def get_dynamic_elements_ena(self, args):
"""
function generates dynamic stages for ENA based on the study type
:param args:
:return:
"""
args = args.split(",")
# args: stub_ref
stub_ref = args[0]
study_type = self.get_batch_attributes()["study_type"][0]
if not study_type:
return list()
study_type = study_type['study_type']
# get protocols
protocols = ISAHelpers().get_protocols_parameter_values(study_type)
# get study assay schema
schema_fields = getattr(DataSchemas("COPO").get_ui_template_as_obj().copo, study_type).fields
# generate dynamic stages from protocols
dynamic_stages = list()
# get message dictionary
message_dict = d_utils.json_to_pytype(lkup.MESSAGES_LKUPS["datafile_wizard"])["properties"]
for pr in protocols:
if len(pr.get("parameterValues", list())) > 0:
title = pr.get("name", str()).title()
ref = pr.get("name", str()).replace(" ", "_")
message = message_dict.get(ref + "_message", dict()).get("text", str())
stage_dict = dict(title=title,
ref=ref,
message=message,
content=str("get_stage_html"),
dependent_on=str("study_type"),
stub_ref=stub_ref,
items=list()
)
for f in schema_fields:
if f.ref in pr.get("parameterValues", list()):
if f.show_in_form:
elem = htags.get_element_by_id(f.id)
elem["id"] = elem['id'].strip(".").rsplit(".", 1)[1]
del elem['ref']
stage_dict.get("items").append(elem)
dynamic_stages.append(stage_dict)
return dynamic_stages
def get_dynamic_elements_ena(datafile_id):
# function mainly based on ena assays specification, reflective of the study type
study_type = get_stage_data(datafile_id, "study_type")
if not study_type:
return []
study_type = study_type["study_type"]
normalised_ranked_list = EnaCollection().get_normalised_ranked_list(
[], DataSchemas("ENA").get_ui_template()["ena"]["studies"]["study"]["assays"]["assaysTable"][study_type]
)
modified_ranked_list = EnaCollection().get_modified_ranked_list(normalised_ranked_list)
# retrieve protocol nodes with sub items
dynamic_elements = [
elem for elem in modified_ranked_list if elem["name"] == "Protocol REF" and len(elem["items"]) > 0
]
# make dynamic_elements wizard compliant, and remove redundant fields
df_wizard_dict = copy.deepcopy(lkup.DF_WIZARD)
if dynamic_elements:
current_list = dynamic_elements
for dye in dynamic_elements:
indx = current_list.index(dye)
current_list[indx]["title"] = (dye["value"]).title()
try:
current_list[indx]["message"] = df_wizard_dict[current_list[indx]["ref"] + "_message"]["text"]
except:
current_list[indx]["message"] = ""
current_list[indx]["content"] = "get_stage_html"
current_list[indx]["deposition_context"] = "ena"
del current_list[indx]["value"] # remove redundant field
del current_list[indx]["name"]
# sort out items
items_dict = []
for its in current_list[indx]["items"]:
elem = htags.get_element_by_id(its["id"])
elem["id"] = elem["id"].strip(".").rsplit(".", 1)[1]
del elem["ref"]
items_dict.append(elem)
current_list[indx]["items"] = items_dict
dynamic_elements = current_list
return dynamic_elements
