tx.py

import pytest

from bloom_lims.db import BLOOMdb3
from bloom_lims.bobjs import BloomWorkflow, BloomWorkflowStep, BloomObj, BloomReagent
import sys
import os

bob_wf = BloomWorkflow(BLOOMdb3(),cfg_fedex=True)

bob_wfs = BloomWorkflowStep(BLOOMdb3(), cfg_fedex=True)

bob_rg = BloomReagent(BLOOMdb3(), cfg_fedex=True)

idt_plate_euid = bob_rg.create_rgnt_24w_plate_TEST('idt-probes-rare-mendelian')
naoh_plate_euid = bob_rg.create_rgnt_24w_plate_TEST('naoh')

from random import randint

ASSAY = "workflow/assay/hla-typing/1.2" if int(sys.argv[2]) > 0 else "workflow/assay/carrier-screen/3.9"

giab_cx, giab_mx = bob_wf.create_container_with_content(
        ("container", "tube", "tube-generic-10ml", "1.0"),
        ("content", "control", "giab-HG002", "1.0")
    )   
 
cfsynctl_cx, cfsynctl_mx = bob_wf.create_container_with_content(
        ("container", "tube", "tube-10ml-glass", "1.0"),
        ("content", "control", "synthetic-cfdna", "1.0")
    )  

ntc_cx, ntc_mx = bob_wf.create_container_with_content( 
        ("container", "tube", "tube-eppi-1.5ml", "1.0"),
        ("content", "control", "water-ntc", "1.0")
    )

## This needs to be done better
CA = [{"cont_address": {
                  "name": "A1",
                  "row_name": "A",
                  "col_name": "1",
                  "row_idx": "0",
                  "col_idx": "0"
                }},{"cont_address": {
                  "name": "A2",
                  "row_name": "A",
                  "col_name": "2",
                  "row_idx": "1",
                  "col_idx": "0"
                }},{"cont_address": {
                  "name": "A3",
                  "row_name": "A",
                  "col_name": "3",
                  "row_idx": "0",
                  "col_idx": "2"
                }}]
                
rgnt_plate_glob = bob_wf.create_instance_by_template_components(
    "container", "plate", "fixed-plate-24", "1.0"
)
rgnt_plate = rgnt_plate_glob[0][0]
rgnt_plate_wells = rgnt_plate_glob[1]
for i in rgnt_plate_wells:
    bob_wf.create_generic_instance_lineage_by_euids(i.euid, bob_wf.create_instance_by_template_components("content","reagent","naoh","1.0")[0][0].euid)


      
new_rack = bob_wf.create_instance_by_template_components(
    "container", "rack", "tube-rack-4-empty", "1.0"
)[0][0]

bob_wf.create_generic_instance_lineage_by_euids(new_rack.euid, ntc_cx.euid)
ntc_cx.json_addl['cont_address']=CA[0]['cont_address']

bob_wf.create_generic_instance_lineage_by_euids(new_rack.euid, cfsynctl_cx.euid)
cfsynctl_cx.json_addl['cont_address']=CA[1]['cont_address']

bob_wf.create_generic_instance_lineage_by_euids(new_rack.euid, giab_cx.euid)
giab_cx.json_addl['cont_address']=CA[2]['cont_address']


def set_status(b, obj, status):
    action = "action/core/set_object_status/1.0"
    action_group = "core"

    action_ds = obj.json_addl["action_groups"][action_group]["actions"][action]
    action_ds["captured_data"]["object_status"] = status
    b.do_action(obj.euid, action, action_group, action_ds)

TUBES=[]

def create_tubes(n=1):
    ctr = 0
    while ctr < n:

        #records = (
        #    bob_wfs.session.query(bob_wfs.Base.classes.workflow_template)
        #    .filter(
        #        bob_wfs.Base.classes.workflow_template.b_sub_type
        #        == "accession-package-kit-tubes-testreq"
        #    )
        #    .all()
        #)

        #wf = bob_wfs.create_instances(records[0].euid)[0][0]

        # Clinical ACC Queue
        #    accessioning-RnD
         
        #from IPython import embed; embed()
        #raise
        # 
        # 
        wf = bob_wf.query_instance_by_component_v2("workflow", "assay", "accessioning-RnD", "1.0")[0]

        action_group = "accessioning"
        action = "action/accessioning-ay/create_package_and_first_workflow_step_assay_root/1.0"
        action_data = wf.json_addl["action_groups"][action_group]["actions"][action]
        # action_data = wf.json_addl["actions"]["create_package_and_first_workflow_step"]
        action_data["captured_data"]["Tracking Number"] = "1001897582860000245100773464327825"
        action_data["captured_data"]["Fedex Tracking Data"] = {}


        wfs=bob_wf.do_action(wf.euid, action, action_group, action_data)
        set_status(bob_wfs, wfs, "in_progress")

        #wfs = bob_wf.do_action_create_package_and_first_workflow_step_assay(wf.euid, action_data)
    
        assert hasattr(wfs, "euid") == True

        b_action_group = "create_child"  # change to child
        #create_package_and_first_workflow_step_assay
        b_action = "action/workflow_step_accessioning/create_child_container_and_link_child_workflow_step/1.0" # "action/workflow_step_accessioning/create_child_container_and_link_child_workflow_step/1.0"
        wfs_action_data = wfs.json_addl["action_groups"][b_action_group]["actions"][b_action]

        wfs_action_data["captured_data"]["Tracking Number"] = "1001897582860000245100773464327825"
        wfs_action_data["captured_data"]["Fedex Tracking Data"] = {}
        bob_wfs.do_action(wfs.euid, b_action, b_action_group, wfs_action_data)

        
        child_wfs = ""
        for i in wfs.parent_of_lineages:
            if i.child_instance.btype == "accessioning-steps":
                child_wfs = i.child_instance

        assert hasattr(child_wfs, "euid") == True
        c_action_group = "specimen_actions"  # change to child
        c_action = "action/workflow_step_accessioning/create_child_container_and_link_child_workflow_step_specimen/1.0"
        c_wfs_action_data = child_wfs.json_addl["action_groups"][c_action_group]["actions"][
            c_action
        ]

        bob_wfs.do_action(child_wfs.euid, c_action, c_action_group, c_wfs_action_data)
        set_status(bob_wfs, wfs, "complete")

        set_status(bob_wfs, child_wfs, "in_progress")        

        new_child_wfs = ""
        for i in child_wfs.parent_of_lineages:
            if i.child_instance.super_type == "workflow_step":
                new_child_wfs = i.child_instance
        assert hasattr(new_child_wfs, "euid") == True




        trf_wfs = bob_wfs.do_action(
            new_child_wfs.euid,
            "action/workflow_step_accessioning/create_test_req_and_link_child_workflow_step_dup/1.0",
            "test_req",
            new_child_wfs.json_addl["action_groups"]["test_req"]["actions"][
                "action/workflow_step_accessioning/create_test_req_and_link_child_workflow_step_dup/1.0"
            ],
        )
        set_status(bob_wfs, new_child_wfs, "in_progress")
        set_status(bob_wfs, child_wfs, "complete")


        assert hasattr(trf_wfs, "euid") == True


        trf_child_wfs = ""
        trf_child_cont = ""
        for i in trf_wfs.parent_of_lineages:
            if i.child_instance.super_type == "workflow_step":
                trf_child_wfs = i.child_instance
            if i.child_instance.super_type == "container":
                trf_child_cont = i.child_instance

        trf = ""
        for i in trf_child_cont.child_of_lineages:
            if i.parent_instance.super_type == "test_requisition":
                trf = i.parent_instance


        trf_assay_data = trf.json_addl["action_groups"]["test_requisitions"]["actions"][
            "action/test_requisitions/add_container_to_assay_q/1.0"
        ]
        # This is super brittle, how I am currently linking Assay to TestReq...
        # = tr.json_addl["actions"]["add_container_to_assay_q"]
        trf_assay_data["captured_data"]["assay_selection"] = ASSAY
        trf_assay_data["captured_data"]["Container EUID"] = trf_child_cont.euid

        wfs_queue = bob_wfs.do_action(
            trf.euid,
            action_group="test_requisitions",
            action="action/test_requisitions/add_container_to_assay_q/1.0",
            action_ds=trf_assay_data,
        )
        assert hasattr(wfs_queue, "euid") == True
        set_status(bob_wfs, wfs_queue, "in_progress")


        scanned_bcs = trf_child_cont.euid

        ctr = ctr + 1
        print('CCCCCCCCCCC',ctr)
        TUBES.append(trf_child_cont.euid)



        wset_q = wfs
        wset_q_axn = "action/move-queues/move-among-ay-top-queues/1.0"
        wset_q_axn_grp = "acc-queue-move"
        wset_q_ad = wset_q.json_addl["action_groups"][wset_q_axn_grp][
            "actions"][wset_q_axn]  
        wset_q_ad["captured_data"]["q_selection"] = "workflow_step/queue/plasma-isolation-queue-exception/1.0" if randint(0,13) > 10 else "workflow_step/queue/plasma-isolation-queue-removed/1.0"
        bob_wfs.do_action(
            wset_q.euid,
            action_group=wset_q_axn_grp,
            action=wset_q_axn,
            action_ds=wset_q_ad
        )


def fill_plates(tubes=[]):
        # Create some controls to add to the plate!
        giab_cx, giab_mx = bob_wf.create_container_with_content(
            ("container", "tube", "tube-generic-10ml", "1.0"),
            ("content", "control", "giab-HG002", "1.0")
        )   
 
        cfsynctl_cx, cfsynctl_mx = bob_wf.create_container_with_content(
            ("container", "tube", "tube-10ml-glass", "1.0"),
            ("content", "control", "synthetic-cfdna", "1.0")
        )  

        ntc_cx, ntc_mx = bob_wf.create_container_with_content( 
            ("container", "tube", "tube-eppi-1.5ml", "1.0"),
            ("content", "control", "water-ntc", "1.0")
        )
        trf_child_cont = bob_wf.get_by_euid(tubes[-1])
        tubes.append(giab_cx.euid)
        tubes.append(cfsynctl_cx.euid)
        tubes.append(ntc_cx.euid)

        scanned_bcs = "\n".join(tubes)
        q_wfs = ""
        for i in trf_child_cont.child_of_lineages:
            if i.parent_instance.b_sub_type == "plasma-isolation-queue-available":
                q_wfs = i.parent_instance

        piso_q_action_data = q_wfs.json_addl["action_groups"]["tube_xfer"]["actions"][
            "action/workflow_step_queue/link_tubes_auto/1.0"
        ]
        piso_q_action_data["captured_data"]["discard_barcodes"] = scanned_bcs
        wfs_plasma = bob_wfs.do_action(
            q_wfs.euid,
            action_group="tube_xfer",
            action="action/workflow_step_queue/link_tubes_auto/1.0",
            action_ds=piso_q_action_data,
        )  # _link_tubes_auto(wfs_queue.euid, piso_q_action_data)

        plasma_cont = None
        for i in trf_child_cont.parent_of_lineages:
            if i.child_instance.b_sub_type == "tube-generic-10ml":
                plasma_cont = i.child_instance
        scanned_bcs_plasma = plasma_cont.euid

        for i in plasma_cont.child_of_lineages:
            if i.parent_instance.super_type == "workflow_step":
                pi_wfs = i.parent_instance
        
        wfset_wf = pi_wfs.child_of_lineages[0].parent_instance
        
        action_ds_plasma = pi_wfs.json_addl["action_groups"]["fill_plate"]["actions"][
            "action/workflow_step_queue/fill_plate_undirected/1.0"
        ]
        # wfs_plasma.json_addl["actions"]["fill_plate_undirected"]
        action_ds_plasma["captured_data"]["discard_barcodes"] = scanned_bcs_plasma
        wfs_plt = bob_wfs.do_action(
            pi_wfs.euid,
            action_group="fill_plate",
            action="action/workflow_step_queue/fill_plate_undirected/1.0",
            action_ds=action_ds_plasma,
        )
        set_status(bob_wfs, pi_wfs, "complete")

        ### ENDING WITH ANEXTRACTION PLATE!  Need to check quant and add more from here.

        plt_fill_wfs = ""
        for i in wfs_plt.parent_of_lineages:
            if i.child_instance.super_type == "workflow_step":
                plt_fill_wfs = i.child_instance

        action_data_dat = plt_fill_wfs.json_addl["action_groups"]["plate_operations"][
            "actions"
        ]["action/workflow_step_plate_operations/cfdna_quant/1.0"]
        # action_data_dat = wfs_plt.json_addl["actions"]["cfdna_quant"]
        action_data_dat["captured_data"]["gdna_quant"] = ""
        yy = bob_wfs.do_action(
            plt_fill_wfs.euid,
            action_group="plate_operations",
            action="action/workflow_step_plate_operations/cfdna_quant/1.0",
            action_ds=action_data_dat,
        )
        set_status(bob_wfs, plt_fill_wfs, "complete")

        eplt = None
        for i in plt_fill_wfs.parent_of_lineages:
            if i.child_instance.super_type == "workflow_step":
                eplt = i.child_instance
        set_status(bob_wfs, eplt, "in_progress")

        next_plate = ""
        for i in plt_fill_wfs.parent_of_lineages:
            if i.child_instance.btype == "plate":
                next_plate = i.child_instance.euid

        stamp_action_data = plt_fill_wfs.json_addl["action_groups"]["plate_operations"][
            "actions"
        ]["action/workflow_step_plate_operations/stamp_copy_plate/1.0"]
        stamp_action_data["captured_data"]["plate_euid"] = next_plate

        xx = bob_wfs.do_action(
            plt_fill_wfs.euid,
            action_group="plate_operations",
            action="action/workflow_step_plate_operations/stamp_copy_plate/1.0",
            action_ds=stamp_action_data,
        )

        for i in plt_fill_wfs.parent_of_lineages:
            if i.child_instance.btype == "plate-operations":
                sec_stamp_wfs = i.child_instance

        for i in sec_stamp_wfs.parent_of_lineages:
            if i.child_instance.super_type == "container":
                next_plate2 = i.child_instance.euid

        stamp_action_data2 = sec_stamp_wfs.json_addl["action_groups"]["plate_operations"][
            "actions"
        ]["action/workflow_step_plate_operations/stamp_copy_plate/1.0"]
        stamp_action_data2["captured_data"]["plate_euid"] = next_plate2
        stamp_wfs2 = bob_wfs.do_action(
            sec_stamp_wfs.euid,
            action_group="plate_operations",
            action="action/workflow_step_plate_operations/stamp_copy_plate/1.0",
            action_ds=stamp_action_data2,
        )


        # make a control
        rgnt = bob_wfs.create_instance_by_template_components(
            "content", "control", "giab-HG002", "1.0"
        )[0][0]
        # put in a tube
        tube = bob_wfs.create_instance_by_template_components(
            "container", "tube", "tube-generic-10ml", "1.0"
        )[0][0]
        # put the reagent in the tube

        bob_wfs.create_generic_instance_lineage_by_euids(tube.euid, rgnt.euid)


        wset_q = wfset_wf
        wset_q_axn = "action/move-queues/move-among-ay-top-queues/1.0"
        wset_q_axn_grp = "queue-move"
        wset_q_ad = wset_q.json_addl["action_groups"][wset_q_axn_grp][
            "actions"][wset_q_axn]  
        wset_q_ad["captured_data"]["q_selection"] = "workflow_step/queue/plasma-isolation-queue-exception/1.0" if randint(0,5) > 4 else "workflow_step/queue/plasma-isolation-queue-removed/1.0"
        bob_wfs.do_action(
            wset_q.euid,
            action_group=wset_q_axn_grp,
            action=wset_q_axn,
            action_ds=wset_q_ad
        )
        

n_tubes = 20 if int(sys.argv[1]) > 20 else int(sys.argv[1])

create_tubes(n_tubes)

fill_plates(tubes=TUBES)