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Merge branch 'release_23.0' into dev

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This commit is contained in:
mvdbeek
2023-02-10 09:13:38 +01:00
parent 1d761ba2df 45c0701885
commit 6c47dca69c
8 changed files with 94 additions and 26 deletions
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client/src/components/Panels/Common/ToolSearch.vue
+1
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@@ -4,6 +4,7 @@
<DelayedInput
:class="!showAdvanced && 'mb-3'"
:query="query"
:delay="100"
:show-advanced="showAdvanced"
:enable-advanced="enableAdvanced"
:placeholder="showAdvanced ? 'any name' : placeholder"
client/src/components/Workflow/Run/WorkflowRunSuccess.vue
+22 -11
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@@ -2,16 +2,17 @@
<div>
<div class="donemessagelarge">
<p>
Successfully invoked workflow <b>{{ workflowName }}</b
><em v-if="multipleInvocations"> - {{ timesExecuted }} times</em>.
Successfully invoked workflow <b>{{ workflowName }}</b>
<em v-if="multipleInvocations"> - {{ timesExecuted }} times</em>.
</p>
<p v-if="multipleInvocations">
<p v-if="multipleHistoryTargets">
This workflow will generate results in multiple histories. You can observe progress in the
<a :href="historyTarget">history multi-view</a>.
<a :href="multiHistoryView">history multi-view</a>.
</p>
<p v-else-if="wasNewHistoryTarget">
This workflow will generate results in a new history.
<a class="workflow-new-history-target-link" :href="historyTarget">Switch to that history now</a>.
<a class="workflow-new-history-target-link" :href="newHistoryTarget">Switch to that history now</a>.
</p>
<p v-else>You can check the status of queued jobs and view the resulting data the History panel.</p>
</div>
@@ -53,12 +54,22 @@ export default {
multipleInvocations() {
return this.timesExecuted > 1;
},
historyTarget() {
if (this.multipleInvocations) {
return `${getAppRoot()}histories/view_multiple`;
} else {
return `${getAppRoot()}history/switch_to_history?hist_id=${this.invocations[0].history_id}`;
}
multipleHistoryTargets() {
return this.targetHistories.length > 1;
},
targetHistories() {
return this.invocations.reduce((histories, invocation) => {
if (invocation.history_id && !histories.includes(invocation.history_id)) {
histories.push(invocation.history_id);
}
return histories;
}, []);
},
multiHistoryView() {
return `${getAppRoot()}histories/view_multiple`;
},
newHistoryTarget() {
return `${getAppRoot()}history/switch_to_history?hist_id=${this.invocations[0].history_id}`;
},
wasNewHistoryTarget() {
if (this.invocations.length < 1) {
client/src/schema/schema.ts
+4 -4
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@@ -520,7 +520,7 @@ export interface paths {
};
"/api/histories/{history_id}/contents/{id}": {
/**
* Return detailed information about an HDA within a history.
* Return detailed information about an HDA within a history. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
* @deprecated
* @description Return detailed information about an `HDA` or `HDCA` within a history.
*
@@ -528,7 +528,7 @@ export interface paths {
*/
get: operations["history_content_api_histories__history_id__contents__id__get"];
/**
* Updates the values for the history content item with the given ``ID``.
* Updates the values for the history content item with the given ``ID``. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
* @deprecated
* @description Updates the values for the history content item with the given ``ID``.
*/
@@ -10605,7 +10605,7 @@ export interface operations {
};
history_content_api_histories__history_id__contents__id__get: {
/**
* Return detailed information about an HDA within a history.
* Return detailed information about an HDA within a history. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
* @deprecated
* @description Return detailed information about an `HDA` or `HDCA` within a history.
*
@@ -10658,7 +10658,7 @@ export interface operations {
};
update_api_histories__history_id__contents__id__put: {
/**
* Updates the values for the history content item with the given ``ID``.
* Updates the values for the history content item with the given ``ID``. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
* @deprecated
* @description Updates the values for the history content item with the given ``ID``.
*/
lib/galaxy/dependencies/pinned-requirements.txt
+1 -1
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@@ -117,7 +117,7 @@ pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9
prompt-toolkit==3.0.36 ; python_version >= "3.7" and python_version < "3.12"
prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12"
psutil==5.9.4 ; python_version >= "3.7" and python_version < "3.12"
pulsar-galaxy-lib==0.15.0.dev0 ; python_version >= "3.7" and python_version < "3.12"
pulsar-galaxy-lib==0.15.0.dev1 ; python_version >= "3.7" and python_version < "3.12"
pyasn1==0.4.8 ; python_version >= "3.7" and python_version < "3.12"
pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
pycryptodome==3.17 ; python_version >= "3.7" and python_version < "3.12"
lib/galaxy/jobs/runners/pulsar.py
+5 -1
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@@ -99,6 +99,10 @@ PULSAR_PARAM_SPECS = dict(
map=specs.to_str_or_none,
default=None,
),
amqp_key_prefix=dict(
map=specs.to_str_or_none,
default=None,
),
galaxy_url=dict(
map=specs.to_str_or_none,
default=None,
@@ -968,7 +972,7 @@ class PulsarMQJobRunner(PulsarJobRunner):
)
DEFAULT_PULSAR_CONTAINER = "galaxy/pulsar-pod-staging:0.15.0.1"
DEFAULT_PULSAR_CONTAINER = "galaxy/pulsar-pod-staging:0.15.0.2"
COEXECUTION_DESTENTATION_DEFAULTS = {
"default_file_action": "remote_transfer",
"rewrite_parameters": "true",
lib/galaxy/managers/markdown_util.py
+12 -7
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@@ -110,13 +110,7 @@ class GalaxyInternalMarkdownDirectiveHandler(metaclass=abc.ABCMeta):
raise MalformedContents(f"Missing object identifier [{line}].")
def _remap(container, line):
id_match = re.search(UNENCODED_ID_PATTERN, line)
object_id = None
encoded_id = None
if id_match:
object_id = int(id_match.group(2))
encoded_id = trans.security.encode_id(object_id)
line = line.replace(id_match.group(), f"{id_match.group(1)}={encoded_id}")
line, object_id, encoded_id = self._encode_line(trans, line)
if container == "history_link":
_check_object(object_id, line)
history = history_manager.get_accessible(object_id, trans.user)
@@ -196,11 +190,22 @@ class GalaxyInternalMarkdownDirectiveHandler(metaclass=abc.ABCMeta):
try:
return _remap(container, line)
except Exception as e:
line, *_ = self._encode_line(trans, line)
return self.handle_error(container, line, str(e))
export_markdown = _remap_galaxy_markdown_calls(_remap_container, internal_galaxy_markdown)
return export_markdown
def _encode_line(self, trans, line):
id_match = re.search(UNENCODED_ID_PATTERN, line)
object_id = None
encoded_id = None
if id_match:
object_id = int(id_match.group(2))
encoded_id = trans.security.encode_id(object_id)
line = line.replace(id_match.group(), f"{id_match.group(1)}={encoded_id}")
return line, object_id, encoded_id
@abc.abstractmethod
def handle_history_link(self, line, history):
pass
lib/galaxy/model/migrations/dbscript.py
+2
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@@ -34,6 +34,8 @@ REVISION_TAGS = {
"22.01": "base",
"release_22.05": "186d4835587b",
"22.05": "186d4835587b",
"release_23.0": "186d4835587b",
"23.0": "186d4835587b",
}
test/integration/test_coexecution.py
+47 -2
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@@ -8,7 +8,7 @@ communicate job status updates back.
For this reason, this test will only work out of the box currently with Docker for Mac,
rabbitmq installed via Homebrew, and if a fixed port is set for the test.
GALAXY_TEST_PORT=9234 pytest test/integration/test_kubernetes_staging.py
GALAXY_TEST_PORT=9234 pytest test/integration/test_coexecution.py
"""
import os
@@ -186,6 +186,37 @@ tools:
"""
TES_CONTAINERIZED_TEMPLATE_CUSTOM_AMQP_KEY = """
runners:
local:
load: galaxy.jobs.runners.local:LocalJobRunner
workers: 1
pulsar_tes:
load: galaxy.jobs.runners.pulsar:PulsarTesJobRunner
amqp_url: ${amqp_url}
amqp_key_prefix: pulsar_foobar34_
execution:
default: pulsar_tes_environment
environments:
pulsar_tes_environment:
runner: pulsar_tes
tes_url: ${tes_url}
docker_enabled: true
docker_default_container_id: busybox:ubuntu-14.04
pulsar_app_config:
message_queue_url: '${container_amqp_url}'
env:
- name: SOME_ENV_VAR
value: '42'
local_environment:
runner: local
tools:
- id: __DATA_FETCH__
environment: local_environment
"""
def tes_job_config(template_str: str, jobs_directory: str) -> str:
job_conf_template = string.Template(template_str)
assert AMQP_URL
@@ -312,6 +343,20 @@ class TestTesCoexecutionContainerIntegration(TestCoexecution):
set_infrastucture_url(config)
@integration_util.skip_unless_environ("FUNNEL_SERVER_TARGET")
class TestTesCoexecutionCustomAmqpKeyContainerIntegration(TestCoexecution):
@classmethod
def handle_galaxy_config_kwds(cls, config) -> None:
config["jobs_directory"] = cls.jobs_directory
config["file_path"] = cls.jobs_directory
config["job_config_file"] = tes_job_config(TES_CONTAINERIZED_TEMPLATE_CUSTOM_AMQP_KEY, cls.jobs_directory)
config["default_job_shell"] = "/bin/sh"
# Disable tool dependency resolution.
config["tool_dependency_dir"] = "none"
set_infrastucture_url(config)
@integration_util.skip_unless_environ("FUNNEL_SERVER_TARGET")
class TestTesDependencyResolutionIntegration(TestCoexecution):
@classmethod
@@ -342,7 +387,7 @@ def to_infrastructure_uri(uri: str) -> str:
# remap MQ or file server URI hostnames for in-container versions, this is sloppy
# should actually parse the URI and rebuild with correct host
# Copied from Pulsar's integraiton tests.
infrastructure_host = os.environ.get("GALAXY_TEST_INFRASTRUCTURE_HOST")
infrastructure_host = GALAXY_TEST_INFRASTRUCTURE_HOST
if infrastructure_host == "_PLATFORM_AUTO_":
system = platform.system()
if system in ["Darwin", "Windows"]: