X

bloom_lims/bobjs.py

@@ -1889,8 +1889,8 @@ def handle_jsonb_filter(key, value, conditions):
         return [result.euid for result in results]
 
 class BloomContainer(BloomObj):
-    def __init__(self, bdb):
-        super().__init__(bdb)
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
     def create_empty_container(self, template_euid):
         return self.create_instances(template_euid)
@@ -1909,8 +1909,8 @@ def unlink_content(self, container_euid, content_euid):
 
 
 class BloomContainerPlate(BloomContainer):
-    def __init__(self, bdb):
-        super().__init__(bdb)
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
     def create_empty_plate(self, template_euid):
         return self.create_instances(template_euid)
@@ -1969,8 +1969,8 @@ def organize_wells(self, wells, parent_container):
 
 
 class BloomContent(BloomObj):
-    def __init__(self, bdb):
-        super().__init__(bdb)
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
     def create_empty_content(self, template_euid):
         """_summary_
@@ -1986,8 +1986,8 @@ def create_empty_content(self, template_euid):
 
 
 class BloomWorkflow(BloomObj):
-    def __init__(self, bdb):
-        super().__init__(bdb)
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
     # This can be made more widely useful now that i've detangled the wf-wfs special relationship
     def get_sorted_uuid(self, workflow_id):
@@ -2098,8 +2098,8 @@ def do_action_create_package_and_first_workflow_step(self, wf_euid, action_ds={}
 
 
 class BloomWorkflowStep(BloomObj):
-    def __init__(self, bdb):
-        super().__init__(bdb)
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
     def create_empty_workflow_step(self, template_euid):
         return self.create_instances(template_euid)
@@ -2660,8 +2660,8 @@ def do_action_create_test_req_and_link_child_workflow_step(
 
 
 class BloomReagent(BloomObj):
-    def __init__(self, bdb):
-        super().__init__(bdb)
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
     def create_rgnt_24w_plate_TEST(self, rg_code="idt-probes-rare-mendelian"):
         # I am taking a short cut and not taking time to think about making this generic.
@@ -2700,26 +2700,26 @@ def create_rgnt_24w_plate_TEST(self, rg_code="idt-probes-rare-mendelian"):
 
 
 class BloomEquipment(BloomObj):
-    def __init__(self, bdb):
-        super().__init__(bdb)
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
     def create_empty_equipment(self, template_euid):
         return self.create_instances(template_euid)
 
 
 class BloomObjectSet(BloomObj):
-    def __init__(self, bdb):
-        super().__init__(bdb)
-
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
+# TODO -- is this used at all, and if so, is it used correctly?
 class AuditLog(BloomObj):
     def __init__(self, session, base):
         super().__init__(session, base)
 
 
 class BloomHealthEvent(BloomObj):
-    def __init__(self, bdb):
-        super().__init__(bdb)
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
     def create_event(self):
 
@@ -2734,9 +2734,10 @@ def create_event(self):
 
 
 class BloomFile(BloomObj):
-    def __init__(self, bdb, bucket_prefix=None):
-        super().__init__(bdb)
-
+
+    def __init__(self, bdb, bucket_prefix=None, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
+
         if bucket_prefix is None:
             bucket_prefix = os.environ.get(
                 "BLOOM_DEWEY_S3_BUCKET_PREFIX", "set-a-bucket-prefix-in-the-dotenv-file"
@@ -3338,9 +3339,8 @@ def create_presigned_url(self,
 # As in expiring s3 links and so on. Potentially allow sharing of files with hosting protocols like SFTP, etc...
 class BloomFileReference(BloomObj):
 
-    def __init__(self, bdb):
-        super().__init__(bdb)
-
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
 
     def create_file_reference(self, file_euid=None, reference_type='presigned', visibility='public', valid_duration=0, start_datetime=None, end_datetime=None, comments="", status="active", presigned_url="", file_set_euid=None, rclone_config={}):
@@ -3457,8 +3457,8 @@ def create_file_reference(self, file_euid=None, reference_type='presigned', visi
         return file_reference
 
 class BloomFileSet(BloomObj):
-    def __init__(self, bdb):
-        super().__init__(bdb)
+    def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
+        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
 
     def create_file_set(self, file_uids=[], file_set_metadata={}):
         file_set = self.create_instance(

tx.py

@@ -5,18 +5,18 @@
 import sys
 import os
 
-bob_wf = BloomWorkflow(BLOOMdb3())
+bob_wf = BloomWorkflow(BLOOMdb3(),cfg_fedex=True)
 
-bob_wfs = BloomWorkflowStep(BLOOMdb3())
+bob_wfs = BloomWorkflowStep(BLOOMdb3(), cfg_fedex=True)
 
-bob_rg = BloomReagent(BLOOMdb3())
+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 randint(0,9) > 99 else "workflow/assay/carrier-screen/3.9"
+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"),