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Andrew Charlwood adc1dbfc58 feat: complete Task 2.2 - test refresh pipeline with Snowflake data

Tested full refresh pipeline end-to-end with real Snowflake data:
- Fixed trust filter to read Name column from defaultTrusts.csv
- Fixed Decimal type handling in calculate_cost_per_patient_per_annum
- Fixed array handling in convert_to_records for average_administered
- Added required reference CSV files to data/ directory
- Configured Snowflake connection (account, warehouse, user)

Results:
- Snowflake fetch: 656,695 records in ~7s
- Transformations: 519,848 records after UPID/drug/directory
- Pathway nodes: 293 for all_6mo (8 trusts, 14 directories)
- Total processing time: ~6.2 minutes

2026-02-05 00:20:12 +00:00

2.4 KiB

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1	Drug	Include
2	ABATACEPT	1
3	ACALABRUTINIB	1
4	ADALIMUMAB	1
5	AFLIBERCEPT	1
6	ALIROCUMAB	1
7	ALITRETINOIN	0
8	AMIKACIN	0
9	AMPHOTERICIN B LIPOSOMAL	0
10	ANAKINRA	0
11	ANDEXANET ALFA	0
12	ANIDULAFUNGIN	0
13	APALUTAMIDE	0
14	APOMORPHINE	0
15	APREMILAST	1
16	ATEZOLIZUMAB	1
17	AVELUMAB	0
18	AXITINIB	0
19	AZACITIDINE	0
20	AZATHIOPRINE	0
21	BACILLUS CALMETTE-GUERIN	0
22	BARICITINIB	1
23	BASILIXIMAB	0
24	BENDAMUSTINE	0
25	BENRALIZUMAB	0
26	BEROTRALSTAT	0
27	BEVACIZUMAB	1
28	BEXAROTENE	0
29	BIMEKIZUMAB	1
30	BLEOMYCIN	0
31	BORTEZOMIB	0
32	BOTULINUM A TOXIN	1
33	BRENTUXIMAB VEDOTIN	0
34	BRODALUMAB	1
35	BUSULFAN	0
36	C1-ESTERASE INHIBITOR	0
37	CABOZANTINIB	0
38	CAPECITABINE	0
39	CARBOPLATIN	0
40	CARFILZOMIB	0
41	CERTOLIZUMAB PEGOL	1
42	CETUXIMAB	0
43	CHLORAMBUCIL	0
44	CICLOSPORIN	0
45	CINACALCET	0
46	CISPLATIN	0
47	COLISTIMETHATE	0
48	COLISTIN	0
49	COPAXONE	0
50	CYCLOPHOSPHAMIDE	0
51	DARBEPOETIN ALFA	0
52	DAROLUTAMIDE	0
53	DASATINIB	0
54	DEFERASIROX	0
55	DENOSUMAB	1
56	DESFERRIOXAMINE	0
57	DEXAMETHASONE	1
58	DIGOXIN IMMUNE FAB	0
59	DIMETHYL FUMARATE	1
60	DOCETAXEL	1
61	DOXORUBICIN	0
62	DUPILUMAB	1
63	ECULIZUMAB	0
64	EFUDIX	0
65	ELTROMBOPAG	0
66	EMTRICITABINE	0
67	ENZALUTAMIDE	0
68	EPIRUBICIN	0
69	EPOETIN	0
70	EPOETIN ALFA	0
71	EPOETIN BETA	0
72	ERENUMAB	1
73	ETANERCEPT	1
74	EVOLOCUMAB	1
75	FARICIMAB	1
76	FIDAXOMICIN	0
77	FILGOTINIB	1
78	FILGRASTIM	0
79	FLUOCINOLONE	1
80	FLUOCINOLONE ACETONIDE	1
81	FLUOROURACIL	0
82	FOMEPIZOLE	0
83	FREMANEZUMAB	1
84	FULVESTRANT	0
85	GALCANEZUMAB	1
86	GEMCITABINE	0
87	GENERIC	0
88	GOLIMUMAB	1
89	GUSELKUMAB	1
90	HYDROXYCARBAMIDE	0
91	IBRUTINIB	0
92	IDARUBICIN	0
93	IDARUCIZUMAB	1
94	IFOSFAMIDE	0
95	ILOPROST	0
96	ILOPROST	0
97	IMATINIB	1
98	IMMUNOGLOBULIN	1
99	INFLIXIMAB	1
100	INSULIN HUMAN	0
101	IRINOTECAN	0
102	ISATUXIMAB	0
103	IXEKIZUMAB	1
104	JYSELECA	0
105	KAFTRIO	0
106	LANREOTIDE	0
107	LENALIDOMIDE	0
108	LENOGRASTIM	0
109	LETERMOVIR	0
110	LIOTHYRONINE	0
111	LUCENTIS	1
112	MEPOLIZUMAB	0
113	METHOTREXATE	0
114	METRELEPTIN	0
115	MITOMYCIN	0
116	MOFETIL	0
117	MOLNUPIRAVIR	0
118	MYCOPHENOLATE	0
119	NERATINIB	0
120	NIRAPARIB	0
121	NORDITROPIN	0
122	NUSINERSEN	0
123	OBINUTUZUMAB	1
124	OCRIPLASMIN	0
125	OCTREOTIDE	1
126	OLAPARIB	0
127	OMALIZUMAB	1
128	OMNITROPE	0
129	OXALIPLATIN	0
130	PACLITAXEL	0
131	PALBOCICLIB	0
132	PALIVIZUMAB	0
133	PARENTERAL	0
134	PEGINTERFERON	0
135	RANIBIZUMAB	1
136	RASBURICASE	0
137	REMDESIVIR	0
138	REMICADE	1
139	RILUZOLE	1
140	RISANKIZUMAB	1
141	RITUXIMAB	1
142	RIXATHON	1
143	ROMIPLOSTIM	0
144	SACITUZUMAB	1
145	SARILUMAB	1
146	SECUKINUMAB	1
147	SERVICE	0
148	SEVELAMER	0
149	SILDENAFIL	0
150	SIMPONI	0
151	SIROLIMUS	0
152	SOLRIAMFETOL	0
153	SOMATROPIN	0
154	SOMATROPINÅ¸	0
155	SOTROVIMAB	0
156	STIRIPENTOL	0
157	TACROLIMUS	0
158	TERIPARATIDE	1
159	TILDRAKIZUMAB	1
160	TOCILIZUMAB	1
161	TOFACITINIB	1
162	TOLVAPTAN	0
163	TRASTUZUMAB	0
164	TRUXIMA	0
165	UNIT	0
166	UPADACITINIB	1
167	USTEKINUMAB	1
168	VABYSMO	0
169	VANCOMYCIN	0
170	VEDOLIZUMAB	1
171	VERTEPORFIN	0
172	VINBLASTINE	0
173	VISMODEGIB	0
174	VORICONAZOLE	0
175	ZANUBRUTINIB	0

2.4 KiB Raw Permalink Blame History

2.4 KiB

Raw Permalink Blame History