make it possible for excel2flapjack to add sboluris

Author: JMante1

excel2flapjack/excel2flapjack/main.py

@@ -1,29 +1,11 @@
 import pandas as pd
-import random
 from flapjack import Flapjack
 
 
-# # this is for testing without flapjack
-# # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-# class id_thing():
-#     def __init__(self, id_in):
-#         self.id = [id_in]
-
-
-# class Flapjack():
-
-#     def create(self, *args):
-
-#         # UNCOMMENT ONE OF THE TWO
-#         print(args)
-#         # temp = args
-
-#         return id_thing(random.randint(1, 100))
-# # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-
 # still requires some work to ensure studies etc created too
-def flapjack_upload(fj_url, fj_user, fj_pass, excel_path):
+def flapjack_upload(fj_url, fj_user, fj_pass, excel_path, sbol_hash_map={},
+                    add_sbol_uris=False, flapjack_override=False,
+                    print_progress=False):
     hash_map = {}
 
     # UNCOMMENT BELOW TO USE FLAPJACK
@@ -32,16 +14,14 @@ def flapjack_upload(fj_url, fj_user, fj_pass, excel_path):
     fj.log_in(username=fj_user, password=fj_pass)
 
     # read in Excel Data
-    #xls = pd.read_excel(excel_path,sheet_name=None)
     xls = pd.ExcelFile(excel_path)
     fj_conv_sht = xls.parse('FlapjackCols', skiprows=0)
 
     # order is important as Chemicals and DNA must be created before
     # they can be referenced
     types = ['Chemical', 'DNA', 'Supplement', 'Vector', 'Strain', 'Media',
              'Signal', 'Study', 'Assay', 'Sample', 'Measurement']
-    #types = ['DNA', 'Supplement', 'Vector', 'Strain', 'Media',
-             #'Signal', 'Measurement']
+
     # initiate hashmap for linking to chemicals
     hash_map = {}
 
@@ -68,31 +48,25 @@ def flapjack_upload(fj_url, fj_user, fj_pass, excel_path):
         # Create a dictionary of the data for flapjack
         obj_dict = obj_df.to_dict('index')
 
-        # REMOVE THIS LINE WHEN USING FLAPJACK
-        #fj = Flapjack()
-
         # Upload all the objects to flapjack
         for key in obj_dict:
+            if print_progress:
+                print(key)
             data = obj_dict[key]
 
+            if key in sbol_hash_map and add_sbol_uris:
+                data['sboluri'] = sbol_hash_map[key]
+
             # Change to flapjack id rather than name for chemicals and dnas
             lookups = {'chemical', 'dnas', 'study', 'vector', 'strain', 'media', 'assay', 'sample', 'signal'}
             lk_inter = lookups.intersection(set(data.keys()))
-            print(lk_inter)
             for it in list(lk_inter):
                 data[it] = hash_map[data[it]]
 
-            # CHANGE THIS WHEN USING FLAPJACK
-            # add ** infront of data later when not patched!!!!!!!!
-            print(obj)
             data['model'] = obj.lower()
-            print(data)
-
-            flapjack_id = fj.create(**data)
-            # flapjack_id = fj.create(data)
+            flapjack_id = fj.create(**data, confirm=not(flapjack_override))
 
             # add Chemical and DNA to hash map to allow cross referencing
-            print(flapjack_id)
             hash_map[key] = flapjack_id.id[0]
 
     return hash_map

excel2flapjack/excel2flapjack/temp.py

@@ -3,13 +3,16 @@
 
 #fj_url = "localhost:8000"
 fj_url = "flapjack.rudge-lab.org:8000" #Web Instance
-fj_user = "saisam17"
-fj_pass = "Il0vem$her"
+fj_user = ""
+fj_pass = ""
 
 direct = __file__
 test_file_path = os.path.join(os.path.split(os.path.split(direct)[0])[0],
                               'tests', 'test_files')
-excel_path = os.path.join(test_file_path, "flapjack_excel_converter_v028.xlsx")
+excel_path = os.path.join(test_file_path, "flapjack_excel_converter_v030.xlsx")
 
-hash_map = e2f.flapjack_upload(fj_url, fj_user, fj_pass, excel_path)
+shm = {'Study1': 'https://synbiohub.org/user/JVM/Flapjack/Study1/1', 'Assay1': 'https://synbiohub.org/user/JVM/Flapjack/Assay1/1', 'Assay2': 'https://synbiohub.org/user/JVM/Flapjack/Assay2/1', 'Sample1': 'https://synbiohub.org/user/JVM/Flapjack/Sample1/1', 'Sample2': 'https://synbiohub.org/user/JVM/Flapjack/Sample2/1', 'Sample3': 'https://synbiohub.org/user/JVM/Flapjack/Sample3/1', 'Sample4': 'https://synbiohub.org/user/JVM/Flapjack/Sample4/1', 'M9Glucose': 'https://synbiohub.org/user/JVM/Flapjack/M9Glucose/1', 'Signal1': 'https://synbiohub.org/user/JVM/Flapjack/Signal1/1', 'Signal9': 'https://synbiohub.org/user/JVM/Flapjack/Signal9/1', 'EcoliT7': 'https://synbiohub.org/user/JVM/Flapjack/EcoliT7/1', 'Rep_HIGH_degrate_plasmid': 'https://synbiohub.org/user/JVM/Flapjack/Rep_HIGH_degrate_plasmid/1', 'Rep_LOW_degrate_plasmid': 'https://synbiohub.org/user/JVM/Flapjack/Rep_LOW_degrate_plasmid/1', 'DNA1': 'https://synbiohub.org/user/JVM/Flapjack/DNA1/1', 'DNA2': 'https://synbiohub.org/user/JVM/Flapjack/DNA2/1', 'DNA3': 'https://synbiohub.org/user/JVM/Flapjack/DNA3/1'}
+
+hash_map = e2f.flapjack_upload(fj_url, fj_user, fj_pass, excel_path, sbol_hash_map=shm,
+                    add_sbol_uris=True, flapjack_override=True, print_progress=True)
 print(hash_map)

excel2flapjack/excel2flapjack/temp2.py

@@ -1,3 +1,3 @@
 pyflapjack==1.0.5
-pandas==1.4.4
+pandas==1.3.3
 openpyxl==3.0.9