTUAL_ENV_2 $GALAXY_VIRTUAL_ENV_3; do \
GALAXY_VIRTUAL_ENV=$VENV ./scripts/common_startup.sh --dev-wheels && \
$VENV/bin/pip install psycopg2-binary; done && \
virtualenv -p /usr/bin/python3 $GALAXY_VIRTUAL_ENV && \
./scripts/common_startup.sh --dev-wheels && \
$GALAXY_VIRTUAL_ENV/bin/pip install psycopg2-binary && \
rm -rf ~/.cache/pip
RUN cd $GALAXY_ROOT && \
echo "Prepopulating postgres database" && \
su -c '/usr/lib/postgresql/${POSTGRES_MAJOR}/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \
sleep 3 && \
GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/galaxy" bash create_db.sh && \
echo "Prepopulating sqlite database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/galaxy.sqlite" bash create_db.sh && \
echo "Prepopulating toolshed postgres database" && \
TOOL_SHED_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/toolshed" bash create_db.sh tool_shed && \
echo "Prepopulating toolshed sqlite database" && \
TOOL_SHED_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/toolshed.sqlite" bash create_db.sh tool_shed
#========================================
# Add Selenium user with passwordless sudo
#========================================
test/docker/base/ansible_vars.yml
+2 -1
View File
@@ -17,7 +17,7 @@ galaxy_db_log: /tmp/pSQL.log
psql_galaxyftp_password: ignoredthis
galaxy_config_file: "{{ galaxy_server_dir }}/config/galaxy.ini"
configure_docker: no
postgresql_bin_dir: /usr/lib/postgresql/9.5/bin
postgresql_bin_dir: /usr/lib/postgresql/10/bin
galaxy_manage_database: no
# avoid some packages unneeded packages install by ansible-galaxy-os
install_maintainance_packages: false
@@ -25,6 +25,7 @@ galaxy_user_name: "root"
galaxy_extras_install_packages: true
galaxy_job_conf_path: "/etc/galaxy/job_conf.xml"
galaxy_build_client: no
galaxy_virtualenv_python: python3
galaxy_web_processes: 1
galaxy_handler_processes: 2
test/docker/base/run_test_wrapper.sh
+5 -13
View File
@@ -4,7 +4,7 @@ set -e
if [ ! -z "$USE_SELENIUM" ];
then
# Start Selenium.
sudo -H -E -u seluser /opt/bin/entry_point.sh &
sudo -E -H -u seluser /opt/bin/entry_point.sh &
fi
echo "Deleting galaxy user - it may not exist and this is fine."
@@ -16,16 +16,15 @@ echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and
groupadd -r galaxy -g "$GALAXY_TEST_UID" | true
echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and this is fine."
useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash | true
mkdir -p /home/galaxy/.singularity
echo "Setting galaxy user password - the operation may fail."
echo "galaxy:galaxy" | chpasswd | true
chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "${GALAXY_VIRTUAL_ENV:-/galaxy_venv}" /home/galaxy/
chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "${GALAXY_VIRTUAL_ENV:-/galaxy_venv}"
: ${GALAXY_TEST_DATABASE_TYPE:-"postgres"}
if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
then
echo "Starting postgres and then sleeping for 3 seconds"
su -c '/usr/lib/postgresql/9.5/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
su -c '/usr/lib/postgresql/10/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
sleep 3
GALAXY_TEST_INSTALL_DB_MERGED="true"
GALAXY_TEST_DBURI="postgresql://root@localhost:5930/galaxy?client_encoding=utf8"
@@ -49,15 +48,8 @@ cd /galaxy
: ${GALAXY_VIRTUAL_ENV:=.venv}
HOME=/home/galaxy
echo "Running common startup for updated dependencies (if any)"
sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh --dev-wheels || { echo "common_startup.sh failed"; exit 1; }
echo "Upgrading test database..."
sudo -E -u "#${GALAXY_TEST_UID}" GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI" sh manage_db.sh upgrade
echo "Upgrading tool shed database... $TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION"
sudo -E -u "#${GALAXY_TEST_UID}" TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION="$TOOL_SHED_TEST_DBURI" sh manage_db.sh upgrade tool_shed
sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh --dev-wheels || { echo "common_startup.sh failed"; exit 1; }
# Ensure Selenium is running before starting tests.
if [ ! -z "$USE_SELENIUM" ];
@@ -78,7 +70,7 @@ fi
if [ -z "$GALAXY_NO_TESTS" ];
then
sudo -E -u "#${GALAXY_TEST_UID}" sh run_tests.sh --skip-common-startup $@
sudo -E -H -u "#${GALAXY_TEST_UID}" sh run_tests.sh --skip-common-startup $@
else
GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI"
TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION="$TOOL_SHED_TEST_DBURI"
test/integration/test_fail_job_tool_unavailable.py
+5 -4
View File
@@ -27,20 +27,21 @@ class FailJobWhenToolUnavailableTestCase(integration_util.IntegrationTestCase):
self.workflow_populator.run_workflow("""
class: GalaxyWorkflow
steps:
- label: sleep
sleep:
run:
class: GalaxyTool
command: sleep 20s && echo 'hello world 2' > '$output1'
outputs:
output1:
format: txt
- tool_id: cat1
cat:
tool_id: cat1
state:
input1:
$link: sleep#output1
$link: sleep/output1
queries:
input2:
$link: sleep#output1
$link: sleep/output1
""", history_id=self.history_id, assert_ok=False, wait=False)
# Wait until workflow is fully scheduled, otherwise can't test effect of removing tool from queued job
time.sleep(10)