def __init__(self,
sh_type=StepHelperType.CREATE_NEW_TEMPLATE,
previous_template_id=-1,
previous_plan_id=-1):
self.sh_type = sh_type
self.previous_template_id = previous_template_id
self.previous_plan_id = previous_plan_id
self.parentName = None
if (sh_type in [
StepHelperType.EDIT_PLAN, StepHelperType.EDIT_PLAN_BY_SAMPLE,
StepHelperType.EDIT_RUN, StepHelperType.EDIT_TEMPLATE
] and previous_template_id == -1 and previous_plan_id == -1):
logger.error(
"step_helper - StepHelper.init() for EDIT should have an existing ID."
)
raise ValueError("You must pass in a plan id or a template id.")
self.steps = OrderedDict()
if sh_type == StepHelperType.CREATE_NEW_PLAN_BY_SAMPLE or sh_type == StepHelperType.EDIT_PLAN_BY_SAMPLE or sh_type == StepHelperType.COPY_PLAN_BY_SAMPLE:
steps_list = [
IonreporterStepData(),
ApplicationStepData(),
KitsStepData(),
MonitoringStepData(),
ReferenceStepData(),
PluginsStepData(),
BarcodeBySampleStepData(),
OutputStepData(),
SavePlanBySampleStepData()
]
elif sh_type == StepHelperType.CREATE_NEW_TEMPLATE_BY_SAMPLE:
steps_list = [
IonreporterStepData(),
ApplicationStepData(),
KitsStepData(),
MonitoringStepData(),
ReferenceStepData(),
PluginsStepData(),
OutputStepData(),
SaveTemplateBySampleStepData()
]
else:
steps_list = [
IonreporterStepData(),
ApplicationStepData(),
KitsStepData(),
MonitoringStepData(),
ReferenceStepData(),
PluginsStepData(),
OutputStepData(),
SaveTemplateStepData(),
SavePlanStepData()
]
for step in steps_list:
self.steps[step.getStepName()] = step
self.update_dependent_steps(self.steps[StepNames.APPLICATION])
def __init__(self, sh_type=StepHelperType.CREATE_NEW_TEMPLATE, previous_template_id=-1, previous_plan_id=-1):
self.sh_type = sh_type
self.previous_template_id = previous_template_id
self.previous_plan_id = previous_plan_id
self.parentName = None
self.steps = OrderedDict()
if sh_type == StepHelperType.CREATE_NEW_PLAN_BY_SAMPLE or sh_type == StepHelperType.EDIT_PLAN_BY_SAMPLE or sh_type == StepHelperType.COPY_PLAN_BY_SAMPLE:
steps_list = [IonreporterStepData(), ApplicationStepData(), KitsStepData(), MonitoringStepData(),
ReferenceStepData(), PluginsStepData(), BarcodeBySampleStepData(),
OutputStepData(), SavePlanBySampleStepData()]
elif sh_type == StepHelperType.CREATE_NEW_TEMPLATE_BY_SAMPLE:
steps_list = [IonreporterStepData(), ApplicationStepData(), KitsStepData(), MonitoringStepData(),
ReferenceStepData(), PluginsStepData(),
OutputStepData(), SaveTemplateBySampleStepData()]
else:
steps_list = [IonreporterStepData(), ApplicationStepData(), KitsStepData(), MonitoringStepData(),
ReferenceStepData(), PluginsStepData(), OutputStepData(),
SaveTemplateStepData(), SavePlanStepData()]
for step in steps_list:
self.steps[step.getStepName()] = step
self.update_dependant_steps(self.steps[StepNames.APPLICATION])
def __init__(self,
sh_type=StepHelperType.CREATE_NEW_TEMPLATE,
previous_template_id=-1,
previous_plan_id=-1,
experiment_id=-1):
self.sh_type = sh_type
self.previous_template_id = previous_template_id
self.previous_plan_id = previous_plan_id
self.experiment_id = experiment_id
self.parentName = None
self.isFromScratch = False
# set to true if we are creating a plan or template from a system template
self.isParentSystem = False
if (sh_type in [
StepHelperType.EDIT_PLAN, StepHelperType.EDIT_PLAN_BY_SAMPLE,
StepHelperType.EDIT_RUN, StepHelperType.EDIT_TEMPLATE
] and previous_template_id == -1 and previous_plan_id == -1):
logger.error(
"step_helper - StepHelper.init() for EDIT should have an existing ID."
)
raise ValueError("You must pass in a plan id or a template id.")
self.steps = OrderedDict()
if sh_type == StepHelperType.CREATE_NEW_PLAN_BY_SAMPLE or sh_type == StepHelperType.EDIT_PLAN_BY_SAMPLE or sh_type == StepHelperType.COPY_PLAN_BY_SAMPLE:
referenceStepData = ReferenceStepData(sh_type)
barcodeBySampleStepData = BarcodeBySampleStepData(sh_type)
analysisParamsStepData = AnalysisParamsStepData(sh_type)
steps_list = [
IonreporterStepData(sh_type),
ApplicationStepData(sh_type),
KitsStepData(sh_type), referenceStepData,
analysisParamsStepData,
PluginsStepData(sh_type), barcodeBySampleStepData,
OutputStepData(sh_type),
SavePlanBySampleStepData(sh_type)
]
# some section can appear in multiple chevrons, key is the step name and value is the step_data object
barcodeBySampleStepData.step_sections.update(
{StepNames.REFERENCE: referenceStepData})
barcodeBySampleStepData.step_sections.update(
{StepNames.ANALYSIS_PARAMS: analysisParamsStepData})
elif sh_type == StepHelperType.CREATE_NEW_TEMPLATE_BY_SAMPLE:
referenceStepData = ReferenceStepData(sh_type)
saveTemplateBySampleData = SaveTemplateBySampleStepData(sh_type)
analysisParamsStepData = AnalysisParamsStepData(sh_type)
steps_list = [
IonreporterStepData(sh_type),
ApplicationStepData(sh_type),
KitsStepData(sh_type), referenceStepData,
analysisParamsStepData,
PluginsStepData(sh_type),
OutputStepData(sh_type), saveTemplateBySampleData
]
saveTemplateBySampleData.step_sections.update(
{StepNames.REFERENCE: referenceStepData})
saveTemplateBySampleData.step_sections.update(
{StepNames.ANALYSIS_PARAMS: analysisParamsStepData})
elif sh_type == StepHelperType.COPY_TEMPLATE or sh_type == StepHelperType.CREATE_NEW_TEMPLATE or sh_type == StepHelperType.EDIT_TEMPLATE:
referenceStepData = ReferenceStepData(sh_type)
saveTemplateStepData = SaveTemplateStepData(sh_type)
analysisParamsStepData = AnalysisParamsStepData(sh_type)
steps_list = [
IonreporterStepData(sh_type),
ApplicationStepData(sh_type),
KitsStepData(sh_type), referenceStepData,
analysisParamsStepData,
PluginsStepData(sh_type),
OutputStepData(sh_type), saveTemplateStepData
]
saveTemplateStepData.step_sections.update(
{StepNames.REFERENCE: referenceStepData})
saveTemplateStepData.step_sections.update(
{StepNames.ANALYSIS_PARAMS: analysisParamsStepData})
else:
referenceStepData = ReferenceStepData(sh_type)
# SaveTemplateStepData is needed for the last chevron during plan creation
saveTemplateStepData = SaveTemplateStepData(sh_type)
savePlanStepData = SavePlanStepData(sh_type)
analysisParamsStepData = AnalysisParamsStepData(sh_type)
steps_list = [
IonreporterStepData(sh_type),
ApplicationStepData(sh_type),
KitsStepData(sh_type), referenceStepData,
analysisParamsStepData,
PluginsStepData(sh_type),
OutputStepData(sh_type), saveTemplateStepData, savePlanStepData
]
savePlanStepData.step_sections.update({
StepNames.REFERENCE:
referenceStepData
}) ###referenceStepData.sectionParentStep = savePlanStepData
savePlanStepData.step_sections.update(
{StepNames.ANALYSIS_PARAMS: analysisParamsStepData})
for step in steps_list:
self.steps[step.getStepName()] = step
self.update_dependent_steps(self.steps[StepNames.APPLICATION])
def __init__(
self,
sh_type=StepHelperType.CREATE_NEW_TEMPLATE,
previous_template_id=-1,
previous_plan_id=-1,
experiment_id=-1,
):
self.sh_type = sh_type
self.previous_template_id = previous_template_id
self.previous_plan_id = previous_plan_id
self.experiment_id = experiment_id
self.parentName = None
self.isFromScratch = False
# set to true if we are creating a plan or template from a system template
self.isParentSystem = False
if (sh_type in [
StepHelperType.EDIT_PLAN,
StepHelperType.EDIT_PLAN_BY_SAMPLE,
StepHelperType.EDIT_RUN,
StepHelperType.EDIT_TEMPLATE,
] and previous_template_id == -1 and previous_plan_id == -1):
logger.error(
"step_helper - StepHelper.init() for EDIT should have an existing ID."
)
raise ValueError(
validation.
invalid_required_at_least_one_polymorphic_type_value(
validation.Entity_EntityFieldName(Plan.verbose_name, "id"),
validation.Entity_EntityFieldName(
PlanTemplate.verbose_name, "id"),
)) # "You must pass in a Plan id or a Template id."
self.steps = OrderedDict()
steps_list = []
if settings.FEATURE_FLAGS.IONREPORTERUPLOADER:
steps_list.append(IonreporterStepData(sh_type))
steps_list.append(ApplicationStepData(sh_type))
else:
steps_list.append(IonreporterStepData(sh_type, next_step_url=None))
steps_list.append(ApplicationStepData(sh_type, prev_step_url=None))
if (sh_type == StepHelperType.CREATE_NEW_PLAN_BY_SAMPLE
or sh_type == StepHelperType.EDIT_PLAN_BY_SAMPLE
or sh_type == StepHelperType.COPY_PLAN_BY_SAMPLE):
referenceStepData = ReferenceStepData(sh_type)
barcodeBySampleStepData = BarcodeBySampleStepData(sh_type)
analysisParamsStepData = AnalysisParamsStepData(sh_type)
steps_list.extend([
KitsStepData(sh_type),
referenceStepData,
analysisParamsStepData,
PluginsStepData(sh_type),
barcodeBySampleStepData,
OutputStepData(sh_type),
SavePlanBySampleStepData(sh_type),
])
# some section can appear in multiple chevrons, key is the step name and value is the step_data object
barcodeBySampleStepData.step_sections.update(
{StepNames.REFERENCE: referenceStepData})
barcodeBySampleStepData.step_sections.update(
{StepNames.ANALYSIS_PARAMS: analysisParamsStepData})
elif sh_type == StepHelperType.CREATE_NEW_TEMPLATE_BY_SAMPLE:
referenceStepData = ReferenceStepData(sh_type)
saveTemplateBySampleData = SaveTemplateBySampleStepData(sh_type)
analysisParamsStepData = AnalysisParamsStepData(sh_type)
steps_list.extend([
KitsStepData(sh_type),
referenceStepData,
analysisParamsStepData,
PluginsStepData(sh_type),
OutputStepData(sh_type),
saveTemplateBySampleData,
])
saveTemplateBySampleData.step_sections.update(
{StepNames.REFERENCE: referenceStepData})
saveTemplateBySampleData.step_sections.update(
{StepNames.ANALYSIS_PARAMS: analysisParamsStepData})
elif (sh_type == StepHelperType.COPY_TEMPLATE
or sh_type == StepHelperType.CREATE_NEW_TEMPLATE
or sh_type == StepHelperType.EDIT_TEMPLATE):
referenceStepData = ReferenceStepData(sh_type)
saveTemplateStepData = SaveTemplateStepData(sh_type)
analysisParamsStepData = AnalysisParamsStepData(sh_type)
steps_list.extend([
KitsStepData(sh_type),
referenceStepData,
analysisParamsStepData,
PluginsStepData(sh_type),
OutputStepData(sh_type),
saveTemplateStepData,
])
saveTemplateStepData.step_sections.update(
{StepNames.REFERENCE: referenceStepData})
saveTemplateStepData.step_sections.update(
{StepNames.ANALYSIS_PARAMS: analysisParamsStepData})
else:
referenceStepData = ReferenceStepData(sh_type)
# SaveTemplateStepData is needed for the last chevron during plan creation
saveTemplateStepData = SaveTemplateStepData(sh_type)
savePlanStepData = SavePlanStepData(sh_type)
analysisParamsStepData = AnalysisParamsStepData(sh_type)
steps_list.extend([
KitsStepData(sh_type),
referenceStepData,
analysisParamsStepData,
PluginsStepData(sh_type),
OutputStepData(sh_type),
saveTemplateStepData,
savePlanStepData,
])
savePlanStepData.step_sections.update({
StepNames.REFERENCE:
referenceStepData
}) ###referenceStepData.sectionParentStep = savePlanStepData
savePlanStepData.step_sections.update(
{StepNames.ANALYSIS_PARAMS: analysisParamsStepData})
for step in steps_list:
self.steps[step.getStepName()] = step
self.update_dependent_steps(self.steps[StepNames.APPLICATION])