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Merge pull request #14688 from mvdbeek/dev

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Merge 22.05 into dev
This commit is contained in:
Marius van den Beek
2022-09-26 15:19:53 +02:00
committed by GitHub
parent 4274683543 cbd38554f1
commit 955815ca11
12 changed files with 245 additions and 160 deletions
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client/src/components/Workflow/Run/WorkflowRunDefaultStep.vue
+52 -28
View File
@@ -2,13 +2,19 @@
<div :step-label="model.step_label">
<FormCard :title="model.fixed_title" :icon="icon" :collapsible="true" :expanded.sync="expanded">
<template v-slot:body>
<FormMessage :message="errorText" variant="danger" :persistent="true" />
<FormDisplay
v-if="hasInputs"
:inputs="inputs"
:inputs="modelInputs"
:sustain-repeats="true"
:sustain-conditionals="true"
:replace-params="replaceParams"
:validation-scroll-to="validationScrollTo"
collapsed-enable-text="Edit"
collapsed-enable-icon="fa fa-edit"
collapsed-disable-text="Undo"
collapsed-disable-icon="fa fa-undo"
@onChange="onChange"
@onValidation="onValidation" />
<div v-else class="py-2">No options available.</div>
</template>
</FormCard>
</div>
@@ -17,52 +23,43 @@
<script>
import WorkflowIcons from "components/Workflow/icons";
import FormDisplay from "components/Form/FormDisplay";
import FormMessage from "components/Form/FormMessage";
import FormCard from "components/Form/FormCard";
import { visitInputs } from "components/Form/utilities";
import { getTool } from "./services";
export default {
components: {
FormDisplay,
FormCard,
FormMessage,
},
props: {
model: {
type: Object,
required: true,
},
replaceParams: {
type: Object,
default: null,
},
validationScrollTo: {
type: Array,
required: true,
},
historyId: {
type: String,
default: null,
},
},
data() {
return {
expanded: this.model.expanded,
errorText: null,
modelIndex: {},
modelInputs: this.model.inputs,
};
},
computed: {
icon() {
return WorkflowIcons[this.model.step_type];
},
isSimpleInput() {
return (
this.model.step_type.startsWith("data_input") ||
this.model.step_type.startsWith("data_collection_input")
);
},
inputs() {
this.model.inputs.forEach((input) => {
input.flavor = "module";
input.hide_label = this.isSimpleInput;
});
if (this.model.inputs && this.model.inputs.length > 0) {
return this.model.inputs;
}
return [];
},
hasInputs() {
return this.inputs.length > 0;
},
},
watch: {
validationScrollTo() {
if (this.validationScrollTo.length > 0) {
@@ -70,8 +67,35 @@ export default {
}
},
},
computed: {
icon() {
return WorkflowIcons[this.model.step_type];
},
},
methods: {
onChange(data) {
onCreateIndex() {
this.modelIndex = {};
visitInputs(this.modelInputs, (input, name) => {
this.modelIndex[name] = input;
});
},
onChange(data, refreshRequest) {
if (refreshRequest) {
getTool(this.model.id, this.model.version, data, this.historyId).then(
(newModel) => {
this.onCreateIndex();
visitInputs(newModel.inputs, (newInput, name) => {
const input = this.modelIndex[name];
input.options = newInput.options;
input.textable = newInput.textable;
});
this.modelInputs = JSON.parse(JSON.stringify(this.modelInputs));
},
(errorText) => {
this.errorText = errorText;
}
);
}
this.$emit("onChange", this.model.index, data);
},
onValidation(validation) {
client/src/components/Workflow/Run/WorkflowRunForm.vue
+8 -7
View File
@@ -36,15 +36,15 @@
</template>
</FormCard>
<div v-for="step in model.steps" :key="step.index">
<WorkflowRunToolStep
v-if="step.step_type == 'tool'"
<WorkflowRunDefaultStep
v-if="step.step_type == 'tool' || step.step_type == 'subworkflow'"
:model="step"
:replace-params="getReplaceParams(step.inputs)"
:validation-scroll-to="getValidationScrollTo(step.index)"
:history-id="currentHistoryId"
@onChange="onToolStepInputs"
@onValidation="onValidation" />
<WorkflowRunDefaultStep
<WorkflowRunInputStep
v-else
:model="step"
:validation-scroll-to="getValidationScrollTo(step.index)"
@@ -64,7 +64,7 @@ import FormCard from "components/Form/FormCard";
import FormElement from "components/Form/FormElement";
import UserHistories from "components/providers/UserHistories";
import WorkflowRunDefaultStep from "./WorkflowRunDefaultStep";
import WorkflowRunToolStep from "./WorkflowRunToolStep";
import WorkflowRunInputStep from "./WorkflowRunInputStep";
import { allowCachedJobs } from "components/Tool/utilities";
import { getReplacements } from "./model";
import { invokeWorkflow } from "./services";
@@ -78,7 +78,7 @@ export default {
FormElement,
UserHistories,
WorkflowRunDefaultStep,
WorkflowRunToolStep,
WorkflowRunInputStep,
},
props: {
model: {
@@ -93,6 +93,7 @@ export default {
stepValidations: {},
stepScrollTo: {},
wpData: {},
inputs: {},
historyData: {},
useCachedJobs: false,
historyInputs: [
@@ -155,8 +156,7 @@ export default {
return [];
},
onDefaultStepInputs(stepId, data) {
this.stepData[stepId] = data;
this.stepData = Object.assign({}, this.stepData);
this.inputs[stepId] = data.input;
},
onToolStepInputs(stepId, data) {
this.stepData[stepId] = data;
@@ -201,6 +201,7 @@ export default {
resource_params: this.resourceData,
replacement_params: this.wpData,
use_cached_job: this.useCachedJobs,
inputs: this.inputs,
parameters: parameters,
// Tool form will submit flat maps for each parameter
// (e.g. "repeat_0|cond|param": "foo" instead of nested
client/src/components/Workflow/Run/WorkflowRunInputStep.vue
+83
View File
@@ -0,0 +1,83 @@
<template>
<div :step-label="model.step_label">
<FormCard :title="model.fixed_title" :icon="icon" :collapsible="true" :expanded.sync="expanded">
<template v-slot:body>
<FormDisplay
v-if="hasInputs"
:inputs="inputs"
:validation-scroll-to="validationScrollTo"
@onChange="onChange"
@onValidation="onValidation" />
<div v-else class="py-2">No options available.</div>
</template>
</FormCard>
</div>
</template>
<script>
import WorkflowIcons from "components/Workflow/icons";
import FormDisplay from "components/Form/FormDisplay";
import FormCard from "components/Form/FormCard";
export default {
components: {
FormDisplay,
FormCard,
},
props: {
model: {
type: Object,
required: true,
},
validationScrollTo: {
type: Array,
required: true,
},
},
data() {
return {
expanded: this.model.expanded,
};
},
computed: {
icon() {
return WorkflowIcons[this.model.step_type];
},
isSimpleInput() {
return (
this.model.step_type.startsWith("data_input") ||
this.model.step_type.startsWith("data_collection_input")
);
},
inputs() {
this.model.inputs.forEach((input) => {
input.flavor = "module";
input.hide_label = this.isSimpleInput;
});
if (this.model.inputs && this.model.inputs.length > 0) {
return this.model.inputs;
}
return [];
},
hasInputs() {
return this.inputs.length > 0;
},
},
watch: {
validationScrollTo() {
if (this.validationScrollTo.length > 0) {
this.expanded = true;
}
},
},
methods: {
onChange(data) {
console.log("emitting default change", data);
this.$emit("onChange", this.model.index, data);
},
onValidation(validation) {
this.$emit("onValidation", this.model.index, validation);
},
},
};
</script>
client/src/components/Workflow/Run/WorkflowRunToolStep.vue
-100
View File
@@ -1,100 +0,0 @@
<template>
<div :step-label="model.step_label">
<FormCard :title="model.fixed_title" icon="fa-wrench" :collapsible="true" :expanded.sync="expanded">
<template v-slot:body>
<FormMessage :message="errorText" variant="danger" :persistent="true" />
<FormDisplay
:inputs="modelInputs"
:sustain-repeats="true"
:sustain-conditionals="true"
:replace-params="replaceParams"
:validation-scroll-to="validationScrollTo"
collapsed-enable-text="Edit"
collapsed-enable-icon="fa fa-edit"
collapsed-disable-text="Undo"
collapsed-disable-icon="fa fa-undo"
@onChange="onChange"
@onValidation="onValidation" />
</template>
</FormCard>
</div>
</template>
<script>
import FormDisplay from "components/Form/FormDisplay";
import FormMessage from "components/Form/FormMessage";
import FormCard from "components/Form/FormCard";
import { visitInputs } from "components/Form/utilities";
import { getTool } from "./services";
export default {
components: {
FormDisplay,
FormCard,
FormMessage,
},
props: {
model: {
type: Object,
required: true,
},
replaceParams: {
type: Object,
default: null,
},
validationScrollTo: {
type: Array,
required: true,
},
historyId: {
type: String,
default: null,
},
},
data() {
return {
expanded: this.model.expanded,
errorText: null,
modelIndex: {},
modelInputs: this.model.inputs,
};
},
watch: {
validationScrollTo() {
if (this.validationScrollTo.length > 0) {
this.expanded = true;
}
},
},
methods: {
onCreateIndex() {
this.modelIndex = {};
visitInputs(this.modelInputs, (input, name) => {
this.modelIndex[name] = input;
});
},
onChange(data, refreshRequest) {
if (refreshRequest) {
getTool(this.model.id, this.model.version, data, this.historyId).then(
(newModel) => {
this.onCreateIndex();
visitInputs(newModel.inputs, (newInput, name) => {
const input = this.modelIndex[name];
input.options = newInput.options;
input.textable = newInput.textable;
});
this.modelInputs = JSON.parse(JSON.stringify(this.modelInputs));
},
(errorText) => {
this.errorText = errorText;
}
);
}
this.$emit("onChange", this.model.index, data);
},
onValidation(validation) {
this.$emit("onValidation", this.model.index, validation);
},
},
};
</script>
client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
+2 -12
View File
@@ -86,6 +86,7 @@
<script>
import { mapCacheActions } from "vuex-cache";
import { mapGetters, mapActions } from "vuex";
import WorkflowIcons from "components/Workflow/icons";
import JobStep from "./JobStep";
import ParameterStep from "./ParameterStep";
import GenericHistoryItem from "components/History/Content/GenericItem";
@@ -134,18 +135,7 @@ export default {
return ["data_input", "data_collection_input"].includes(this.workflowStepType);
},
stepIcon() {
switch (this.workflowStepType) {
case "data_input":
return "fa-file";
case "data_collection_input":
return "fa-folder-o";
case "parameter_input":
return "fa-pencil";
case "subworkflow":
return "fa-tasks";
default:
return "fa-wrench";
}
return WorkflowIcons[this.workflowStepType];
},
stepLabel() {
return this.labelForWorkflowStep(this.workflowStep.id);
lib/galaxy/model/__init__.py
+13 -3
View File
@@ -7034,6 +7034,10 @@ class WorkflowStep(Base, RepresentById):
self.uuid = uuid4()
self._input_connections_by_name = None
@reconstructor
def init_on_load(self):
self._input_connections_by_name = None
@property
def tool_uuid(self):
return self.dynamic_tool and self.dynamic_tool.uuid
@@ -7047,13 +7051,17 @@ class WorkflowStep(Base, RepresentById):
@property
def input_default_value(self):
tool_inputs = self.tool_inputs
tool_state = tool_inputs
tool_state = self.tool_inputs
default_value = tool_state.get("default")
if default_value:
default_value = json.loads(default_value)["value"]
return default_value
@property
def input_optional(self):
tool_state = self.tool_inputs
return tool_state.get("optional") or False
def get_input(self, input_name):
for step_input in self.inputs:
if step_input.name == input_name:
@@ -7196,7 +7204,9 @@ class WorkflowStep(Base, RepresentById):
copied_step.workflow_outputs = copy_list(self.workflow_outputs, copied_step)
def log_str(self):
return "WorkflowStep[index=%d,type=%s]" % (self.order_index, self.type)
return (
f"WorkflowStep[index={self.order_index},type={self.type},label={self.label},uuid={self.uuid},id={self.id}]"
)
def clear_module_extras(self):
# the module code adds random dynamic state to the step, this
lib/galaxy/workflow/run.py
+5 -7
View File
@@ -450,12 +450,10 @@ class WorkflowProgress:
step_id = step.id
if step_id not in self.inputs_by_step_id and "output" not in outputs:
default_value = step.input_default_value
if default_value:
if default_value or step.input_optional:
outputs["output"] = default_value
else:
template = "Step with id %s not found in inputs_step_id (%s)"
message = template % (step.log_str(), self.inputs_by_step_id)
raise ValueError(message)
raise ValueError(f"{step.log_str()} not found in inputs_step_id {self.inputs_by_step_id}")
elif step_id in self.inputs_by_step_id:
outputs["output"] = self.inputs_by_step_id[step_id]
@@ -536,9 +534,9 @@ class WorkflowProgress:
subworkflow_inputs = {}
for input_subworkflow_step in subworkflow.input_steps:
connection_found = False
subworkflow_step_id = input_subworkflow_step.id
for input_connection in step.input_connections:
if input_connection.input_subworkflow_step == input_subworkflow_step:
subworkflow_step_id = input_subworkflow_step.id
if input_connection.input_subworkflow_step_id == subworkflow_step_id:
is_data = input_connection.output_step.type != "parameter_input"
replacement = self.replacement_for_connection(
input_connection,
@@ -548,7 +546,7 @@ class WorkflowProgress:
connection_found = True
break
if not connection_found:
if not connection_found and not input_subworkflow_step.input_optional:
raise Exception("Could not find connections for all subworkflow inputs.")
return WorkflowProgress(
lib/galaxy/workflow/run_request.py
+1 -1
View File
@@ -110,7 +110,7 @@ def _normalize_inputs(
if possible_input_key in inputs:
inputs_key = possible_input_key
default_value = step.tool_inputs.get("default")
optional = step.tool_inputs.get("optional") or False
optional = step.input_optional
# Need to be careful here to make sure 'default' has correct type - not sure how to do that
# but asserting 'optional' is definitely a bool and not a String->Bool or something is a good
# start to ensure tool state is being preserved and loaded in a type safe way.
lib/galaxy_test/api/test_workflows.py
+36
View File
@@ -16,6 +16,7 @@ from typing import (
from uuid import uuid4
import pytest
import yaml
from requests import (
delete,
get,
@@ -41,6 +42,7 @@ from galaxy_test.base.workflow_fixtures import (
WORKFLOW_ONE_STEP_DEFAULT,
WORKFLOW_OPTIONAL_FALSE_INPUT_COLLECTION,
WORKFLOW_OPTIONAL_FALSE_INPUT_DATA,
WORKFLOW_OPTIONAL_INPUT_DELAYED_SCHEDULING,
WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION,
WORKFLOW_OPTIONAL_TRUE_INPUT_DATA,
WORKFLOW_PARAMETER_INPUT_INTEGER_DEFAULT,
@@ -3168,6 +3170,40 @@ input1:
content = self.dataset_populator.get_history_dataset_content(history_id)
assert "No input selected" in content
def test_run_with_optional_data_unspecified_survives_delayed_step(self):
with self.dataset_populator.test_history() as history_id:
self._run_workflow(
WORKFLOW_OPTIONAL_INPUT_DELAYED_SCHEDULING,
history_id=history_id,
wait=True,
assert_ok=True,
)
def test_run_subworkflow_with_optional_data_unspecified(self):
with self.dataset_populator.test_history() as history_id:
subworkflow = yaml.safe_load(
"""
class: GalaxyWorkflow
inputs:
required: data
steps:
nested_workflow:
in:
required: required
test_data:
required:
value: 1.bed
type: File
"""
)
subworkflow["steps"]["nested_workflow"]["run"] = yaml.safe_load(WORKFLOW_OPTIONAL_INPUT_DELAYED_SCHEDULING)
self._run_workflow(
subworkflow,
history_id=history_id,
wait=True,
assert_ok=True,
)
def test_run_with_non_optional_data_unspecified_fails_invocation(self):
with self.dataset_populator.test_history() as history_id:
error = self._run_jobs(
lib/galaxy_test/base/populators.py
+5 -2
View File
@@ -1746,8 +1746,11 @@ class BaseWorkflowPopulator(BasePopulator):
if test_data is None:
if jobs_descriptions is None:
assert source_type != "path"
assert isinstance(has_workflow, str)
jobs_descriptions = yaml.safe_load(has_workflow)
if isinstance(has_workflow, dict):
jobs_descriptions = has_workflow
else:
assert isinstance(has_workflow, str)
jobs_descriptions = yaml.safe_load(has_workflow)
test_data_dict = jobs_descriptions.get("test_data", {})
elif not isinstance(test_data, dict):
lib/galaxy_test/base/workflow_fixtures.py
+38
View File
@@ -614,6 +614,44 @@ steps:
"""
WORKFLOW_OPTIONAL_INPUT_DELAYED_SCHEDULING = """
class: GalaxyWorkflow
inputs:
required:
type: data
optional:
type: data
optional: true
outputs:
out1:
outputSource: count_multi_file/out_file1
steps:
expression:
tool_id: expression_parse_int
state:
input1: 1
head:
tool_id: head
in:
input: required
state:
lineNum:
$link: expression/out1
count_multi_file:
tool_id: count_multi_file
in:
input1:
- optional
- head/out_file1
out:
out_file1: out_file1
test_data:
required:
value: 1.bed
type: File
"""
WORKFLOW_RUNTIME_PARAMETER_SIMPLE = """
class: GalaxyWorkflow
inputs:
test/unit/workflows/test_workflow_progress.py
+2
View File
@@ -189,6 +189,8 @@ class WorkflowProgressTestCase(unittest.TestCase):
subworkflow_invocation = self.invocation.create_subworkflow_invocation_for_step(
self.invocation.workflow.step_by_index(1)
)
self.app.model.session.add(subworkflow_invocation)
self.app.model.session.flush()
progress = self._new_workflow_progress()
remaining_steps = progress.remaining_steps()
(subworkflow_step, subworkflow_invocation_step) = remaining_steps[0]