diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index f16715e..1971fdf 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -8,10 +8,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.9 diff --git a/.github/workflows/schema.yml b/.github/workflows/schema.yml index 8feda16..ef86799 100644 --- a/.github/workflows/schema.yml +++ b/.github/workflows/schema.yml @@ -9,10 +9,10 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.9 @@ -29,7 +29,7 @@ jobs: cd pyxb_build python setup.py bdist_wheel - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: name: ukrdc_schema_wheel path: pyxb_build/dist/*.whl @@ -39,7 +39,7 @@ jobs: if: startsWith(github.ref, 'refs/tags/') with: user: __token__ - password: ${{ secrets.PYPI_API_TOKEN }} + password: ${{ secrets.PYPI_API_TOKEN_SCHEMA }} packages_dir: pyxb_build/dist @@ -48,10 +48,10 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.9 @@ -66,7 +66,7 @@ jobs: ./build.sh python setup.py bdist_wheel - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: name: ukrdc_xsdata_wheel path: xsdata_build/dist/*.whl @@ -76,7 +76,7 @@ jobs: if: startsWith(github.ref, 'refs/tags/') with: user: __token__ - password: ${{ secrets.PYPI_API_TOKEN }} + password: ${{ secrets.PYPI_API_TOKEN_XSDATA }} packages_dir: xsdata_build/dist github-release: @@ -86,7 +86,7 @@ jobs: if: startsWith(github.ref, 'refs/tags/') steps: - - uses: actions/download-artifact@v2 + - uses: actions/download-artifact@v4.1.7 - name: Release uses: softprops/action-gh-release@v1 diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index c1d6d91..3bbfd8d 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -11,18 +11,13 @@ jobs: working-directory: scripts steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.8 - - name: Set up SSH keys - uses: webfactory/ssh-agent@v0.5.3 - with: - ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }} - - name: Install dependencies run: | python -m pip install --upgrade pip diff --git a/.github/workflows/validate_samples.yml b/.github/workflows/validate_samples.yml index d54b2cc..2cd1c6b 100644 --- a/.github/workflows/validate_samples.yml +++ b/.github/workflows/validate_samples.yml @@ -8,10 +8,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v6 with: python-version: 3.9 diff --git a/codes/README.md b/codes/README.md new file mode 100644 index 0000000..79b7fd0 --- /dev/null +++ b/codes/README.md @@ -0,0 +1,3 @@ +# Registry codes +Historically this directory was used to store csv files containing picklists and mappings for the codes which were used by the UKRDC. They have been now moved to a repo exclusively for this purpose which can be found [here](https://github.com/renalreg/registry-codes). + diff --git a/codes/code_lists/edta2.csv b/codes/code_lists/edta2.csv deleted file mode 100644 index 71ce7c1..0000000 --- a/codes/code_lists/edta2.csv +++ /dev/null @@ -1,287 +0,0 @@ -EDTA2,2513,AA amyloid secondary to chronic inflammation -EDTA2,1768,Acquired obstructive nephropathy due to neurogenic bladder -EDTA2,1752,Acquired obstructive uropathy / nephropathy -EDTA2,3442,Acute cortical necrosis -EDTA2,3380,Acute kidney injury -EDTA2,3403,Acute kidney injury due to circulatory failure -EDTA2,3398,Acute kidney injury due to hypovolaemia -EDTA2,3435,Acute kidney injury due to nephrotoxicity -EDTA2,3426,Acute kidney injury due to rhabdomyolysis -EDTA2,3419,Acute kidney injury due to sepsis -EDTA2,3457,Acute pyelonephritis -EDTA2,2196,Acute urate nephropathy - histologically proven -EDTA2,2183,Acute urate nephropathy - no histology -EDTA2,1003,Adult nephrotic syndrome - no histology -EDTA2,2392,Ageing kidney - no histology -EDTA2,2521,AL amyloid secondary to plasma cell dyscrasia -EDTA2,3071,Alagille syndrome -EDTA2,2760,Alport syndrome - histologically proven -EDTA2,2756,Alport syndrome - no histology -EDTA2,1472,Anti-Glomerular basement membrane (GBM) disease / Goodpasture's syndrome - histologically proven -EDTA2,1464,Anti-Glomerular basement membrane (GBM) disease / Goodpasture's syndrome - no histology -EDTA2,3118,Apparent mineralocorticoid excess -EDTA2,1995,Aristolochic acid nephropathy (Balkan / Chinese herb / endemic nephropathy) - histologically proven -EDTA2,1982,Aristolochic acid nephropathy (Balkan / Chinese herb / endemic nephropathy) - no histology -EDTA2,2448,Atheroembolic renal disease - histologically proven -EDTA2,2430,Atheroembolic renal disease - no histology -EDTA2,2623,Atypical haemolytic uraemic syndrome (HUS) - diarrhoea negative -EDTA2,2718,Autosomal dominant (AD) polycystic kidney disease -EDTA2,2725,Autosomal dominant (AD) polycystic kidney disease type I -EDTA2,2739,Autosomal dominant (AD) polycystic kidney disease type II -EDTA2,2741,Autosomal recessive (AR) polycystic kidney disease -EDTA2,3085,Bartter syndrome -EDTA2,2773,Benign familial haematuria -EDTA2,1710,Bladder exstrophy -EDTA2,3322,Branchio-oto-renal syndrome -EDTA2,1845,Calcium oxalate urolithiasis -EDTA2,1832,Calculus nephropathy / urolithiasis -EDTA2,2482,Cardiorenal syndrome -EDTA2,2363,Chronic hypertensive nephropathy - histologically proven -EDTA2,2359,Chronic hypertensive nephropathy - no histology -EDTA2,3564,Chronic kidney disease (CKD) / chronic renal failure (CRF) - aetiology uncertain / unknown - histologically proven -EDTA2,3555,Chronic kidney disease (CKD) / chronic renal failure (CRF) - aetiology uncertain / unknown - no histology -EDTA2,3529,Chronic kidney disease (CKD) / chronic renal failure (CRF) caused by tumour nephrectomy -EDTA2,3540,Chronic kidney disease (CKD) / chronic renal failure (CRF) due to donor nephrectomy -EDTA2,3538,Chronic kidney disease (CKD) / chronic renal failure (CRF) due to traumatic loss of kidney -EDTA2,3708,Chronic renal failure -EDTA2,3643,Chronic renal failure due to systemic infection -EDTA2,2203,Chronic urate nephropathy - histologically proven -EDTA2,3636,Chronic urate nephropathy - no histology -EDTA2,1440,Churg-Strauss syndrome - histologically proven -EDTA2,1438,Churg-Strauss syndrome - no histology -EDTA2,1625,Congenital dysplasia / hypoplasia -EDTA2,2652,Congenital haemolytic uraemic syndrome (HUS) -EDTA2,1088,Congenital nephrotic syndrome (CNS) - congenital infection -EDTA2,1057,Congenital nephrotic syndrome (CNS) - diffuse mesangial sclerosis -EDTA2,1042,Congenital nephrotic syndrome (CNS) - Finnish type - histologically proven -EDTA2,1035,Congenital nephrotic syndrome (CNS) - Finnish type - no histology -EDTA2,1061,Congenital nephrotic syndrome (CNS) - focal segmental glomerulosclerosis (FSGS) -EDTA2,1026,Congenital nephrotic syndrome (CNS) - no histology -EDTA2,1706,Congenital neurogenic bladder -EDTA2,1660,Congenital pelvi-ureteric junction obstruction -EDTA2,1673,Congenital vesico-ureteric junction obstruction -EDTA2,1570,Cryoglobulinaemia secondary to hepatitis C - histologically proven -EDTA2,1562,Cryoglobulinaemia secondary to hepatitis C - no histology -EDTA2,1591,Cryoglobulinaemia secondary to systemic disease - histologically proven -EDTA2,1589,Cryoglobulinaemia secondary to systemic disease - no histology -EDTA2,2794,Cystic kidney disease -EDTA2,2964,Cystinosis -EDTA2,2955,Cystinuria -EDTA2,2929,Dent disease -EDTA2,1074,Denys-Drash syndrome -EDTA2,2328,Diabetic nephropathy in type I diabetes - histologically proven -EDTA2,2316,Diabetic nephropathy in type I diabetes - no histology -EDTA2,2344,Diabetic nephropathy in type II diabetes - histologically proven -EDTA2,2337,Diabetic nephropathy in type II diabetes - no histology -EDTA2,1331,Diffuse endocapillary glomerulonephritis -EDTA2,3028,Distal renal tubular acidosis (RTA) - type I -EDTA2,3037,Distal renal tubular acidosis with sensorineural deafness - gene mutations -EDTA2,2005,Drug-induced tubulointerstitial nephritis - no histology -EDTA2,2014,Drug-induced tubulointerstitial nephritis - histologically proven -EDTA2,2005,Drug-induced tubulointerstitial nephritis - no histology -EDTA2,1641,Dysplasia due to fetal ACE-inhibitor exposure -EDTA2,1850,Enteric hyperoxaluria -EDTA2,1558,Essential mixed cryoglobulinaemia - histologically proven -EDTA2,1543,Essential mixed cryoglobulinaemia - no histology -EDTA2,3230,Fabry disease - histologically proven -EDTA2,3224,Fabry disease - no histology -EDTA2,2566,Familial AA amyloid secondary to familial Mediterranean fever / TRAPS (Hibernian fever) - histologically proven -EDTA2,2550,Familial AA amyloid secondary to familial Mediterranean fever / TRAPS (Hibernian fever) - no histology -EDTA2,2545,Familial amyloid secondary to protein mutations - histologically proven -EDTA2,2532,Familial amyloid secondary to protein mutations - no histology -EDTA2,1308,Familial focal segmental glomerulosclerosis (FSGS) - autosomal dominant - histologically proven -EDTA2,1298,Familial focal segmental glomerulosclerosis (FSGS) - autosomal dominant - no histology -EDTA2,1280,Familial focal segmental glomerulosclerosis (FSGS) - autosomal recessive - histologically proven -EDTA2,1279,Familial focal segmental glomerulosclerosis (FSGS) - autosomal recessive - no histology -EDTA2,2668,Familial haemolytic uraemic syndrome (HUS) -EDTA2,3173,Familial hypercalciuric hypocalcaemia -EDTA2,3160,Familial hypocalciuric hypercalcaemia -EDTA2,3187,Familial hypomagnesaemia -EDTA2,1144,Familial IgA nephropathy - histologically proven -EDTA2,1137,Familial IgA nephropathy - no histology -EDTA2,1911,Familial interstitial nephropathy - histologically proven -EDTA2,1907,Familial interstitial nephropathy - no histology -EDTA2,3379,Familial nephropathy -EDTA2,1618,Familial reflux nephropathy -EDTA2,2675,Familial thrombotic thrombocytopenic purpura (TTP) -EDTA2,2453,Fibromuscular dysplasia of renal artery -EDTA2,1354,Focal and segmental proliferative glomerulonephritis -EDTA2,3754,Focal segmental glomerulosclerosis (FSGS) secondary to HIV -EDTA2,3765,Focal segmental glomerulosclerosis (FSGS) secondary to lithium -EDTA2,1320,Focal segmental glomerulosclerosis (FSGS) secondary to obesity - histologically proven -EDTA2,1312,Focal segmental glomerulosclerosis (FSGS) secondary to obesity - no histology -EDTA2,3777,Focal segmental glomerulosclerosis (FSGS) secondary to sickle cell -EDTA2,3314,Frasier syndrome -EDTA2,3092,Gitelman syndrome -EDTA2,1656,Glomerulocystic disease -EDTA2,1377,Glomerulonephritis - histologically indeterminate -EDTA2,3749,Glomerulonephritis - no histology -EDTA2,1365,Glomerulonephritis - secondary to other systemic disease -EDTA2,1365,Glomerulonephritis - secondary to systemic disease -EDTA2,3125,Glucocorticoid suppressible hyperaldosteronism -EDTA2,1417,Granulomatosis with polyangiitis - histologically proven -EDTA2,1401,Granulomatosis with polyangiitis - no histology -EDTA2,3572,Haematuria and proteinuria - no histology -EDTA2,2610,Haemolytic uraemic syndrome (HUS) - diarrhoea associated -EDTA2,2647,Haemolytic uraemic syndrome (HUS) secondary to systemic disease -EDTA2,2257,Hantavirus nephropathy -EDTA2,1515,Henoch-Schönlein purpura / nephritis - histologically proven -EDTA2,1504,Henoch-Schönlein purpura / nephritis - no histology -EDTA2,2495,Hepatorenal syndrome -EDTA2,3305,Horse-shoe kidney -EDTA2,3662,Hypercalcaemic nephropathy -EDTA2,2993,Hypophosphataemic rickets autosomal recessive (AR) -EDTA2,2986,Hypophosphataemic rickets X-linked (XL) -EDTA2,1251,Idiopathic rapidly progressive (crescentic) glomerulonephritis -EDTA2,1813,Idiopathic retroperitoneal fibrosis -EDTA2,1128,IgA nephropathy - histologically proven -EDTA2,1116,IgA nephropathy - no histology -EDTA2,1163,IgA nephropathy secondary to liver cirrhosis - histologically proven -EDTA2,1159,IgA nephropathy secondary to liver cirrhosis - no histology -EDTA2,1171,IgM - associated nephropathy -EDTA2,2606,Immunotactoid / fibrillary nephropathy -EDTA2,3823,Infiltration by lymphoma - histologically proven -EDTA2,3139,Inherited / genetic diabetes mellitus type II -EDTA2,2940,Inherited aminoaciduria -EDTA2,2972,Inherited renal glycosuria -EDTA2,2407,Ischaemic nephropathy - no histology -EDTA2,2411,Ischaemic nephropathy / microvascular disease - histologically proven -EDTA2,3712,Isolated haematuria - no histology -EDTA2,3720,Isolated proteinuria - no histology -EDTA2,3810,Kidney stones due to ARPT deficiency -EDTA2,3461,Kidney tumour -EDTA2,3351,Lawrence-Moon-Biedl / Bardet-Biedl syndrome -EDTA2,2177,Lead induced nephropathy - histologically proven -EDTA2,2165,Lead induced nephropathy - no histology -EDTA2,2242,Leptospirosis -EDTA2,3059,Lesch Nyhan syndrome - hypoxanthine guanine phosphoribosyl transferase deficiency -EDTA2,3102,Liddle syndrome -EDTA2,2597,Light chain deposition disease -EDTA2,2938,Lowe syndrome (oculocerebrorenal syndrome) -EDTA2,1866,Magnesium ammonium phosphate (struvite) urolithiasis -EDTA2,2385,Malignant hypertensive nephropathy / accelerated hypertensive nephropathy - histologically proven -EDTA2,2371,Malignant hypertensive nephropathy / accelerated hypertensive nephropathy - no histology -EDTA2,2804,Medullary cystic kidney disease type I -EDTA2,2815,Medullary cystic kidney disease type II -EDTA2,3295,Medullary sponge kidneys -EDTA2,1723,Megacystis-megaureter -EDTA2,1205,Membranous nephropathy - drug induced -EDTA2,1185,Membranous nephropathy - idiopathic -EDTA2,1214,Membranous nephropathy - infection associated -EDTA2,1192,Membranous nephropathy - malignancy associated -EDTA2,1349,Mesangial proliferative glomerulonephritis -EDTA2,1222,Mesangiocapillary glomerulonephritis type 1 -EDTA2,1233,Mesangiocapillary glomerulonephritis type 2 (dense deposit disease) -EDTA2,1246,Mesangiocapillary glomerulonephritis type 3 -EDTA2,3501,Mesoblastic nephroma - histologically proven -EDTA2,1429,Microscopic polyangiitis - histologically proven -EDTA2,1100,Minimal change nephropathy - histologically proven -EDTA2,1090,Minimal change nephropathy - no histology -EDTA2,3367,Mitochondrial cytopathy -EDTA2,1639,Multicystic dysplastic kidneys -EDTA2,2584,Myeloma cast nephropathy - histologically proven -EDTA2,2578,Myeloma kidney - no histology -EDTA2,3253,Nail-patella syndrome -EDTA2,3044,Nephrogenic diabetes insipidus -EDTA2,2836,Nephronophthisis -EDTA2,2843,Nephronophthisis - type 1 (juvenile type) -EDTA2,2858,Nephronophthisis - type 2 (infantile type) -EDTA2,2862,Nephronophthisis - type 3 (adolescent type) -EDTA2,2870,Nephronophthisis - type 4 (juvenile type) -EDTA2,2889,Nephronophthisis - type 5 -EDTA2,2891,Nephronophthisis - type 6 -EDTA2,2098,Nephropathy due to aminoglycosides - histologically proven -EDTA2,2080,Nephropathy due to aminoglycosides - no histology -EDTA2,2112,Nephropathy due to amphotericin - histologically proven -EDTA2,2108,Nephropathy due to amphotericin - no histology -EDTA2,2033,Nephropathy due to analgesic drugs - histologically proven -EDTA2,2022,Nephropathy due to analgesic drugs - no histology -EDTA2,2051,Nephropathy due to ciclosporin - histologically proven -EDTA2,2046,Nephropathy due to ciclosporin - no histology -EDTA2,2131,Nephropathy due to cisplatin - histologically proven -EDTA2,2120,Nephropathy due to cisplatin - no histology -EDTA2,2154,Nephropathy due to lithium - histologically proven -EDTA2,2149,Nephropathy due to lithium - no histology -EDTA2,2681,Nephropathy due to eclampsia -EDTA2,3834,Nephropathy due to pre- eclampsia -EDTA2,2079,Nephropathy due to tacrolimus - histologically proven -EDTA2,2067,Nephropathy due to tacrolimus - no histology -EDTA2,2288,Nephropathy related to HIV - histologically proven -EDTA2,2274,Nephropathy related to HIV - no histology -EDTA2,3615,Nephrotic syndrome of childhood - no trial of steroids - no histology -EDTA2,3604,Nephrotic syndrome of childhood - steroid resistant - no histology -EDTA2,1019,Nephrotic syndrome of childhood - steroid sensitive - no histology -EDTA2,1799,Obstructive nephropathy due to bladder cancer -EDTA2,1809,Obstructive nephropathy due to other malignancies -EDTA2,1781,Obstructive nephropathy due to prostate cancer -EDTA2,1775,Obstructive nephropathy due to prostatic hypertrophy -EDTA2,1734,Oligomeganephronia -EDTA2,2300,Other specific infection -EDTA2,3063,Phosphoribosyl pyrophosphate synthetase (PRPPS) superactivity -EDTA2,1455,Polyarteritis nodosa -EDTA2,1687,Posterior urethral valves -EDTA2,2901,Primary Fanconi syndrome -EDTA2,1267,Primary focal segmental glomerulosclerosis (FSGS) -EDTA2,3194,Primary hyperoxaluria -EDTA2,3207,Primary hyperoxaluria type I -EDTA2,3211,Primary hyperoxaluria type II -EDTA2,3731,Primary hyperoxaluria type III -EDTA2,1602,Primary reflux nephropathy - sporadic -EDTA2,3000,Primary renal tubular acidosis (RTA) -EDTA2,3016,Proximal renal tubular acidosis (RTA) - type II -EDTA2,3141,Pseudohypoaldosteronism type 1 -EDTA2,3156,Pseudohypoaldosteronism type 2 (Gordon syndrome) -EDTA2,2219,Radiation nephritis -EDTA2,2226,Renal / perinephric abscess -EDTA2,2509,Renal amyloidosis -EDTA2,2469,Renal arterial thrombosis / occlusion -EDTA2,2424,Renal artery stenosis -EDTA2,3474,Renal cell carcinoma - histologically proven -EDTA2,3658,Renal coloboma syndrome -EDTA2,3627,Renal cysts and diabetes syndrome -EDTA2,1641,Renal dysplasia due to fetal ACE-inhibitor exposure -EDTA2,3691,Renal failure -EDTA2,1747,Renal papillary necrosis -EDTA2,3796,Renal papillary necrosis caused by analgesics -EDTA2,3783,Renal papillary necrosis caused by diabetes -EDTA2,3806,Renal papillary necrosis caused by sickle cell -EDTA2,1976,Renal sarcoidosis - histologically proven -EDTA2,1969,Renal sarcoidosis - no histology -EDTA2,1536,Renal scleroderma / systemic sclerosis - histologically proven -EDTA2,1527,Renal scleroderma / systemic sclerosis - no histology -EDTA2,2235,Renal tuberculosis -EDTA2,2476,Renal vein thrombosis -EDTA2,3689,Retroperitoneal fibrosis secondary to drugs -EDTA2,1821,Retroperitoneal fibrosis secondary to malignancies -EDTA2,3670,Retroperitoneal fibrosis secondary to peri-aortitis -EDTA2,3269,Rubinstein-Taybi syndrome -EDTA2,2290,Schistosomiasis -EDTA2,2702,Sickle cell nephropathy - histologically proven -EDTA2,2699,Sickle cell nephropathy - no histology -EDTA2,3517,Single kidney identified in adulthood -EDTA2,1694,Syndrome of agenesis of abdominal muscles - prune belly syndrome -EDTA2,1493,Systemic lupus erythematosus / nephritis - histologically proven -EDTA2,1486,Systemic lupus erythematosus / nephritis - no histology -EDTA2,1383,Systemic vasculitis - ANCA negative - histologically proven -EDTA2,3847,Systemic vasculitis - ANCA negative - no histology -EDTA2,3852,Systemic vasculitis - ANCA positive - histologically proven -EDTA2,1396,Systemic vasculitis - ANCA positive - no histology -EDTA2,2787,Thin basement membrane disease -EDTA2,2634,Thrombotic thrombocytopenic purpura (TTP) -EDTA2,3346,Townes-Brocks syndrome -EDTA2,3488,Transitional cell carcinoma - histologically proven -EDTA2,3276,Tuberous sclerosis -EDTA2,2917,Tubular disorder as part of inherited metabolic diseases -EDTA2,1897,Tubulointerstitial nephritis - histologically proven -EDTA2,1884,Tubulointerstitial nephritis - no histology -EDTA2,1930,Tubulointerstitial nephritis associated with autoimmune disease - histologically proven -EDTA2,1924,Tubulointerstitial nephritis associated with autoimmune disease - no histology -EDTA2,1953,Tubulointerstitial nephritis with uveitis (TINU) - histologically proven -EDTA2,1948,Tubulointerstitial nephritis with uveitis (TINU) - no histology -EDTA2,1878,Uric acid urolithiasis -EDTA2,2827,Uromodulin-associated nephropathy (familial juvenile hyperuricaemic nephropathy) -EDTA2,3282,Von Hippel-Lindau disease -EDTA2,3333,Williams syndrome -EDTA2,3490,Wilms tumour - histologically proven -EDTA2,3248,Xanthinuria -EDTA2,2261,Xanthogranulomatous pyelonephritis diff --git a/codes/code_lists/snomed.csv b/codes/code_lists/snomed.csv deleted file mode 100644 index 2b9e460..0000000 --- a/codes/code_lists/snomed.csv +++ /dev/null @@ -1,232 +0,0 @@ -SNOMED,52254009,Nephrotic syndrome -SNOMED,445119005,Steroid sensitive nephrotic syndrome of childhood -SNOMED,48796009,Congenital nephrotic syndrome -SNOMED,197601003,Finnish congenital nephrotic syndrome -SNOMED,722369003,Congenital nephrotic syndrome -SNOMED,236384008,Congenital nephrotic syndrome with focal glomerulosclerosis -SNOMED,236385009,Drash syndrome -SNOMED,722118005,Congenital nephrotic syndrome -SNOMED,44785005,Minimal change disease -SNOMED,236407003,IgA nephropathy -SNOMED,445404003,Familial immunoglobulin A nephropathy -SNOMED,282364005,IgA nephropathy associated with liver disease -SNOMED,236411009,IgM nephropathy -SNOMED,722119002,Idiopathic membranous glomerulonephritis -SNOMED,722086002,Membranous glomerulonephritis due to malignant neoplastic disease -SNOMED,722120008,Drug-induced membranous glomerulonephritis -SNOMED,722168002,Membranous glomerulonephritis with infectious disease -SNOMED,75888001,"Mesangiocapillary glomerulonephritis, type I " -SNOMED,722760002,"Mesangiocapillary glomerulonephritis, type II " -SNOMED,236409000,Mesangiocapillary glomerulonephritis type III -SNOMED,197697005, -SNOMED,236404005,Classical focal segmental glomerulosclerosis -SNOMED,445388002,Autosomal recessive focal segmental glomerulosclerosis -SNOMED,444977005,Autosomal dominant focal segmental glomerulosclerosis -SNOMED,1269761000000101,Focal segmental glomerulosclerosis (FSGS) secondary to obesity -SNOMED,3704008,Diffuse endocapillary proliferative glomerulonephritis -SNOMED,35546006,Mesangial proliferative glomerulonephritis -SNOMED,83866005,Focal AND segmental proliferative glomerulonephritis -SNOMED, 724599009,Systemic vasculitis - histologically proven -SNOMED,722191003,Antineutrophil cytoplasmic antibody positive vasculitis -SNOMED,195353004,Granulomatosis with polyangiitis -SNOMED,1144805008,Microscopic polyarteritis nodosa -SNOMED,82275008,EGPA - eosinophilic granulomatosis with polyangiitis -SNOMED,155441006,Polyarteritis nodosa -SNOMED,50581000,Goodpasture syndrome -SNOMED,68815009,Lupus nephritis -SNOMED,191306005,Henoch-Schönlein purpura -SNOMED,236502006,Renal involvement in scleroderma -SNOMED,239947001,Essential mixed cryoglobulinemia -SNOMED,128971000119101,Cryoglobulinemia due to chronic hepatitis C -SNOMED,30911005,Cryoglobulinemia -SNOMED,197764002,Non-obstructive reflux-associated chronic pyelonephritis -SNOMED,707208009,Familial non-obstructive reflux-associated chronic pyelonephritis -SNOMED,204949001,Renal dysplasia -SNOMED,737562008,Multicystic dysplastic kidney -SNOMED,710571007,Renal dysplasia due to fetal exposure to angiotensin converting enzyme inhibitor -SNOMED,253864004,"Familial hypoplastic, glomerulocystic kidney" -SNOMED,373584008,Congenital pelviureteric junction obstruction -SNOMED,373585009,Congenital ureterovesical obstruction -SNOMED,253900005,Congenital posterior urethral valves -SNOMED,5187006,Prune belly syndrome -SNOMED,445387007,Congenital neurogenic urinary bladder -SNOMED,61758007,Exstrophy of bladder sequence -SNOMED,253904001,Megacystis-megaureter syndrome -SNOMED,18417009,Oligomeganephronic hypoplasia of kidney -SNOMED,90241004,Papillary necrosis -SNOMED,86249007,Obstructive nephropathy -SNOMED,722078002,Obstructive nephropathy due to neurogenic bladder -SNOMED,722082000,Obstructive nephropathy due to benign prostatic hyperplasia -SNOMED,722081007,Obstructive nephropathy due to carcinoma of prostate -SNOMED,722089009,Obstructive nephropathy due to bladder cancer -SNOMED,722088001,Obstructive nephropathy due to malignancy -SNOMED,197808006,Idiopathic retroperitoneal fibrosis -SNOMED,236017004,Malignant retroperitoneal fibrosis -SNOMED,95566004,Urolithiasis -SNOMED,444717006,Calcium oxalate urolithiasis -SNOMED,37497004,Enteric hyperoxaluria -SNOMED,444690001,Magnesium ammonium phosphate urolithiasis -SNOMED,267441009,Uric acid urolithiasis -SNOMED,428255004,Tubulointerstitial nephritis -SNOMED,83923004,Familial interstitial nephritis -SNOMED,45927004,Immunologic mediated tubulointerstitial nephritis -SNOMED,418839003,Tubulointerstitial nephritis with uveitis syndrome -SNOMED,37061001,Granulomatous sarcoid nephropathy -SNOMED,717770008,Aristolochic acid nephropathy -SNOMED,439990003,Drug-induced tubulointerstitial nephritis -SNOMED,59400006,Analgesic nephropathy -SNOMED,704203009,Nephropathy induced by ciclosporin -SNOMED,704205002,Nephropathy induced by tacrolimus -SNOMED,704206001,Nephropathy induced by aminoglycosides -SNOMED,704055002,Nephropathy induced by amphotericin -SNOMED,53556002,Cis-platinum nephropathy -SNOMED,4390004,Lithium nephropathy -SNOMED,704204003,Nephropathy induced by lead -SNOMED,236496000,Acute urate nephropathy -SNOMED,7725007,Radiation nephritis -SNOMED,197772000,Renal abscess OR Perirenal abscess -SNOMED,44323002,Tuberculosis of kidney -SNOMED,77377001,Leptospirosis -SNOMED,716864001,Haemorrhagic fever with renal syndrome -SNOMED,38898003,Xanthogranulomatous pyelonephritis -SNOMED,713504001,HIV-associated nephropathy -SNOMED,236706006,Urinary schistosomiasis -SNOMED,40733004,Infectious disease -SNOMED,96441000119101,Chronic kidney disease due to type 1 diabetes mellitus -SNOMED,771000119108,Chronic kidney disease due to type 2 diabetes mellitus -SNOMED,38481006,Hypertensive renal disease -SNOMED,65443008,Malignant hypertensive renal disease -SNOMED,445108007,Age related reduction of renal function -SNOMED,710565001,Ischaemic nephropathy -SNOMED,302233006,Renal artery stenosis -SNOMED,51677000,Atheroembolism of renal arteries -SNOMED,783730009,Fibromuscular dysplasia of renal artery -SNOMED,236488005,Renal artery occlusion -SNOMED,15842009,Thrombosis of renal vein -SNOMED,445236007,Cardiorenal syndrome -SNOMED,51292008,Hepatorenal syndrome -SNOMED,48713002,Renal amyloidosis -SNOMED,274945004,AA amyloidosis -SNOMED,23132008,AL amyloidosis -SNOMED,66451004,Familial renal amyloidosis -SNOMED,367528006,Amyloid of familial Mediterranean fever -SNOMED,32278006,Myeloma kidney -SNOMED,373604002,Light chain deposition disease -SNOMED,73305009,Fibrillary glomerulonephritis -SNOMED,373421000,Diarrhea-associated hemolytic uremic syndrome -SNOMED,373422007,Atypical haemolytic uraemic syndrome -SNOMED,78129009,Thrombotic thrombocytopenic purpura -SNOMED, 111407006,Hemolytic uremic syndrome -SNOMED,444976001,Congenital hemolytic uremic syndrome -SNOMED,722721004,Familial haemolytic-uraemic syndrome -SNOMED,373420004,Upshaw-Schulman syndrome -SNOMED,736993008,Nephropathy following eclampsia -SNOMED,13886001,Sickle cell nephropathy -SNOMED,765330003,Autosomal dominant polycystic kidney disease -SNOMED,253878003,Autosomal dominant polycystic kidney disease type 1 -SNOMED,253879006,Autosomal dominant polycystic kidney disease type 2 -SNOMED,28770003,Autosomal recessive polycystic kidney disease -SNOMED,770414008,Alport syndrome -SNOMED,236418003,Thin basement membrane disease -SNOMED, 722223000,Cystic kidney disease -SNOMED,726017001,Medullary cystic kidney disease type 1 -SNOMED,723373006,Medullary cystic kidney disease type 2 -SNOMED,46785007,Familial juvenile hyperuricaemia nephropathy -SNOMED,204958008,Nephronophthisis -SNOMED,444830001,Familial juvenile nephronophthisis -SNOMED,444558002,Infantile nephronophthisis -SNOMED,444749006,Adolescent nephronophthisis -SNOMED,446989009,Juvenile nephronophthisis -SNOMED,446991001,Nephronophthisis type 5 -SNOMED,447335007,Nephronophthisis type 6 -SNOMED,236466005,Congenital Fanconi syndrome -SNOMED,197744007,Renal tubulo-interstitial disorders in metabolic diseases -SNOMED,444645005,Dent's disease -SNOMED,79385002,Lowe syndrome -SNOMED,698953004,Inherited aminoaciduria -SNOMED,85020001,Cystinuria -SNOMED,190681003,Cystinosis -SNOMED,226309007,Familial renal glucosuria -SNOMED,82236004,Familial x-linked hypophosphatemic vitamin D refractory rickets -SNOMED,726080006,Autosomal recessive hypophosphatemic vitamin D refractory rickets -SNOMED,1776003,Renal tubular acidosis -SNOMED,24790002,Proximal renal tubular acidosis -SNOMED,236461000,Distal renal tubular acidosis -SNOMED,722468005,Distal renal tubular acidosis with sensorineural hearing loss (SNHL) -SNOMED,111395007,Nephrogenic diabetes insipidus -SNOMED,10406007,Lesch-Nyhan syndrome -SNOMED,35759001,Phosphoribosyl pyrophosphate synthase superactivity -SNOMED,31742004,Alagille syndrome -SNOMED,707742001,Bartter syndrome -SNOMED,707756004,Gitelman syndrome -SNOMED,707747007,Liddle syndrome -SNOMED,237770005,Syndrome of apparent mineralocorticoid excess -SNOMED,237743003,Glucocorticoid-suppressible hyperaldosteronism -SNOMED,237604008,Diabetes mellitus autosomal dominant type II -SNOMED,43941006,"Pseudohypoaldosteronism, type 1 " -SNOMED,15689008,"Pseudohypoaldosteronism, type 2 " -SNOMED,237885008,Familial hypocalciuric hypercalcemia -SNOMED,711152006,Familial hypercalciuric hypocalcaemia -SNOMED,48655003,Isolated familial renal hypomagnesaemia -SNOMED,17901006,Primary hyperoxaluria -SNOMED,65520001,Primary hyperoxaluria type I -SNOMED,40951006,"Primary hyperoxaluria, type II " -SNOMED,16652001,Fabry's disease -SNOMED,190919008,Xanthinuria -SNOMED,22199006,Nail patella-like renal disease -SNOMED,45582004,Rubinstein-Taybi syndrome -SNOMED,7199000,Tuberous sclerosis syndrome -SNOMED,46659004,Von Hippel-Lindau syndrome -SNOMED,236443009,Medullary sponge kidney -SNOMED,41729002,Horseshoe kidney -SNOMED,445431000,Frasier syndrome -SNOMED,290006,Branchio-oto-renal syndrome -SNOMED,63247009,Williams syndrome -SNOMED,24750000,Townes-Brocks syndrome -SNOMED,5619004,Laurence-Moon syndrome -SNOMED,240096000,Mitochondrial cytopathy -SNOMED,236419006,Familial nephropathy -SNOMED,14669001,Acute kidney injury -SNOMED,1048451000000103,Acute kidney injury due to acute tubular necrosis due to hypovolaemia -SNOMED,1048481000000109,Acute kidney injury due to acute tubular necrosis due to circulatory failure -SNOMED,1048491000000106,Acute kidney injury due to acute tubular necrosis due to sepsis -SNOMED,23697004,Acute kidney injury due to rhabdomyolysis -SNOMED,236428007,Acute kidney injury due to nephrotoxicity -SNOMED,444794000,Acute cortical necrosis -SNOMED,36689008,Acute pyelonephritis -SNOMED,126880001,Neoplasm of kidney -SNOMED,702391001,Renal cell carcinoma -SNOMED,408642003,Transitional cell carcinoma of kidney -SNOMED,302849000,Nephroblastoma -SNOMED,307604008,Mesoblastic nephroma -SNOMED,824131000000108,Solitary kidney -SNOMED,722149000,Chronic kidney disease (CKD) caused by tumour nephrectomy -SNOMED,722467000,Chronic kidney disease due to traumatic loss of kidney -SNOMED,722098007,Chronic kidney disease after donor nephrectomy -SNOMED,709044004,Chronic kidney disease - aetiology uncertain / unknown -SNOMED,449820008,Steroid resistant nephrotic syndrome of childhood -SNOMED,705065000,Childhood nephrotic syndrome -SNOMED,609572000,Renal cysts and diabetes syndrome -SNOMED,190829000,Chronic urate nephropathy -SNOMED,722150000,Chronic kidney disease due to systemic infection -SNOMED,446449009,Renal coloboma syndrome -SNOMED,33763006,Hypercalcemic nephropathy -SNOMED,49120005,Retroperitoneal fibrosis -SNOMED,236015007,Drug-induced retroperitoneal fibrosis -SNOMED,42399005,Renal failure syndrome -SNOMED,90688005,Chronic renal failure syndrome -SNOMED,53298003,Hematuria -SNOMED,53298000,Hematuria syndrome -SNOMED,12491000132101,Proteinuria -SNOMED,734990008,"Primary hyperoxaluria, type III " -SNOMED,36171008,Glomerulonephritis -SNOMED, 713887002,Focal segmental glomerulosclerosis co-occurrent with human immunodeficiency virus infection -SNOMED, 722139003,Focal segmental glomerulosclerosis caused by lithium -SNOMED,722147003,Focal segmental glomerulosclerosis due to sickle cell disease -SNOMED,723074006,Renal papillary necrosis due to diabetes mellitus -SNOMED,722077007,Renal papillary necrosis caused by analgesic drug -SNOMED, 722085003,Renal papillary necrosis due to sickle cell disease -SNOMED, 95570007,Kidney stone -SNOMED,118600007,Malignant lymphoma  -SNOMED,736992003,Nephropathy following pre-eclampsia -SNOMED,6956008,Systemic Vasculitis diff --git a/codes/code_mappings/edta2_to_snomed.csv b/codes/code_mappings/edta2_to_snomed.csv deleted file mode 100644 index a59e02e..0000000 --- a/codes/code_mappings/edta2_to_snomed.csv +++ /dev/null @@ -1,283 +0,0 @@ -EDTA2,1003,SNOMED,52254009 -EDTA2,1019,SNOMED,445119005 -EDTA2,1026,SNOMED,48796009 -EDTA2,1035,SNOMED,197601003 -EDTA2,1042,SNOMED,197601003 -EDTA2,1057,SNOMED,722369003 -EDTA2,1061,SNOMED,236384008 -EDTA2,1074,SNOMED,236385009 -EDTA2,1088,SNOMED,722118005 -EDTA2,1090,SNOMED,44785005 -EDTA2,1100,SNOMED,44785005 -EDTA2,1116,SNOMED,236407003 -EDTA2,1128,SNOMED,236407003 -EDTA2,1137,SNOMED,445404003 -EDTA2,1144,SNOMED,445404003 -EDTA2,1159,SNOMED,282364005 -EDTA2,1163,SNOMED,282364005 -EDTA2,1171,SNOMED,236411009 -EDTA2,1185,SNOMED,722119002 -EDTA2,1192,SNOMED,722086002 -EDTA2,1205,SNOMED,722120008 -EDTA2,1214,SNOMED,722168002 -EDTA2,1222,SNOMED,75888001 -EDTA2,1233,SNOMED,722760002 -EDTA2,1246,SNOMED,236409000 -EDTA2,1251,SNOMED,197697005 -EDTA2,1267,SNOMED,236404005 -EDTA2,1279,SNOMED,445388002 -EDTA2,1280,SNOMED,445388002 -EDTA2,1298,SNOMED,444977005 -EDTA2,1308,SNOMED,444977005 -EDTA2,1312,SNOMED,1269761000000101 -EDTA2,1320,SNOMED,1269761000000101 -EDTA2,1331,SNOMED,3704008 -EDTA2,1349,SNOMED,35546006 -EDTA2,1354,SNOMED,83866005 -EDTA2,1365,SNOMED,36171008 -EDTA2,1377,SNOMED, 36171008 -EDTA2,1383,SNOMED, 724599009 -EDTA2,1396,SNOMED,722191003 -EDTA2,1401,SNOMED,195353004 -EDTA2,1417,SNOMED,195353004 -EDTA2,1429,SNOMED,1144805008 -EDTA2,1438,SNOMED,82275008 -EDTA2,1440,SNOMED,82275008 -EDTA2,1455,SNOMED,155441006 -EDTA2,1464,SNOMED,50581000 -EDTA2,1472,SNOMED,50581000 -EDTA2,1486,SNOMED,68815009 -EDTA2,1493,SNOMED,68815009 -EDTA2,1504,SNOMED,191306005 -EDTA2,1515,SNOMED,191306005 -EDTA2,1527,SNOMED,236502006 -EDTA2,1536,SNOMED,236502006 -EDTA2,1543,SNOMED,239947001 -EDTA2,1558,SNOMED,239947001 -EDTA2,1562,SNOMED,128971000119101 -EDTA2,1570,SNOMED,128971000119101 -EDTA2,1589,SNOMED,30911005 -EDTA2,1591,SNOMED,30911005 -EDTA2,1602,SNOMED,197764002 -EDTA2,1618,SNOMED,707208009 -EDTA2,1625,SNOMED,204949001 -EDTA2,1639,SNOMED,737562008 -EDTA2,1641,SNOMED,710571007 -EDTA2,1656,SNOMED,253864004 -EDTA2,1660,SNOMED,373584008 -EDTA2,1673,SNOMED,373585009 -EDTA2,1687,SNOMED,253900005 -EDTA2,1694,SNOMED,5187006 -EDTA2,1706,SNOMED,445387007 -EDTA2,1710,SNOMED,61758007 -EDTA2,1723,SNOMED,253904001 -EDTA2,1734,SNOMED,18417009 -EDTA2,1747,SNOMED,90241004 -EDTA2,1752,SNOMED,86249007 -EDTA2,1768,SNOMED,722078002 -EDTA2,1775,SNOMED,722082000 -EDTA2,1781,SNOMED,722081007 -EDTA2,1799,SNOMED,722089009 -EDTA2,1809,SNOMED,722088001 -EDTA2,1813,SNOMED,197808006 -EDTA2,1821,SNOMED,236017004 -EDTA2,1832,SNOMED,95566004 -EDTA2,1845,SNOMED,444717006 -EDTA2,1850,SNOMED,37497004 -EDTA2,1866,SNOMED,444690001 -EDTA2,1878,SNOMED,267441009 -EDTA2,1884,SNOMED,428255004 -EDTA2,1897,SNOMED,428255004 -EDTA2,1907,SNOMED,83923004 -EDTA2,1911,SNOMED,83923004 -EDTA2,1924,SNOMED,45927004 -EDTA2,1930,SNOMED,45927004 -EDTA2,1948,SNOMED,418839003 -EDTA2,1953,SNOMED,418839003 -EDTA2,1969,SNOMED,37061001 -EDTA2,1976,SNOMED,37061001 -EDTA2,1982,SNOMED,717770008 -EDTA2,1995,SNOMED,717770008 -EDTA2,2005,SNOMED,439990003 -EDTA2,2014,SNOMED,439990003 -EDTA2,2022,SNOMED,59400006 -EDTA2,2033,SNOMED,59400006 -EDTA2,2046,SNOMED,704203009 -EDTA2,2051,SNOMED,704203009 -EDTA2,2067,SNOMED,704205002 -EDTA2,2079,SNOMED,704205002 -EDTA2,2080,SNOMED,704206001 -EDTA2,2098,SNOMED,704206001 -EDTA2,2108,SNOMED,704055002 -EDTA2,2112,SNOMED,704055002 -EDTA2,2120,SNOMED,53556002 -EDTA2,2131,SNOMED,53556002 -EDTA2,2149,SNOMED,4390004 -EDTA2,2154,SNOMED,4390004 -EDTA2,2165,SNOMED,704204003 -EDTA2,2177,SNOMED,704204003 -EDTA2,2183,SNOMED,236496000 -EDTA2,2196,SNOMED,236496000 -EDTA2,2203,SNOMED,190829000 -EDTA2,2219,SNOMED,7725007 -EDTA2,2226,SNOMED,197772000 -EDTA2,2235,SNOMED,44323002 -EDTA2,2242,SNOMED,77377001 -EDTA2,2257,SNOMED,716864001 -EDTA2,2261,SNOMED,38898003 -EDTA2,2274,SNOMED,713504001 -EDTA2,2288,SNOMED,713504001 -EDTA2,2290,SNOMED,236706006 -EDTA2,2300,SNOMED,40733004 -EDTA2,2316,SNOMED,96441000119101 -EDTA2,2328,SNOMED,96441000119101 -EDTA2,2337,SNOMED,771000119108 -EDTA2,2344,SNOMED,771000119108 -EDTA2,2359,SNOMED,38481006 -EDTA2,2363,SNOMED,38481006 -EDTA2,2371,SNOMED,65443008 -EDTA2,2385,SNOMED,65443008 -EDTA2,2392,SNOMED,445108007 -EDTA2,2407,SNOMED,710565001 -EDTA2,2411,SNOMED,710565001 -EDTA2,2424,SNOMED,302233006 -EDTA2,2430,SNOMED,51677000 -EDTA2,2448,SNOMED,51677000 -EDTA2,2453,SNOMED,783730009 -EDTA2,2469,SNOMED,236488005 -EDTA2,2476,SNOMED,15842009 -EDTA2,2482,SNOMED,445236007 -EDTA2,2495,SNOMED,51292008 -EDTA2,2509,SNOMED,48713002 -EDTA2,2513,SNOMED,274945004 -EDTA2,2521,SNOMED,23132008 -EDTA2,2532,SNOMED,66451004 -EDTA2,2545,SNOMED,66451004 -EDTA2,2550,SNOMED,367528006 -EDTA2,2566,SNOMED,367528006 -EDTA2,2578,SNOMED,32278006 -EDTA2,2584,SNOMED,32278006 -EDTA2,2597,SNOMED,373604002 -EDTA2,2606,SNOMED,73305009 -EDTA2,2610,SNOMED,373421000 -EDTA2,2623,SNOMED,373422007 -EDTA2,2634,SNOMED,78129009 -EDTA2,2647,SNOMED, 111407006 -EDTA2,2652,SNOMED,444976001 -EDTA2,2668,SNOMED,722721004 -EDTA2,2675,SNOMED,373420004 -EDTA2,2681,SNOMED,736993008 -EDTA2,2699,SNOMED,13886001 -EDTA2,2702,SNOMED,13886001 -EDTA2,2718,SNOMED,765330003 -EDTA2,2725,SNOMED,253878003 -EDTA2,2739,SNOMED,253879006 -EDTA2,2741,SNOMED,28770003 -EDTA2,2756,SNOMED,770414008 -EDTA2,2760,SNOMED,770414008 -EDTA2,2773,SNOMED,236418003 -EDTA2,2787,SNOMED,236418003 -EDTA2,2794,SNOMED, 722223000 -EDTA2,2804,SNOMED,726017001 -EDTA2,2815,SNOMED,723373006 -EDTA2,2827,SNOMED,46785007 -EDTA2,2836,SNOMED,204958008 -EDTA2,2843,SNOMED,444830001 -EDTA2,2858,SNOMED,444558002 -EDTA2,2862,SNOMED,444749006 -EDTA2,2870,SNOMED,446989009 -EDTA2,2889,SNOMED,446991001 -EDTA2,2891,SNOMED,447335007 -EDTA2,2901,SNOMED,236466005 -EDTA2,2917,SNOMED,197744007 -EDTA2,2929,SNOMED,444645005 -EDTA2,2938,SNOMED,79385002 -EDTA2,2940,SNOMED,698953004 -EDTA2,2955,SNOMED,85020001 -EDTA2,2964,SNOMED,190681003 -EDTA2,2972,SNOMED,226309007 -EDTA2,2986,SNOMED,82236004 -EDTA2,2993,SNOMED,726080006 -EDTA2,3000,SNOMED,1776003 -EDTA2,3016,SNOMED,24790002 -EDTA2,3028,SNOMED,236461000 -EDTA2,3037,SNOMED,722468005 -EDTA2,3044,SNOMED,111395007 -EDTA2,3059,SNOMED,10406007 -EDTA2,3063,SNOMED,35759001 -EDTA2,3071,SNOMED,31742004 -EDTA2,3085,SNOMED,707742001 -EDTA2,3092,SNOMED,707756004 -EDTA2,3102,SNOMED,707747007 -EDTA2,3118,SNOMED,237770005 -EDTA2,3125,SNOMED,237743003 -EDTA2,3139,SNOMED,237604008 -EDTA2,3141,SNOMED,43941006 -EDTA2,3156,SNOMED,15689008 -EDTA2,3160,SNOMED,237885008 -EDTA2,3173,SNOMED,711152006 -EDTA2,3187,SNOMED,48655003 -EDTA2,3194,SNOMED,17901006 -EDTA2,3207,SNOMED,65520001 -EDTA2,3211,SNOMED,40951006 -EDTA2,3224,SNOMED,16652001 -EDTA2,3230,SNOMED,16652001 -EDTA2,3248,SNOMED,190919008 -EDTA2,3253,SNOMED,22199006 -EDTA2,3269,SNOMED,45582004 -EDTA2,3276,SNOMED,7199000 -EDTA2,3282,SNOMED,46659004 -EDTA2,3295,SNOMED,236443009 -EDTA2,3305,SNOMED,41729002 -EDTA2,3314,SNOMED,445431000 -EDTA2,3322,SNOMED,290006 -EDTA2,3333,SNOMED,63247009 -EDTA2,3346,SNOMED,24750000 -EDTA2,3351,SNOMED,5619004 -EDTA2,3367,SNOMED,240096000 -EDTA2,3379,SNOMED,236419006 -EDTA2,3380,SNOMED,14669001 -EDTA2,3398,SNOMED,1048451000000103 -EDTA2,3403,SNOMED,1048481000000109 -EDTA2,3419,SNOMED,1048491000000106 -EDTA2,3426,SNOMED,23697004 -EDTA2,3435,SNOMED,236428007 -EDTA2,3442,SNOMED,444794000 -EDTA2,3457,SNOMED,36689008 -EDTA2,3461,SNOMED,126880001 -EDTA2,3474,SNOMED,702391001 -EDTA2,3488,SNOMED,408642003 -EDTA2,3490,SNOMED,302849000 -EDTA2,3501,SNOMED,307604008 -EDTA2,3517,SNOMED,824131000000108 -EDTA2,3529,SNOMED,722149000 -EDTA2,3538,SNOMED,722467000 -EDTA2,3540,SNOMED,722098007 -EDTA2,3555,SNOMED,709044004 -EDTA2,3564,SNOMED,709044004 -EDTA2,3604,SNOMED,449820008 -EDTA2,3615,SNOMED,705065000 -EDTA2,3627,SNOMED,609572000 -EDTA2,3636,SNOMED,190829000 -EDTA2,3643,SNOMED,722150000 -EDTA2,3658,SNOMED,446449009 -EDTA2,3662,SNOMED,33763006 -EDTA2,3670,SNOMED,49120005 -EDTA2,3689,SNOMED,236015007 -EDTA2,3691,SNOMED,42399005 -EDTA2,3708,SNOMED,90688005 -EDTA2,3712,SNOMED,53298000 -EDTA2,3720,SNOMED,12491000132101 -EDTA2,3731,SNOMED,734990008 -EDTA2,3749,SNOMED,36171008 -EDTA2,3754,SNOMED, 713887002 -EDTA2,3765,SNOMED, 722139003 -EDTA2,3777,SNOMED,722147003 -EDTA2,3783,SNOMED,723074006 -EDTA2,3796,SNOMED,722077007 -EDTA2,3806,SNOMED, 722085003 -EDTA2,3810,SNOMED, 95570007 -EDTA2,3823,SNOMED,118600007 -EDTA2,3834,SNOMED,736992003 -EDTA2,3847,SNOMED,6956008 -EDTA2,3852,SNOMED,6956008 diff --git a/codes/code_mappings/snomed_to_edta2.csv b/codes/code_mappings/snomed_to_edta2.csv deleted file mode 100644 index 9cb0e70..0000000 --- a/codes/code_mappings/snomed_to_edta2.csv +++ /dev/null @@ -1,234 +0,0 @@ -SNOMED,52254009,EDTA2,1003 -SNOMED,445119005,EDTA2,1019 -SNOMED,48796009,EDTA2,1026 -SNOMED,197601003,EDTA2,1035 -SNOMED,722369003,EDTA2,1057 -SNOMED,236384008,EDTA2,1061 -SNOMED,236385009,EDTA2,1074 -SNOMED,722118005,EDTA2,1088 -SNOMED,44785005,EDTA2,1090 -SNOMED,236407003,EDTA2,1116 -SNOMED,445404003,EDTA2,1137 -SNOMED,282364005,EDTA2,1159 -SNOMED,236411009,EDTA2,1171 -SNOMED,722119002,EDTA2,1185 -SNOMED,722086002,EDTA2,1192 -SNOMED,722120008,EDTA2,1205 -SNOMED,722168002,EDTA2,1214 -SNOMED,75888001,EDTA2,1222 -SNOMED,722760002,EDTA2,1233 -SNOMED,236409000,EDTA2,1246 -SNOMED,197697005,EDTA2,1251 -SNOMED,236404005,EDTA2,1267 -SNOMED,445388002,EDTA2,1279 -SNOMED,444977005,EDTA2,1298 -SNOMED,1269761000000101,EDTA2,1312 -SNOMED,3704008,EDTA2,1331 -SNOMED,35546006,EDTA2,1349 -SNOMED,83866005,EDTA2,1354 -SNOMED, 36171008,EDTA2,1377 -SNOMED, 724599009,EDTA2,1383 -SNOMED,722191003,EDTA2,1396 -SNOMED,195353004,EDTA2,1401 -SNOMED,1144805008,EDTA2,1429 -SNOMED,82275008,EDTA2,1438 -SNOMED,155441006,EDTA2,1455 -SNOMED,50581000,EDTA2,1464 -SNOMED,68815009,EDTA2,1486 -SNOMED,191306005,EDTA2,1504 -SNOMED,236502006,EDTA2,1527 -SNOMED,239947001,EDTA2,1543 -SNOMED,128971000119101,EDTA2,1562 -SNOMED,30911005,EDTA2,1589 -SNOMED,197764002,EDTA2,1602 -SNOMED,707208009,EDTA2,1618 -SNOMED,204949001,EDTA2,1625 -SNOMED,737562008,EDTA2,1639 -SNOMED,710571007,EDTA2,1641 -SNOMED,253864004,EDTA2,1656 -SNOMED,373584008,EDTA2,1660 -SNOMED,373585009,EDTA2,1673 -SNOMED,253900005,EDTA2,1687 -SNOMED,5187006,EDTA2,1694 -SNOMED,445387007,EDTA2,1706 -SNOMED,61758007,EDTA2,1710 -SNOMED,253904001,EDTA2,1723 -SNOMED,18417009,EDTA2,1734 -SNOMED,90241004,EDTA2,1747 -SNOMED,86249007,EDTA2,1752 -SNOMED,722078002,EDTA2,1768 -SNOMED,722082000,EDTA2,1775 -SNOMED,722081007,EDTA2,1781 -SNOMED,722089009,EDTA2,1799 -SNOMED,722088001,EDTA2,1809 -SNOMED,197808006,EDTA2,1813 -SNOMED,236017004,EDTA2,1821 -SNOMED,95566004,EDTA2,1832 -SNOMED,444717006,EDTA2,1845 -SNOMED,37497004,EDTA2,1850 -SNOMED,444690001,EDTA2,1866 -SNOMED,267441009,EDTA2,1878 -SNOMED,428255004,EDTA2,1884 -SNOMED,83923004,EDTA2,1907 -SNOMED,45927004,EDTA2,1924 -SNOMED,418839003,EDTA2,1948 -SNOMED,37061001,EDTA2,1969 -SNOMED,717770008,EDTA2,1982 -SNOMED,439990003,EDTA2,2005 -SNOMED,59400006,EDTA2,2022 -SNOMED,704203009,EDTA2,2046 -SNOMED,704205002,EDTA2,2067 -SNOMED,704206001,EDTA2,2080 -SNOMED,704055002,EDTA2,2108 -SNOMED,53556002,EDTA2,2120 -SNOMED,4390004,EDTA2,2149 -SNOMED,704204003,EDTA2,2165 -SNOMED,236496000,EDTA2,2183 -SNOMED,7725007,EDTA2,2219 -SNOMED,197772000,EDTA2,2226 -SNOMED,44323002,EDTA2,2235 -SNOMED,77377001,EDTA2,2242 -SNOMED,716864001,EDTA2,2257 -SNOMED,38898003,EDTA2,2261 -SNOMED,713504001,EDTA2,2274 -SNOMED,236706006,EDTA2,2290 -SNOMED,40733004,EDTA2,2300 -SNOMED,96441000119101,EDTA2,2316 -SNOMED,771000119108,EDTA2,2337 -SNOMED,38481006,EDTA2,2359 -SNOMED,65443008,EDTA2,2371 -SNOMED,445108007,EDTA2,2392 -SNOMED,710565001,EDTA2,2407 -SNOMED,302233006,EDTA2,2424 -SNOMED,51677000,EDTA2,2430 -SNOMED,783730009,EDTA2,2453 -SNOMED,236488005,EDTA2,2469 -SNOMED,15842009,EDTA2,2476 -SNOMED,445236007,EDTA2,2482 -SNOMED,51292008,EDTA2,2495 -SNOMED,48713002,EDTA2,2509 -SNOMED,274945004,EDTA2,2513 -SNOMED,23132008,EDTA2,2521 -SNOMED,66451004,EDTA2,2532 -SNOMED,367528006,EDTA2,2550 -SNOMED,32278006,EDTA2,2578 -SNOMED,373604002,EDTA2,2597 -SNOMED,73305009,EDTA2,2606 -SNOMED,373421000,EDTA2,2610 -SNOMED,373422007,EDTA2,2623 -SNOMED,78129009,EDTA2,2634 -SNOMED, 111407006,EDTA2,2647 -SNOMED,444976001,EDTA2,2652 -SNOMED,722721004,EDTA2,2668 -SNOMED,373420004,EDTA2,2675 -SNOMED,736993008,EDTA2,2681 -SNOMED,13886001,EDTA2,2699 -SNOMED,765330003,EDTA2,2718 -SNOMED,253878003,EDTA2,2725 -SNOMED,253879006,EDTA2,2739 -SNOMED,28770003,EDTA2,2741 -SNOMED,770414008,EDTA2,2756 -SNOMED,236418003,EDTA2,2787 -SNOMED, 722223000,EDTA2,2794 -SNOMED,726017001,EDTA2,2804 -SNOMED,723373006,EDTA2,2815 -SNOMED,46785007,EDTA2,2827 -SNOMED,204958008,EDTA2,2836 -SNOMED,444830001,EDTA2,2843 -SNOMED,444558002,EDTA2,2858 -SNOMED,444749006,EDTA2,2862 -SNOMED,446989009,EDTA2,2870 -SNOMED,446991001,EDTA2,2889 -SNOMED,447335007,EDTA2,2891 -SNOMED,236466005,EDTA2,2901 -SNOMED,197744007,EDTA2,2917 -SNOMED,444645005,EDTA2,2929 -SNOMED,79385002,EDTA2,2938 -SNOMED,698953004,EDTA2,2940 -SNOMED,85020001,EDTA2,2955 -SNOMED,190681003,EDTA2,2964 -SNOMED,226309007,EDTA2,2972 -SNOMED,82236004,EDTA2,2986 -SNOMED,726080006,EDTA2,2993 -SNOMED,1776003,EDTA2,3000 -SNOMED,24790002,EDTA2,3016 -SNOMED,236461000,EDTA2,3028 -SNOMED,722468005,EDTA2,3037 -SNOMED,111395007,EDTA2,3044 -SNOMED,10406007,EDTA2,3059 -SNOMED,35759001,EDTA2,3063 -SNOMED,31742004,EDTA2,3071 -SNOMED,707742001,EDTA2,3085 -SNOMED,707756004,EDTA2,3092 -SNOMED,707747007,EDTA2,3102 -SNOMED,237770005,EDTA2,3118 -SNOMED,237743003,EDTA2,3125 -SNOMED,237604008,EDTA2,3139 -SNOMED,43941006,EDTA2,3141 -SNOMED,15689008,EDTA2,3156 -SNOMED,237885008,EDTA2,3160 -SNOMED,711152006,EDTA2,3173 -SNOMED,48655003,EDTA2,3187 -SNOMED,17901006,EDTA2,3194 -SNOMED,65520001,EDTA2,3207 -SNOMED,40951006,EDTA2,3211 -SNOMED,16652001,EDTA2,3224 -SNOMED,190919008,EDTA2,3248 -SNOMED,22199006,EDTA2,3253 -SNOMED,45582004,EDTA2,3269 -SNOMED,7199000,EDTA2,3276 -SNOMED,46659004,EDTA2,3282 -SNOMED,236443009,EDTA2,3295 -SNOMED,41729002,EDTA2,3305 -SNOMED,445431000,EDTA2,3314 -SNOMED,290006,EDTA2,3322 -SNOMED,63247009,EDTA2,3333 -SNOMED,24750000,EDTA2,3346 -SNOMED,5619004,EDTA2,3351 -SNOMED,240096000,EDTA2,3367 -SNOMED,236419006,EDTA2,3379 -SNOMED,14669001,EDTA2,3380 -SNOMED,1048451000000103,EDTA2,3398 -SNOMED,1048481000000109,EDTA2,3403 -SNOMED,1048491000000106,EDTA2,3419 -SNOMED,23697004,EDTA2,3426 -SNOMED,236428007,EDTA2,3435 -SNOMED,444794000,EDTA2,3442 -SNOMED,36689008,EDTA2,3457 -SNOMED,126880001,EDTA2,3461 -SNOMED,702391001,EDTA2,3474 -SNOMED,408642003,EDTA2,3488 -SNOMED,302849000,EDTA2,3490 -SNOMED,307604008,EDTA2,3501 -SNOMED,824131000000108,EDTA2,3517 -SNOMED,722149000,EDTA2,3529 -SNOMED,722467000,EDTA2,3538 -SNOMED,722098007,EDTA2,3540 -SNOMED,709044004,EDTA2,3555 -SNOMED,34436003,EDTA2,3572 -SNOMED,29738008,EDTA2,3572 -SNOMED,449820008,EDTA2,3604 -SNOMED,705065000,EDTA2,3615 -SNOMED,609572000,EDTA2,3627 -SNOMED,190829000,EDTA2,3636 -SNOMED,722150000,EDTA2,3643 -SNOMED,446449009,EDTA2,3658 -SNOMED,33763006,EDTA2,3662 -SNOMED,49120005,EDTA2,3670 -SNOMED,236015007,EDTA2,3689 -SNOMED,42399005,EDTA2,3691 -SNOMED,90688005,EDTA2,3708 -SNOMED,53298000,EDTA2,3712 -SNOMED,12491000132101,EDTA2,3720 -SNOMED,734990008,EDTA2,3731 -SNOMED,36171008,EDTA2,3749 -SNOMED, 713887002,EDTA2,3754 -SNOMED, 722139003,EDTA2,3765 -SNOMED,722147003,EDTA2,3777 -SNOMED,723074006,EDTA2,3783 -SNOMED,722077007,EDTA2,3796 -SNOMED, 722085003,EDTA2,3806 -SNOMED, 95570007,EDTA2,3810 -SNOMED,118600007,EDTA2,3823 -SNOMED,736992003,EDTA2,3834 -SNOMED,6956008,EDTA2,3847 diff --git a/docs_build/main.py b/docs_build/main.py index 81c58a5..d4521be 100644 --- a/docs_build/main.py +++ b/docs_build/main.py @@ -1,8 +1,10 @@ import os +import re import sys -import lxml.etree as ET -from typing import List from pathlib import Path +from typing import List + +import lxml.etree as ET in_path = Path(sys.argv[1]) out_path = Path(sys.argv[2]) @@ -13,6 +15,31 @@ xslt = ET.parse(xsl_path.as_posix()) transform = ET.XSLT(xslt) +type_paths = {} + + +def replace_strings(html_document, lookup_dict): + pattern = r'XXX(\w+)YYY' # Regular expression pattern to match XXXValueYYY + + if isinstance(html_document, bytes): + html_document = html_document.decode() + + def replace(match): + value = match.group(1) + + type_path = lookup_dict.get(value, None) + + if type_path: + replacement = f"Type: {value}" + else: + replacement = f"Type: {value}" + + return replacement + + replaced_html = re.sub(pattern, replace, html_document) + + return replaced_html + def make_index(title: str, dir_links: List[str], file_links: List[str]): file_links.sort() @@ -38,6 +65,32 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): content += "" return content +for path, dirs, files in os.walk(in_path): + + path_relative_to_base = Path(path).relative_to(in_path) + page_dir = out_path.joinpath(path_relative_to_base) + page_dir.mkdir(exist_ok=True) + + for xsd_file in [f for f in files if f.endswith(".xsd")]: + + in_file = Path(path).joinpath(xsd_file) + dom = ET.parse(in_file.as_posix()) + + namespace = "http://www.w3.org/2001/XMLSchema" + xpath_expr = "//xs:complexType/@name|//xs:simpleType/@name" + xsd_types = dom.xpath(xpath_expr, namespaces={"xs": namespace}) + + for xsd_type in xsd_types: + type_path = str(in_file).replace('schema/ukrdc/', '') + + type_path_list = type_path.split('/') + if len(type_path_list) > 1: + if type_path_list[0] == type_path_list[1]: + type_path = "/".join(type_path_list[1:]) + # HACK: This only fixes a specific case. + # type_path.replace('Types/Types/', 'Types/') + + type_paths[xsd_type] = str(type_path)[:-4] + ".html" for path, dirs, files in os.walk(in_path): @@ -62,9 +115,16 @@ def make_index(title: str, dir_links: List[str], file_links: List[str]): dom = ET.parse(in_file.as_posix()) newdom = transform(dom) + + html_string = ET.tostring(newdom, pretty_print=True) + + # TODO: This doesn't work if the definition is in a different + # file in the same folder as it's being used in. + # The replace function needs to take account of the current path. + html_string = replace_strings(html_string, type_paths) - with open(out_file, "wb") as html: - html.write(ET.tostring(newdom, pretty_print=True)) + with open(out_file, "w") as html_file: + html_file.write(html_string) index_path = out_path.joinpath(path_relative_to_base, "index.html") with open(index_path, "w") as html: diff --git a/docs_build/stylesheet.xsl b/docs_build/stylesheet.xsl index 205c39a..6d54ab4 100644 --- a/docs_build/stylesheet.xsl +++ b/docs_build/stylesheet.xsl @@ -1,5 +1,5 @@ - + + +
+ Should be submitted for: +
+
+ +
+
@@ -165,8 +173,11 @@ + + Type: + - + XXXYYY @@ -236,6 +247,7 @@ + @@ -245,8 +257,74 @@ + + Type: + - + XXXYYY +
+ + + + + + + + + + @@ -352,6 +430,8 @@ + + diff --git a/pyxb_build/setup.py b/pyxb_build/setup.py index e28ac7b..81e789d 100644 --- a/pyxb_build/setup.py +++ b/pyxb_build/setup.py @@ -6,7 +6,7 @@ match_pat = r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]' version = re.search(match_pat, f.read(), re.MULTILINE).group(1) -data = {'ukrdc_schema': ['transforms/*.xsl'], } +data = {'ukrdc_schema': ['transforms/*.xsl', 'py.typed'], } setup( name='ukrdc_schema', version=version, diff --git a/pyxb_build/ukrdc_schema/__init__.py b/pyxb_build/ukrdc_schema/__init__.py index ff04168..f0bddce 100644 --- a/pyxb_build/ukrdc_schema/__init__.py +++ b/pyxb_build/ukrdc_schema/__init__.py @@ -1 +1 @@ -__version__ = "3.3.1" +__version__ = "4.2.0" \ No newline at end of file diff --git a/pyxb_build/ukrdc_schema/py.typed b/pyxb_build/ukrdc_schema/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/sample_files/ukrdc/fullDemographics.xml b/sample_files/ukrdc/fullDemographics.xml index a6b1d29..2b60c73 100644 --- a/sample_files/ukrdc/fullDemographics.xml +++ b/sample_files/ukrdc/fullDemographics.xml @@ -1,5 +1,5 @@ - ABC123 + ABC123 UKRDC diff --git a/sample_files/ukrdc/fullFile.xml b/sample_files/ukrdc/fullFile.xml index 9b4f31b..2c95a4e 100644 --- a/sample_files/ukrdc/fullFile.xml +++ b/sample_files/ukrdc/fullFile.xml @@ -1,5 +1,5 @@ - ABC123 + ABC123 UKRDC @@ -188,11 +188,6 @@ 2006-05-04T18:13:51.0 2006-05-04T18:13:51.0 2006-05-04T18:13:51.0 - - RR1+ - ABC123 - Test Hospital - 2006-05-04T18:13:51.0 5555555555 @@ -205,15 +200,11 @@ 2006-05-04T18:13:51.0 2006-05-04T18:13:51.0 2006-05-04T18:13:51.0 - - RR1+ - ABC123 - Test Hospital 1 - 2006-05-04T18:13:51.0 778787876878 + PRIMARY EDTA_COD 14 @@ -225,6 +216,7 @@ 211111221 + PRIMARY EDTA2 13 @@ -259,16 +251,16 @@ CF_RR23 l - Description61 + Litre Frequency0 Comments17 0 - CodingStandard62 - Code62 - Description62 + CF_RR23 + other + Other Indication0 EncounterNumber2 @@ -286,11 +278,6 @@ Haemodialysis 2006-05-04T18:13:51.0 - - ODS - ABC123 - Dr Foster - RR1+ ABC123 @@ -298,16 +285,6 @@ 2006-05-04T18:13:51.0 787878787 - - Y - NLN - BB - Y - 100 - 200 - 300 - U - @@ -315,17 +292,7 @@ Code82 Description82 - - ODS - Code83 - Description83 - 2006-05-04T18:13:51.0 - - ODS - Code84 - Description84 - ODS Code85 @@ -333,16 +300,6 @@ 2006-05-04T18:13:51.0 ExternalId20 - - Y - NLN - BB - Y - 100 - 200 - 300 - L - @@ -352,11 +309,6 @@ PEX 2006-05-04T18:13:51.0 - - ODS - ABC123 - Dr Foster - RR1+ ABC123 @@ -364,36 +316,6 @@ 2006-05-04T18:13:51.0 1222333444 - - 2006-05-04T18:13:51.0 - 14 - 2006-05-04T18:13:51.0 - 2006-05-04T18:13:51.0 - 21 - DBD - NEG - NEG - 27 - 1 - NEG - NEG - 0 - 0 - 0 - Y - Y - Y - Y - Y - 90 - Y - 0 - 1 - 2 - Y - 10 - 10 - @@ -402,11 +324,6 @@ Construction of arteriovenous fistula 2006-05-04T18:13:51.0 - - ODS - ABC123 - Dr Foster - RR1+ ABC123 @@ -467,15 +384,7 @@ Another Hospital - 100 - 200 - 300 - 400 - HOSP - 1 - Y - 1 - 2006-05-04T18:13:51.0 + INCENTRE 2006-05-04T18:13:51.0 3343433432234 diff --git a/sample_files/ukrdc/minimalDemographics.xml b/sample_files/ukrdc/minimalDemographics.xml index 32d0ba5..ef6a0e3 100644 --- a/sample_files/ukrdc/minimalDemographics.xml +++ b/sample_files/ukrdc/minimalDemographics.xml @@ -1,5 +1,5 @@ - ABC123 + ABC123 UKRDC diff --git a/schema/rrtf/RRTF_4.xsd b/schema/rrtf/RRTF_4.xsd index e0289aa..edf6104 100644 --- a/schema/rrtf/RRTF_4.xsd +++ b/schema/rrtf/RRTF_4.xsd @@ -1688,6 +1688,116 @@ + + + + + + Non-melanoma skin cancer, BCC, SCC + + + + + + + Melanoma + + + + + + + Breast + + + + + + + Upper GI (oesophagus/stomach) + + + + + + + Lower GI (small/large bowel) + + + + + + + Lung + + + + + + + Urological NOT prostate + + + + + + + Prostate + + + + + + + Testicular + + + + + + + Leukaemia + + + + + + + Lymphoma + + + + + + + Myeloma + + + + + + + CNS Tumour + + + + + + + Musculo-skeletal + + + + + + + Other + + + + + + @@ -3593,6 +3703,37 @@ + + + + RR_DATE_FIRST_CKD1 + + + + + + RR_DATE_FIRST_CKD2 + + + + + + RR_DATE_FIRST_CKD3 + + + + + + RR_DATE_FIRST_CKD4 + + + + + + RR_DATE_FIRST_CKD5 + + + @@ -3654,14 +3795,12 @@ Pre dialysis Creatinine at 1st RRT / ERF treatment - - @@ -4073,7 +4212,7 @@ - + @@ -4970,6 +5109,8 @@ + + diff --git a/schema/ukrdc/Allergies/Allergy.xsd b/schema/ukrdc/Allergies/Allergy.xsd index 9858141..eb14c6a 100644 --- a/schema/ukrdc/Allergies/Allergy.xsd +++ b/schema/ukrdc/Allergies/Allergy.xsd @@ -5,42 +5,70 @@ + + + Allergies. This item should not be submitted without checking with the UKRR. + + Substance to which the patient is allergic. (SNOMED) + Type of Allergy (HL7 00204) + Severity (HL7 00206) + Diagnosing Clinician - allergy.discoverytime + Reported Date - allergy.confirmedtime + Confirmed Time - allergy.commenttext + + Advice given to the patient @@ -51,13 +79,19 @@ - allergy.inactivetime + Resolved Time - allergy.freetextallergy + AL1-5 Free text definition of what happened @@ -68,7 +102,10 @@ - allergy.qualifyingdetails + Details if patient or family reported diff --git a/schema/ukrdc/Assessments/Assessment.xsd b/schema/ukrdc/Assessments/Assessment.xsd new file mode 100644 index 0000000..ede3e72 --- /dev/null +++ b/schema/ukrdc/Assessments/Assessment.xsd @@ -0,0 +1,94 @@ + + + + + UKRRv5 + + + + + + + + UKRRv5 + + The Date the Assessment Started + + + + + + UKRRv5 + + The Date the Assessment Ended + + + + + + UKRRv5 + + Assessment Type + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + UKRRv5 + + Assessment Outcome + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/schema/ukrdc/CHANGELOG.md b/schema/ukrdc/CHANGELOG.md index 36b0b46..0641f0c 100644 --- a/schema/ukrdc/CHANGELOG.md +++ b/schema/ukrdc/CHANGELOG.md @@ -1,5 +1,50 @@ # Changelog +## 4.2.0 - 2024-02-26 +### Changed +- Restricted Treatment/VisitDescription to 255 characters +- Increased ResultItem/ResultValue to 30 characters +- Increased Observation/ObservationValue to 30 characters +- Amended Medication UoM to use CF_RR23 type. +- Remove EnteredBy from Procedure +- Allow Multiple PRD/CoD Records +- Make ObservationTime mandatory on ResultItem/Observation + +## 4.1.3 - 2023-12-22 +### Changed +- Remove maxOccurs from PatientNumbers to fix PyXB + +## 4.1.0 - 2023-08-13 +### Changed +- Added Missing EDTA2 PRD Codes +- Added Missing Admisssion Reason Codes +- Reduced Admission Reason Description to 100 characters to match database. +- Changed Mandatory fields in DialysisPrescription +- Modified Diagnosis to allow LOCAL/ICD-10 CodingStandards + +## 4.0.0 - 2023-06-13 +### Added +- Assessment Element Type +- Dialysis Prescription Element Type + +### Changed +- Amended RenalDiagnosis / CauseOfDeath to support Primary/Secondary diagnoses. +- Amended Diagnosis / RenalDiagnosis to allow for refuted or "negative" diagnoses. +- Amended Diagnosis / RenalDiagnosis to allow whether a Biopsy was used to arrive at the diagnosis. +- Amended DialysisSession to remove items not in V5. +- Amended Treatment to remove items not in V5. +- Added V5 Treatment Modality Codes. + + + +### 3.4.5 - 2023-06-14 +### Changed +- Version increment for package build. + +### 3.4.0 - 2023-06-14 +### Changed +- Add ug to the RR23 enumeration. + ## 3.3.0 - 2021-12-16 ### Changed - Add to Clinician/Location Enumeration to support PV diff --git a/schema/ukrdc/ClinicalRelationships/ClinicalRelationship.xsd b/schema/ukrdc/ClinicalRelationships/ClinicalRelationship.xsd index 5c0bddd..23ab271 100644 --- a/schema/ukrdc/ClinicalRelationships/ClinicalRelationship.xsd +++ b/schema/ukrdc/ClinicalRelationships/ClinicalRelationship.xsd @@ -3,24 +3,36 @@ + + + + - clinicalrelationship.fromtime + + Start of the relationship - clinicalrelationship.totime + + End of the relationship - + + + + - + + + + diff --git a/schema/ukrdc/Diagnoses/CauseOfDeath.xsd b/schema/ukrdc/Diagnoses/CauseOfDeath.xsd index df73492..de49251 100644 --- a/schema/ukrdc/Diagnoses/CauseOfDeath.xsd +++ b/schema/ukrdc/Diagnoses/CauseOfDeath.xsd @@ -3,32 +3,94 @@ + + + + - + - causeofdeath.diagnosistype + + + + + + + Primary + + + + + Secondary + + + + + Other + + + + - - - Clinician Coding Death - - - + + Coded Caused of Death (EDTA) - causeofdeath.comments + + Free text about the Diagnosis + + + + The verification status to support or decline the clinical status of the condition or diagnosis. + + + + + + Unconfirmed + + + + + Provisional + + + + + Differential + + + + + Confirmed + + + + + Refuted + + + + + Entered in Error + + + + + - causeofdeath.enteredon + + The date the COD was recorded in the medical record. diff --git a/schema/ukrdc/Diagnoses/Diagnosis.xsd b/schema/ukrdc/Diagnoses/Diagnosis.xsd index e499112..9d4b055 100644 --- a/schema/ukrdc/Diagnoses/Diagnosis.xsd +++ b/schema/ukrdc/Diagnoses/Diagnosis.xsd @@ -1,42 +1,59 @@ - - + + + + + + + + National Clinicial code where possible or other local code if not. - + + SNOMED CT coded diagnoses. This should also include any diagnosis that has been submitted elsewhere as a Primary Renal Diagnosis. + + + + Was a biopsy performed to arrive at this Diagnosis + + + Free text about the Diagnosis + Date of initial diagnosis + Date condition began. + The verification status to support or decline the clinical status of the condition or diagnosis. @@ -76,20 +93,17 @@ + The date the diagnosis was recorded in the medical record. + This is used to associate a Diagnosis with the activity in a particular Encounter record. This element should not be submitted without prior discussion with the UKRR. - - - National code for the hospital providing care - e.g. RXF01 - - diff --git a/schema/ukrdc/Diagnoses/RenalDiagnosis.xsd b/schema/ukrdc/Diagnoses/RenalDiagnosis.xsd index bdf6f09..5289db6 100644 --- a/schema/ukrdc/Diagnoses/RenalDiagnosis.xsd +++ b/schema/ukrdc/Diagnoses/RenalDiagnosis.xsd @@ -2,44 +2,120 @@ + + + + + - + - renaldiagnosis.diagnosistype + + + + + + + Primary + + + + + Secondary + + + + + Other + + + + Clinician Coding Diagnosis - + + Coded Primary Renal Diagnosis + + + + Was a biopsy performed to arrive at this Diagnosis + + + Free text about the Diagnosis - renaldiagnosis.identificationtime + + Date of initial diagnosis - renaldiagnosis.onsettime + + Date condition began. + + + + The verification status to support or decline the clinical status of the condition or diagnosis. + + + + + + Unconfirmed + + + + + Provisional + + + + + Differential + + + + + Confirmed + + + + + Refuted + + + + + Entered in Error + + + + + - renaldiagnosis.enteredon + + The date the diagnosis was recorded in the medical record. diff --git a/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd b/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd new file mode 100644 index 0000000..eefda60 --- /dev/null +++ b/schema/ukrdc/DialysisPrescriptions/DialysisPrescription.xsd @@ -0,0 +1,54 @@ + + + + + UKRRv5 + + + + + + + + The date the Dialysis Prescription was created. + + + + + + Time the Period the Dialysis Prescription Applies To Starts + + + + + + Time the Period the Dialysis Prescription Applies To Ends + + + + + + Session Type (Same as QHD41) + + + + + + Number of Dialysis Sessions per Week + + + + + + Time Dialysed (Minutes) + + + + + + Vascular Access to Use (QHD20) + + + + + \ No newline at end of file diff --git a/schema/ukrdc/DialysisSessions/DialysisSession.xsd b/schema/ukrdc/DialysisSessions/DialysisSession.xsd index 431c451..7c77fc6 100644 --- a/schema/ukrdc/DialysisSessions/DialysisSession.xsd +++ b/schema/ukrdc/DialysisSessions/DialysisSession.xsd @@ -11,211 +11,36 @@ + + + + - - - - - - Symptomatic hypotension - - - - - Vascular Access Used (RR02) - - - - - - Non-Tunneled Line - - - - - Tunneled Line - - - - - Arteriovenous Fistula - - - - - Arteriovenous Graft - - - - - Vein Loop - - - - - PD Catherer - - - - - PD Embedded Catherer - - - - - PD Catherer Temp - - - - - HeRO Graft - - - - - - - - Vascular Access Site (RR41) - - - - - - Brachio-Basilic - - - - - Brachio-Cephalic - - - - - Axillary Vein Line - - - - - Femoral Vein Line - - - - - Intenal Jugular Line - - - - - Subclavian Line - - - - - Popliteal-Long Saphenous - - - - - Radio-Cephalic Wrist - - - - - Radio-Ulnar - - - - - Radio-Cephalic Snuff Box - - - - - Brachio-Basilic and Transposition - - - - - Popliteal-Long Saphenous and Transposition - - - - - Ankle - - - - - Ulna-Cephalic - - - - - Forearm NOS - - - - - Other - - - - - Thigh NOS - - - - - - - - Access in two sites simultaneously - - - - - Blood Flow Rate - - - - - Time Dialysed in Minutes - - - - - Sodium in Dialysate - - - - - Needling Method (RR50) - - - - - - Rope Ladder - - - - - Button Hole - - - - - Unknown - - - - - - - + + + + Symptomatic hypotension (QHD19) + + + + + + Vascular Access Used (QHD20) + + + + + + Vascular Access Site (QHD21) + + + + + + Time Dialysed in Minutes (QHD31) + diff --git a/schema/ukrdc/Documents/Document.xsd b/schema/ukrdc/Documents/Document.xsd index 8318dfc..b0a86e2 100644 --- a/schema/ukrdc/Documents/Document.xsd +++ b/schema/ukrdc/Documents/Document.xsd @@ -1,76 +1,92 @@ - - - - - - - - - Document Creation - - - - - The body of the document as plain text - - - - - For future use. - - - - - The person responsibile for the content of the document - - - - - Document title - - - - - - - - - - ACTIVE or INACTIVE - - - - - Person entering the document as a National Clinicial code where possible or other local code if not. - - - - - Location the document was created at. Use National coding e.g. RXF01 - - - - - The MIME type of the data if supplied as a stream. - - - - - The filename of the document - - - - - This property is used when the Document is binary data, e.g DOC, PDF, JPG - - - - - URL to the document if notetext/stream is not supplied. - - - - - + + + + + + + + + + + + + + Document Creation + + + + + + The body of the document as plain text + + + + + + For future use. + + + + + + The person responsibile for the content of the document + + + + + + Document title + + + + + + + + + + + ACTIVE or INACTIVE + + + + + + Person entering the document as a National Clinicial code where possible or other local code if not. + + + + + + Location the document was created at. Use National coding e.g. RXF01 + + + + + + The MIME type of the data if supplied as a stream. + + + + + + The filename of the document + + + + + + This property is used when the Document is binary data, e.g DOC, PDF, JPG + + + + + + URL to the document if notetext/stream is not supplied. + + + + + diff --git a/schema/ukrdc/Encounters/Encounter.xsd b/schema/ukrdc/Encounters/Encounter.xsd index 14e1d2e..fbec6f9 100644 --- a/schema/ukrdc/Encounters/Encounter.xsd +++ b/schema/ukrdc/Encounters/Encounter.xsd @@ -4,10 +4,15 @@ + + + + + General Encounter Type (PV1-2) @@ -67,51 +72,61 @@ + Time that encounter starts + Time that encounter ends + Responsible Clinician as a National Clinicial code where possible or other local code if not. + Parent renal unit as national ODS code (e.g. RXF01) + Reason for change of care + Parent renal unit as national ODS code (e.g. RXF01) + Reason for Discharge (Transplant, Removed from List etc.) + Parent renal unit as national ODS code (e.g. RXF01) + National code for the hospital providing care - e.g. RXF01 + Details of validation e.g. Date Done, by whom, who provided the info diff --git a/schema/ukrdc/Encounters/TransplantList.xsd b/schema/ukrdc/Encounters/TransplantList.xsd index d872d8d..6775a30 100644 --- a/schema/ukrdc/Encounters/TransplantList.xsd +++ b/schema/ukrdc/Encounters/TransplantList.xsd @@ -1,107 +1,122 @@ - - - - - - - - - - - General Encounter Type (PV1-2) - - - - - - Emergency - - - - - Inpatient - - - - - Outpatient - - - - - N/A - - - - - ? - - - - - Pre-Admit - - - - - ? - - - - - - - - Start of Registration - - - - - End of Registration - - - - - Responsible Clinician as a National Clinicial code where possible or other local code if not. - - - - - Transplant Unit - - - - - Type of Organ - - - - - Referring Unit - - - - - Registration End Status - - - - - Parent renal unit as national ODS code (e.g. RXF01) - - - - - National code for the hospital providing care - e.g. RXF01 - - - - - Details of validation e.g. Date Done, by whom, who provided the info - - - - - + + + + + + + + + + + + + + + + General Encounter Type (PV1-2) + + + + + + Emergency + + + + + Inpatient + + + + + Outpatient + + + + + N/A + + + + + ? + + + + + Pre-Admit + + + + + ? + + + + + + + + + Start of Registration + + + + + + End of Registration + + + + + + Responsible Clinician as a National Clinicial code where possible or other local code if not. + + + + + + Transplant Unit + + + + + + Type of Organ + + + + + + Referring Unit + + + + + + Registration End Status + + + + + + Parent renal unit as national ODS code (e.g. RXF01) + + + + + + National code for the hospital providing care - e.g. RXF01 + + + + + + Details of validation e.g. Date Done, by whom, who provided the info + + + + + diff --git a/schema/ukrdc/Encounters/Treatment.xsd b/schema/ukrdc/Encounters/Treatment.xsd index cbeb1ec..19a5c07 100644 --- a/schema/ukrdc/Encounters/Treatment.xsd +++ b/schema/ukrdc/Encounters/Treatment.xsd @@ -7,232 +7,115 @@ + + + + - treatment.encounternumber + + - - - treatment.encountertype - General Encounter Type (PV1-2) - - - - - - Emergency - - - - - Inpatient - - - - - N/A - - - - - ? - - - - - Pre-Admit - - - - - ? - - - - - Reoccuring Patient - - - - - Obstetrics - - - - - Commercial Account - - - - - Unknown - - - - - - treatment.fromtime + + Start of Treatment (TXT00) - treatment.totime + + End of Treatment (TXT01) + Responsible Clinician as a National Clinicial code where possible or other local code if not. + Treatment Centre (TXT20) + Modality + Prior Main Renal Unit + Reason for Discharge + Destination Main Renal Unit + National code for the hospital providing care - e.g. RXF01 - + - treatment.visitdescription + + Free text about the Treatment record. + + + + + - - - - treatment.hdp01 - Times Per Week - - - - - treatment.hdp02 - Time Dialysed in Minutes - - - - - treatment.hdp03 - Blood Flow Rate - - - - - treatment.hdp04 - Sodium in Dialysate - - - treatment.qbl05 - HD Treatment Location (RR8) + + + HD Treatment Location (RR8) AKA TXT21 - - - Hospital Dialysis Unit - - - - - Satellite Dialysis Unit - - Home Dialysis - - - - - - treatment.qbl06 - HD Shared Care (RR21) - - - - - treatment.qbl07 - Patient Participation - - - - - treatment.erf61 - Assessed for suitability for Transplant by start of Dialysis Date. This should only be supplied for the First RRT Treatment. (RR13) - - - - - - Unsuitable - - - + - Working Up or under discussion + Treatment occurs In-centre - + - On Transplant List - - - - - Suspended on Transplant List - - - - - Not Assessed by Start of Dialysis + Treatment is assisted by a paid carer - - - treatment.pat35 - Date of referral to renal team (i.e. date letter received) - - diff --git a/schema/ukrdc/FamilyHistories/FamilyHistory.xsd b/schema/ukrdc/FamilyHistories/FamilyHistory.xsd index bd73638..02ad586 100644 --- a/schema/ukrdc/FamilyHistories/FamilyHistory.xsd +++ b/schema/ukrdc/FamilyHistories/FamilyHistory.xsd @@ -1,42 +1,52 @@ - - - - - - - - - - Family member - - - - - Diagnosis on family member - - - - - - - - - - - - - - - Beginning of period covered - - - - - End of period covered - - - - - + + + + + + + + + + + + + + + Family member + + + + + + Diagnosis on family member + + + + + + + + + + + + + + + + + + Beginning of period covered + + + + + + End of period covered + + + + + diff --git a/schema/ukrdc/LabOrders/LabOrder.xsd b/schema/ukrdc/LabOrders/LabOrder.xsd index fb040b5..67fafcf 100644 --- a/schema/ukrdc/LabOrders/LabOrder.xsd +++ b/schema/ukrdc/LabOrders/LabOrder.xsd @@ -10,10 +10,12 @@ - - + + + + - + @@ -21,16 +23,28 @@ + + + UKRRv4,UKRRv5,PKB,RADAR + + + + + UKRRv4,UKRRv5,PKB,RADAR + Location or Facility receiving/performing the order. - laborder.placerid - ORC:2 Placer's Order Id + + + UKRRv4,UKRRv5,PKB,RADAR + + ORC:2 Placer (Hospital)'s Order Id @@ -40,7 +54,10 @@ - laborder.fillerid + + + UKRRv4,UKRRv5,PKB,RADAR + ORC:3 Filler (Lab)'s Order Id @@ -49,33 +66,46 @@ - + - ORC:12 Requesting Physician as a nationally coded person. Use the description if this is not coded. + + UKRRv4,UKRRv5,PKB,RADAR + + Requesting Location (as in Hospital, GP, etc.) + + UKRRv4,UKRRv5,PKB,RADAR + OBR:4 Service Id - the identity of the test ordered. - laborder.specimencollectedtime + + + UKRRv4,UKRRv5,PKB,RADAR + OBR:22 - laborder.specimenreceivedtime + + + UKRRv4,UKRRv5,PKB,RADAR + OBR:14 - laborder.status - + + + @@ -86,7 +116,8 @@ - laborder.specimensource + + OBR:15.1 e.g. serum, blood @@ -97,42 +128,52 @@ - laborder.duration + + OBR:27.3 + In patient / out patient - equivalent to PV1:2 Patient Class - laborder.enteredon + + Date Order entered - + + - + + - + + + UKRRv4,UKRRv5,PKB,RADAR + + + - resultitem.resulttype + AT @@ -143,13 +184,16 @@ - resultitem.enteredon - + + - resultitem.prepost + + UKRRv4,UKRRv5,PKB,RADAR + + Was the sample taken PRE or POST dialysis @@ -179,12 +223,15 @@ + + UKRRv4,UKRRv5,PKB,RADAR + Test Code (OBX:3) - resultitem.subid + Sub-Test Id (OBX:4) @@ -195,18 +242,24 @@ - resultitem.resultvalue + + UKRRv4,UKRRv5,PKB,RADAR + + OBX:5 - + - resultitem.resultvalueunits + + UKRRv4,UKRRv5,PKB,RADAR + + OBX:6 @@ -217,7 +270,9 @@ - resultitem.referencerange + + UKRRv4,UKRRv5,PKB,RADAR + OBX:7 @@ -228,7 +283,10 @@ - resultitem.interpretationcodes + + UKRRv4,UKRRv5,PKB,RADAR + + Interpretation Codes (OBX:8) @@ -253,7 +311,7 @@ - resultitem.status + OBX:11 @@ -276,15 +334,15 @@ - + - resultitem.observationtime + OBX:14 - resultitem.commenttext + From NTE:3 @@ -295,8 +353,8 @@ - resultitem.referencecomment - + + diff --git a/schema/ukrdc/Medications/Medication.xsd b/schema/ukrdc/Medications/Medication.xsd index 062f4e2..4ace4a8 100644 --- a/schema/ukrdc/Medications/Medication.xsd +++ b/schema/ukrdc/Medications/Medication.xsd @@ -1,15 +1,22 @@ + + + + + + - medication.prescriptionnumber - Prescription Id + + + Prescription ID @@ -19,28 +26,27 @@ - medication.fromtime + + Start Time of the prescription - medication.totime + + End Time of the prescription - - - Prescriber - National Id - - + Where the Medicine was Prescribed + Medication Route @@ -73,7 +79,8 @@ - medication.frequency + + Frequency @@ -84,7 +91,8 @@ - medication.commenttext + + Other instructions @@ -95,14 +103,16 @@ - medication.dosequantity + + Dose - + - medication.indication + + The condition or problem for which the drug is being prescribed @@ -113,6 +123,7 @@ + This is used to associate the prescribing of a Medication with the activity in a particular Encounter record. This element should not be submitted without prior discussion with the UKRR. diff --git a/schema/ukrdc/Observations/Observation.xsd b/schema/ukrdc/Observations/Observation.xsd index aa5e888..bbaa7ad 100644 --- a/schema/ukrdc/Observations/Observation.xsd +++ b/schema/ukrdc/Observations/Observation.xsd @@ -12,10 +12,15 @@ + + + + - + - observation.observationtime + + When the Observation was made @@ -27,7 +32,8 @@ - observation.observationcodestd + + @@ -38,7 +44,8 @@ - observation.observationcode + + @@ -49,7 +56,8 @@ - observation.observationdesc + + @@ -63,18 +71,20 @@ - observation.observationvalue + + - + - observation.observationunits + + @@ -85,7 +95,8 @@ - observation.prepost + + Was the Observation made PRE or POST dialysis @@ -115,7 +126,8 @@ - observation.commenttext + + @@ -124,11 +136,6 @@ - - - Requesting Physician as a nationally coded person. Use the description if this is not coded. - - diff --git a/schema/ukrdc/OptOuts/OptOut.xsd b/schema/ukrdc/OptOuts/OptOut.xsd index 3f513bc..257f04f 100644 --- a/schema/ukrdc/OptOuts/OptOut.xsd +++ b/schema/ukrdc/OptOuts/OptOut.xsd @@ -3,24 +3,32 @@ + + + + + Person entering the consent as a National Clinicial code where possible or other local code if not. + National code for the trust recording the opt-out - e.g. RXF01 + Name of RDG or study + Free text @@ -31,11 +39,13 @@ + Date of Withdrawal + Date Withdrawal Ended diff --git a/schema/ukrdc/Patient.xsd b/schema/ukrdc/Patient.xsd index 2d5c38f..338f72a 100644 --- a/schema/ukrdc/Patient.xsd +++ b/schema/ukrdc/Patient.xsd @@ -1,26 +1,32 @@ + + + + - - - - + - Every Patient should have one MRN type PatientNumber. This should be the primary identifier for the Patient in the sending system and typically not change. If a National Identifier (such as NHS Number) is used as the MRN it should also be submitted as an NI type PatientNumber. - + + UKRRv4,UKRRv5 + + Patient Numbers + + Names + @@ -31,6 +37,9 @@ + + Addresses + @@ -42,7 +51,7 @@ - Only 1 of each type should be sent. This must only be used for the Patient's own Contact Details and not those of third parties. + Only 1 of each type should be sent. This must only be used for the Patient's own Contact Details and not those of third parties. This should not be submitted for patients who are only being sent as part of the UKRR data collection. diff --git a/schema/ukrdc/Procedures/Procedure.xsd b/schema/ukrdc/Procedures/Procedure.xsd index 8443a26..b1a79d4 100644 --- a/schema/ukrdc/Procedures/Procedure.xsd +++ b/schema/ukrdc/Procedures/Procedure.xsd @@ -4,27 +4,21 @@ + + + + At least code must be entered - - - National Clinicial code where possible or other local code if not. - - The time the Procedure started. - - - Person entering the diagnosis as a National Clinicial code where possible or other local code if not. - - Location the procedure was performed at. Use National coding e.g. RXF01 diff --git a/schema/ukrdc/ProgramMemberships/ProgramMembership.xsd b/schema/ukrdc/ProgramMemberships/ProgramMembership.xsd index 417774b..f8dd936 100644 --- a/schema/ukrdc/ProgramMemberships/ProgramMembership.xsd +++ b/schema/ukrdc/ProgramMemberships/ProgramMembership.xsd @@ -3,19 +3,26 @@ + + + + + Person entering the consent as a National Clinicial code where possible or other local code if not. + National code for the trust recording the consent - e.g. RXF01 + Name of RDG or study @@ -26,6 +33,7 @@ + Free text @@ -36,11 +44,13 @@ + Date Consent Given + Date Consent Withdrawn diff --git a/schema/ukrdc/README.md b/schema/ukrdc/README.md index c803c69..b31d7e5 100644 --- a/schema/ukrdc/README.md +++ b/schema/ukrdc/README.md @@ -6,7 +6,7 @@ [Schema Documentation](https://renalregistry.atlassian.net/wiki/spaces/UD/overview) -[File Transfer Instructions](https://renalregistry.atlassian.net/wiki/spaces/UD/pages/2044133823/UKRDC+File+Transmission) +[Building a Renal Unit to UKRDC Feed](https://renalregistry.atlassian.net/wiki/spaces/UD/pages/2383118357/Building+a+Renal+Unit+to+UKRDC+Feed) ## Technical References diff --git a/schema/ukrdc/SocialHistories/SocialHistory.xsd b/schema/ukrdc/SocialHistories/SocialHistory.xsd index 2c2e96c..ca5f2f6 100644 --- a/schema/ukrdc/SocialHistories/SocialHistory.xsd +++ b/schema/ukrdc/SocialHistories/SocialHistory.xsd @@ -1,14 +1,19 @@ - - - - - - - Social Habits - - - - - + + + + + + + + + + + + Social Habits + + + + + diff --git a/schema/ukrdc/Surveys/Survey.xsd b/schema/ukrdc/Surveys/Survey.xsd index 653f6f7..643be8b 100644 --- a/schema/ukrdc/Surveys/Survey.xsd +++ b/schema/ukrdc/Surveys/Survey.xsd @@ -1,10 +1,13 @@ - - - - + + + + + + + @@ -17,6 +20,10 @@ + + + + @@ -28,6 +35,10 @@ + + + + @@ -38,66 +49,70 @@ - - - - - When the survey was completed. - - - - - Survey Type - - - - - - - - - - - - - - - - - - - - - - - - - - Who completed the survey - - - - - Where the Survey was completed - - + + + + + + + + + When the survey was completed. + + + + + Survey Type + + + + + + + + + + + + + + + + + + + + + + + + + + Who completed the survey + + + + + Where the Survey was completed + + - - - Current Modality - - - - - If Current Modality = HD, where is it performed? - - - - - This is currently only used to flag surveys which were submitted via the SharedHD project. Another field may be more appropriate. - - - - - + + + Current Modality + + + + + If Current Modality = HD, where is it performed? + + + + + This is currently only used to flag surveys which were submitted via the SharedHD project. Another field may be more appropriate. + + + + + diff --git a/schema/ukrdc/Transplants/Transplant.xsd b/schema/ukrdc/Transplants/Transplant.xsd index f204db8..f271b19 100644 --- a/schema/ukrdc/Transplants/Transplant.xsd +++ b/schema/ukrdc/Transplants/Transplant.xsd @@ -2,230 +2,70 @@ - + + + + + - - - - - - transplant.tra64 - Failure Date - - - - - transplant.tra65 - Cause of Failure (RR10) - - - - - - Hyperacute Rejection - - - - - Non-Viable Transplant Kidney - - - - - Primary Non-Function of Transplant Kidney - - - - - Acute Rejection - - - - - Chronic Allograft Nephropathy - - - - - Rejection following withdrawal of immunosuppression - non Medical Reason - - - - - Rejection following withdrawal of immunosuppression - Medical Reason - - - - - - - - transplant.tra66 - Description of Failure - - - - - transplant.tra69 - Date graft nephrectomy if graft failed - - - - - transplant.tra76 - Graft Type (RR24) - - - - - transplant.tra77 - NHSBT Type - - - - - - - - - - - - transplant.tra78 - rCMV - Recipient CMV status at transplant - - - - - transplant.tra79 - rEBV - Recipient EBV status at transplant - - - - - transplant.tra80 - Donor age - - - - - transplant.tra8a - Donor sex - - - - - transplant.tra81 - rCMV - Donor CMV status at transplant - - - - - transplant.tra82 - rEBV - Donor CMV status at transplant - - - - - transplant.tra83 - Mismatch A - - - - - transplant.tra84 - Mismatch B - - - - - transplant.tra85 - Mismatch DR - - - - - transplant.tra86 - ABO compatible - - - - - transplant.tra87 - Plasma exchange - - - - - transplant.tra88 - Immunoadsorption - - - - - transplant.tra89 - Rituximab - - - - - transplant.tra90 - IV immunoglobulin - - - - - transplant.tra91 - Cold ischaemic time in hours - - - - - transplant.tra92 - Primary function - - - - - transplant.tra93 - Anticoagulation (RR15) - - - - - transplant.tra94 - CMV prophylaxis (RR16) - - - - - transplant.tra95 - Pneumocystis prophylaxis (RR17) - - - - - transplant.tra96 - Functioning - - - - - transplant.tra97 - Other organ transplanted simultaneously 1 (RR14) - - - - - transplant.tra98 - Other organ transplanted simultaneously 2 (RR14) - - - - + + + + + NHSBT Type + + + + + + + + + + + + + + Date Registered for Transplantation + + + + + + + Failure Date + + + + + + + Cold ischaemic time in Minutes + + + + + + + Mismatch A + + + + + + + Mismatch B + + + + + + + Mismatch DR + diff --git a/schema/ukrdc/Types/Address.xsd b/schema/ukrdc/Types/Address.xsd index 4d3d3d5..a4b2864 100644 --- a/schema/ukrdc/Types/Address.xsd +++ b/schema/ukrdc/Types/Address.xsd @@ -52,14 +52,14 @@ - + - + diff --git a/schema/ukrdc/Types/CF_EDTA_PRD.xsd b/schema/ukrdc/Types/CF_EDTA_PRD.xsd index 3132814..5e504d6 100644 --- a/schema/ukrdc/Types/CF_EDTA_PRD.xsd +++ b/schema/ukrdc/Types/CF_EDTA_PRD.xsd @@ -1705,6 +1705,51 @@ Glomerulonephritis - No Histology + + + Focal segmental glomerulosclerosis (FSGS) secondary to HIV + + + + + Focal segmental glomerulosclerosis (FSGS) secondary to lithium + + + + + Focal segmental glomerulosclerosis (FSGS) secondary to sickle cell + + + + + Renal papillary necrosis caused by diabetes + + + + + Renal papillary necrosis caused by analgesics + + + + + Renal papillary necrosis caused by sickle cell + + + + + Kidney stones due to ARPT deficiency + + + + + Infiltration by lymphoma - histologically proven + + + + + Nephropathy due to pre-eclampsia + + Systemic vasculitis - ANCA negative - no histology @@ -2857,7 +2902,7 @@ -  Chronic kidney disease following excision of renal neoplasm (disorder) + Chronic kidney disease following excision of renal neoplasm (disorder) diff --git a/schema/ukrdc/Types/CF_RR23.xsd b/schema/ukrdc/Types/CF_RR23.xsd index 60fcc75..526d5be 100644 --- a/schema/ukrdc/Types/CF_RR23.xsd +++ b/schema/ukrdc/Types/CF_RR23.xsd @@ -36,6 +36,11 @@ Miligrams + + + Micrograms + + diff --git a/schema/ukrdc/Types/CF_RR7_Discharge.xsd b/schema/ukrdc/Types/CF_RR7_Discharge.xsd index 9068e18..7efef3b 100644 --- a/schema/ukrdc/Types/CF_RR7_Discharge.xsd +++ b/schema/ukrdc/Types/CF_RR7_Discharge.xsd @@ -11,67 +11,59 @@ - - Graft Failure + Kidney Transplant Failure - - Patient transferred Out + Patient Transferred Out - - + - ARF - Recovered + Treatment Stopped (Renal Function Recovered) - - + - ARF - Stopped Dialysis (without recovery of function) + Treatment Stopped (Without Recovery of Function) - - + - ARF - Transferred Out + Patient - Lost to follow-up - - + + - Patient - Renal Function Recovered + ARF - Recovered - - + - Patient - Treatment Stopped (Without Recovery of Function) + ARF - Stopped Dialysis (without recovery of function) - + - Conservative Management - Treatment stopped without recovery + ARF - Transferred Out - - + - Patient - Lost to follow-up + Conservative Management - Treatment stopped without recovery - - + diff --git a/schema/ukrdc/Types/CF_RR7_Treatment.xsd b/schema/ukrdc/Types/CF_RR7_Treatment.xsd index 8b679f7..eca1478 100644 --- a/schema/ukrdc/Types/CF_RR7_Treatment.xsd +++ b/schema/ukrdc/Types/CF_RR7_Treatment.xsd @@ -26,21 +26,11 @@ Haemodiafiltration - - - Haemodialysis > 4 days per week / daily - - Ultrafiltration - - - Haemodialysis - type unknown - - CAPD Connect @@ -81,149 +71,200 @@ Assisted Cycling PD >= 6 nights/week wet (day dwell) - + - Peritoneal Dialysis - Type Unknown + Transplant; Cadaver Donor - + - Transplant; Cadaver Donor + Transplant; Live Donor - + - Transplant; Live Related - Sibling + Transplant; Type Unknown - + - Transplant; Live Related - Parent or Child + Transplant Clinic Followup - + - Transplant; Live Related - Other + Acute Kidney Injury - Haemodialysis - + - Transplant; Live Genetically Unrelated + Acute Kidney Injury - Haemofiltration - + - Transplant; Cadaver + Transp Other Organ + Acute Kidney Injury - Peritoneal Dialysis - + - Transplant; Live Donor + Transp Other Organ + Acute Kidney Injury receiving RRT not by renal service - + - Transplant; Live donor Non-UK Transplant + First Assessment by Renal Service - + - Transplant; Non-Heart-beating Donor + Conservative Management - Mutual decision not to offer RRT - + - Transplant; Type Unknown + Conservative Management - Clinical decision not to offer RRT - + - Graft acute rejection episode - biopsy proven + Plasmapharesis / Plasma Exchange - + - Graft acute rejection episode - no biopsy + Assisted CAPD - + - Transplant : Live related - father + Assisted APD - + - Transplant : Live related - mother + Hybrid CAPD with HD - + - Transplant : Live related - child + Hybrid APD with HD - + - Acute Renal Failure not dialysed + Hybrid APD with CAPD - + - Acute Haemodialysis - ARF + CKD (Not on RRT) - + - Acute Haemofiltration - ARF + Patient - ESKD with no RRT - + - Acute Peritoneal Dialysis - ARF + Patient - CKD-advanced MDT clinic - + - Conservative Management - Mutual decision not to offer RRT + Patient - CKD-clinic follow-up - + - Conservative Management - Clinical decision not to offer RRT + Patient - CKD-remote monitoring - + + - Plasmapharesis / Plasma Exchange + Haemodialysis > 4 days per week / daily - + - Assisted CAPD + Haemodialysis - type unknown - + - Assisted APD + Peritoneal Dialysis - Type Unknown - + - Hybrid CAPD with HD + Transplant; Live Related - Sibling - + - Hybrid APD with HD + Transplant; Live Related - Parent or Child - + - Hybrid APD with CAPD + Transplant; Live Related - Other - + - CKD (Not on RRT) + Transplant; Live Genetically Unrelated + + + + + Transplant; Cadaver + Transp Other Organ + + + + + Transplant; Live Donor + Transp Other Organ + + + + + Transplant; Live donor Non-UK Transplant + + + + + Transplant; Non-Heart-beating Donor + + + + + Graft acute rejection episode - biopsy proven + + + + + Graft acute rejection episode - no biopsy + + + + + Transplant : Live related - father + + + + + Transplant : Live related - mother + + + + + Transplant : Live related - child + + + + + Acute Renal Failure not dialysed @@ -232,7 +273,7 @@ - + diff --git a/schema/ukrdc/Types/DiagnosisCodeType.xsd b/schema/ukrdc/Types/DiagnosisCodeType.xsd new file mode 100644 index 0000000..41496d4 --- /dev/null +++ b/schema/ukrdc/Types/DiagnosisCodeType.xsd @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/schema/ukrdc/Types/DrugProduct.xsd b/schema/ukrdc/Types/DrugProduct.xsd index df4b2bb..aa78208 100644 --- a/schema/ukrdc/Types/DrugProduct.xsd +++ b/schema/ukrdc/Types/DrugProduct.xsd @@ -13,7 +13,7 @@ - medication.drugproductgeneric + Generic name @@ -24,7 +24,7 @@ - medication.drugproductlabelname + Brand Name diff --git a/schema/ukrdc/Types/FamilyDoctor.xsd b/schema/ukrdc/Types/FamilyDoctor.xsd index 5f2c18e..16bf1b7 100644 --- a/schema/ukrdc/Types/FamilyDoctor.xsd +++ b/schema/ukrdc/Types/FamilyDoctor.xsd @@ -6,7 +6,7 @@ - familydoctor.gppracticeid + National GP Practice Code @@ -18,7 +18,7 @@ - familydoctor.gpid + National GP Code @@ -40,7 +40,7 @@ - familydoctor.email + GP E-mail Address diff --git a/schema/ukrdc/Types/PVData.xsd b/schema/ukrdc/Types/PVData.xsd index 0247265..e49d005 100644 --- a/schema/ukrdc/Types/PVData.xsd +++ b/schema/ukrdc/Types/PVData.xsd @@ -4,7 +4,7 @@ - pvdata.rrtstatus + @@ -15,7 +15,7 @@ - pvdata.tpstatus + @@ -26,13 +26,13 @@ - pvdata.diagnosisdate + - pvdata.bloodgroup + diff --git a/schema/ukrdc/Types/RRTypes.xsd b/schema/ukrdc/Types/RRTypes.xsd index 825859a..2b6cb89 100644 --- a/schema/ukrdc/Types/RRTypes.xsd +++ b/schema/ukrdc/Types/RRTypes.xsd @@ -1,5 +1,14 @@ + + + UKRDC Schema Version in 0.0.0 Format + + + + + + diff --git a/schema/ukrdc/Types/SendingFacility.xsd b/schema/ukrdc/Types/SendingFacility.xsd new file mode 100644 index 0000000..c04bb1c --- /dev/null +++ b/schema/ukrdc/Types/SendingFacility.xsd @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + This should be a reference for the System / Version which generated the file. The intended purpose is to allow us to identify, or temporarily rectify, issues with what a particular extract is generating. + + + + + This should be the time that the extract was generated. + + + + + This should be the version (from the XSD Schema) that the extract has been written against. This is to allow us to process incoming files accordingly as well as track which Units are submitting which version. Note that the RDA Schema version is unrelated to the UKRR Dataset version. + + + + + The batch number as used in the filenames. This should be incremented each time the extract is run, not per-patient + + + + + + \ No newline at end of file diff --git a/schema/ukrdc/UKRDC.xsd b/schema/ukrdc/UKRDC.xsd index a1d6efa..4f86a46 100644 --- a/schema/ukrdc/UKRDC.xsd +++ b/schema/ukrdc/UKRDC.xsd @@ -1,94 +1,122 @@ - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - + + + + ALL + + + The value of this element is the Site or System responsible for the data being sent. + + - + - The extract process within the facility which produced this file. + + ALL + + + The type of data feed. This is used to enable different behaviour when the original source of data was something other than a UKRDC feed (i.e. when "PV XML" is converted to "RDA XML" it is given a SendingExtract of "PV"). Unless told otherwise the value should be set to "UKRDC". + - - + - Lab Orders. These are measurements taken about a patient that have been processed by a Laboratory. Our EHR structure requires that all test results are associated with a lab order. If the details of the lab order are not received by the renal system then a generic lab order should be created to contain all results with a common sample time. + + ALL + + Patient Demographics - + - Other Health Related Behaviours. + + UKRRv4,UKRRv5,PKB,RADAR + Test + + Lab Orders + + + + + + NONE + + Other Health Related Behaviours - + - This is used to record information about conditions diagnosed in the Patient's relatives. This element should not be submitted without prior discussion with the UKRR + + NONE + + Family Histories - + - Observations. These are measurements taken about a patient that do not involve a Laboratory. + + UKRRv4,UKRRv5,PKB,RADAR + + + Observations. These are measurements taken about a patient that do not involve a Laboratory. + - Allergies + + NONE + + + Allergies. + - + @@ -97,18 +125,26 @@ + + UKRRv4,UKRRv5,PKB,RADAR + Co-Morbidities - + + + UKRRv4,UKRRv5,RADAR + Cause of Death - + - Primary Renal Diagnosis. These should be used to record the Primary Renal Disease (defined in the ERA-EDTA PRD spreadsheet, notes for users, sections: 'Description of PRD' and 'Selection of the most appropriate PRD' http://www.era-edta-reg.org/prd.jsp ) for analysis by the UKRR, SRR and ERA. In order for the data to be comparable across countries it needs to be coded in using the EDTA code lists. Consequently we expect that some conditions may appear both as PRD objects and as generic diagnoses coded in SNOMED. Patients who started RRT after 01/01/2014 should be coded using the 2012 "EDTA2" code list. Patients who started before then can continue to be submitted using the older EDTA list. Systems should not automatically convert the older codes to the newer ones as this results in a loss of accuracy. - + + UKRRv4,UKRRv5,PKB,RADAR + + Renal Diagnoses @@ -116,12 +152,30 @@ - Medications. All recorded medications should be submitted whether or not prescribed for the purposes of renal care. + + UKRRv4,UKRRv5,PKB,RADAR + + Medications + + + + + + + + + + + UKRRv5 + + Dialysis Prescriptions - + + + @@ -130,19 +184,35 @@ - - - + + + + NONE + + Procedures (not otherwise Specified) + + + + + + UKRRv4,UKRRv5 + Dialysis Sessions - Transplant Procedures.These should be used to record any Transplants. A single Procedure should be recorded for each organ being transplanted, with multiple organ transplants being identified by multiple transplants occurring on the same day. The record also contains information about the source donor for each transplant. + + UKRRv4,UKRRv5,PKB + + Transplant Procedures + + UKRRv4 + Vascular Access Constructions @@ -151,11 +221,14 @@ + + PKB + Documents - + @@ -164,16 +237,25 @@ + + PKB + This is used to record the duration of something other than a Treatment. This element should not be submitted without prior discussion with the UKRR. + + UKRRv4,UKRRv5,PKB + This is used to record the duration a Patient received a particular type of Care/Treatment at a particular Treatment Facility. It is similar in concept to the UKRR TXT records however at the end of the period it should be end-dated rather than an additional record being sent. It is possible for treatment records to overlap if a patient has multiple treatments (such as post-transplant dialysis). A treatment record should exist for any period of time where they would be considered a patient (so for example code 900 record for pre-RRT CKD and a code 94 record for post-RRT Conservative care). Details of Transplants themselves should be recorded as Procedures but Treatment records should be used to record periods of Transplant related Inpatient/Outpatient care. + + NHSBT + This is only for NHSBT supplied Transplant Waiting List data. @@ -182,47 +264,78 @@ - Program Memberships. These are used to record whether or not a patient wishes to participate in one of the UKRDC’s member projects. In the case of projects such as RADAR the Program Membership record should only be closed if the patient actively wishes to withdraw. It should not be end dated when they leave the unit or die. If a patient decides to leave a project and then re-joins a new Program Membership record should be created (with a different ExternalID) rather than re-opening the original one. + + NONE + + + Program Memberships. These are used to record whether or not a patient wishes to participate in one of the UKRDC’s member projects. In the case of projects such as RADAR the Program Membership record should only be closed if the patient actively wishes to withdraw. It should not be end dated when they leave the unit or die. If a patient decides to leave a project and then re-joins a new Program Membership record should be created (with a different ExternalID) rather than re-opening the original one. + - + + + UKRRv4,UKRRv5 + Opt-Outs - + + + NONE + This is used to record the relationship between a Patient and a Clinician or Care Facility. This element should not be submitted without prior discussion with the UKRR. - + + + NONE + Surveys - + + + + + + + + NONE + + Assessments + + + + - This is used internally to hold data items sent in PV XML files and should not be sent by external parties. + + PKB + + + This is used internally to hold data items sent in PV XML files and should not be sent by external parties. diff --git a/schema/ukrdc/VascularAccesses/VascularAccess.xsd b/schema/ukrdc/VascularAccesses/VascularAccess.xsd index 02b1330..e1f0c93 100644 --- a/schema/ukrdc/VascularAccesses/VascularAccess.xsd +++ b/schema/ukrdc/VascularAccesses/VascularAccess.xsd @@ -1,6 +1,10 @@ + + + + @@ -9,26 +13,31 @@ + Date Access first used for Dialysis + Date of Access Failure + Date of Removal + Reason for Removal of Haemodialysis Access (HD Only) (RR49) + PD Catheter Insertion Technique (PD Only) (RR143) @@ -58,6 +67,7 @@ + Reason for Removal of PD Catheter (PD Only) (RR29) diff --git a/scripts/code_importer.py b/scripts/code_importer.py new file mode 100644 index 0000000..850e2e6 --- /dev/null +++ b/scripts/code_importer.py @@ -0,0 +1,236 @@ +import csv +import argparse +import sys +import os + +import psycopg2 + +from ukrdc.database import Connection + + +class CodeUpdater(object): + def upload(self): + for row in self.rows: + self.add_row(row) + self.connection.commit() + + @property + def connection(self): + return self._connection + + @connection.setter + def connection(self, connection): + self._connection = connection + self.cursor = connection.cursor() + + def insert(self, sql, row): + try: + self.cursor.execute(sql, (row)) + except psycopg2.IntegrityError as e: + self.connection.rollback() + print("Problem with integrity " + str(e)) + except Exception: + print(sql) + print(row) + raise + + def select(self, sql, row): + try: + self.cursor.execute(sql, (row)) + return list(self.cursor.fetchall()) + except psycopg2.Error as e: + print(e) + + +class CodeList(CodeUpdater): + def __init__(self): + self.rows = [] + + def truncate(self): + sqlstring = """ + TRUNCATE TABLE CODE_LIST + """ + self.cursor.execute(sqlstring) + self.connection.commit() + + def get_row(self, *args): + sql = """ + select + coding_standard, code, description, object_type + from + extract.code_list + where + coding_standard = %s and + code = %s and + description = %s and + object_type = %s + """ + return self.insert(sql, args) + + def update(self): + for row in self.rows: + results = self.get_row(row) + if results: + print("Yes we have that row") + else: + self.update_row(row[0], row[1], row) + + def add_row(self, row): + sqlstring = """ + INSERT INTO CODE_LIST + ( + CODING_STANDARD, + CODE, + DESCRIPTION, + OBJECT_TYPE, + UNITS + ) + VALUES (%s, %s, %s, %s, %s) + """ + self.insert(sqlstring, row) + + def read_csv(self): + base_folder = "conf/pv2_codes/code_lists/" + + for filename in os.listdir(base_folder): + print(f"Reading {filename}") + fp = os.path.join(base_folder, filename) + csvreader = csv.reader(open(fp, "r", encoding="utf-8")) + + for row in csvreader: + # Get Row to expected length + row = list(row)[:5] + diff_len = 5 - len(row) + if diff_len > 0: + row = row + [None] * diff_len + if row[0] == "": + print("Empty Row, continue") + continue + self.rows.append(row) + + +class CodeMap(CodeUpdater): + def __init__(self): + self.rows = [] + + def truncate(self): + + sqlstring = """ + TRUNCATE TABLE CODE_MAP + """ + self.cursor.execute(sqlstring) + self.connection.commit() + + def add_row(self, row): + sqlstring = """ + INSERT INTO CODE_MAP + ( + SOURCE_CODING_STANDARD, + SOURCE_CODE, + DESTINATION_CODING_STANDARD, + DESTINATION_CODE + ) + VALUES(%s, %s, %s, %s)""" + self.insert(sqlstring, row) + + def read_csv(self): + # Code Conv List + + base_folder = "conf/pv2_codes/code_conv_lists/" + + for filename in os.listdir(base_folder): + fp = os.path.join(base_folder, filename) + print(fp) + csvreader = csv.reader(open(fp, "r", encoding="utf-8")) + for row in csvreader: + self.rows.append(row) + + +class SatelliteMap(CodeUpdater): + def __init__(self): + self.rows = [] + + def truncate(self): + + sqlstring = """ + TRUNCATE TABLE SATELLITE_MAP + """ + self.cursor.execute(sqlstring) + self.connection.commit() + + def add_row(self, row): + sqlstring = """ + INSERT INTO SATELLITE_MAP + ( + SATELLITE_CODE, + MAIN_UNIT_CODE + ) + VALUES(%s, %s)""" + self.insert(sqlstring, row) + + def read_csv(self): + # Satellite Mapping List + + base_folder = "conf/pv2_codes/satellite_map/" + + for filename in os.listdir(base_folder): + + fp = os.path.join(base_folder, filename) + print(fp) + csvreader = csv.reader(open(fp, "r", encoding="utf-8")) + for row in csvreader: + self.rows.append(row) + + +def main(): + + servers = ["ukrdc_dev", "ukrdc_staging", "ukrdc_live"] + + parser = argparse.ArgumentParser(description="Update codes") + parser.add_argument("--server", nargs="+", default=servers) + parser.add_argument("--upload-codelist", action="store_true") + parser.add_argument("--upload-codemap", action="store_true") + parser.add_argument("--upload-satellitemap", action="store_true") + + if not len(sys.argv) > 1: + parser.print_help() + return + args = parser.parse_args() + if args.upload_codelist: + codelist = CodeList() + codelist.read_csv() + if args.upload_codemap: + codemap = CodeMap() + codemap.read_csv() + if args.upload_satellitemap: + satellitemap = SatelliteMap() + satellitemap.read_csv() + + for server in args.server: + print(f"server: {server}") + engine = Connection.get_engine_from_file(None, server) + connection = engine.raw_connection() + print("Connected") + if args.upload_codelist: + codelist.connection = connection + print("Truncating Code List") + codelist.truncate() + print("Populating Code List") + codelist.upload() + if args.upload_codemap: + codemap.connection = connection + print("Truncating Code Map") + codemap.truncate() + print("Populating Code Map") + codemap.upload() + if args.upload_satellitemap: + satellitemap.connection = connection + print("Truncating Satellite Map") + satellitemap.truncate() + print("Uploading Satellite Map") + satellitemap.upload() + connection.close() + + +if __name__ == "__main__": + main() diff --git a/scripts/code_writer.py b/scripts/code_writer.py new file mode 100644 index 0000000..8722128 --- /dev/null +++ b/scripts/code_writer.py @@ -0,0 +1,67 @@ +# This script converts Shaun's XLS document +# Into 3 CSV files to match the table structure + +import csv +import itertools + + +def main(): + # Code List + + csvreader = csv.reader(open("C:/Temp/PV2_Test_harmonisation.csv", "r")) + + code_list = list() + code_conv_list = list() + unit_conv_list = list() + + next(csvreader) + for row in csvreader: + + test_code = row[0] + unit_code = row[1] + correct_test_code = row[3] + correct_unit_code = row[4] + record_type = row[5] + + # creatinine,µmol/l,68,creatinine,micromol/L,result, + + code_list.append(("PV", correct_test_code, None, record_type)) + if correct_test_code not in ("", None): + code_conv_list.append(("PVMIGRATION", test_code, "PV", correct_test_code)) + if correct_unit_code not in ("", None): + unit_conv_list.append(("PVMIGRATION", unit_code, "PV", correct_unit_code)) + + # Code List + code_list.sort() + code_list = list(code_list for code_list, _ in itertools.groupby(code_list)) + + csvwriter = csv.writer(open("C:/Temp/CodeList.csv", "w", newline="")) + + for row in code_list: + csvwriter.writerow(row) + + # Code Conv List + code_conv_list.sort() + code_conv_list = list( + code_conv_list for code_conv_list, _ in itertools.groupby(code_conv_list) + ) + + csvwriter = csv.writer(open("C:/Temp/CodeConvList.csv", "w", newline="")) + + for row in code_conv_list: + csvwriter.writerow(row) + + # Unit Conv List + unit_conv_list.sort() + unit_conv_list = list( + unit_conv_list for unit_conv_list, _ in itertools.groupby(unit_conv_list) + ) + + csvwriter = csv.writer(open("C:/Temp/UnitConvList.csv", "w", newline="")) + + for row in unit_conv_list: + csvwriter.writerow(row) + + +if __name__ == "__main__": + main() diff --git a/scripts/redis_code_importer.py b/scripts/redis_code_importer.py new file mode 100644 index 0000000..dcc5a1f --- /dev/null +++ b/scripts/redis_code_importer.py @@ -0,0 +1,148 @@ +import csv +import json +import os +from typing import Optional + +import redis +from sshtunnel import SSHTunnelForwarder + +from ukrdc.services.codes import Codes + +UKRDC_INSTANCE = "live_app_ssh" + +code_conv_list_path = "conf/pv2_codes/code_conv_lists/" +code_list_path = "conf/pv2_codes/code_lists/" +code_exclusion_path = "conf/pv2_codes/code_exclusions/" +satellite_map_path = "conf/pv2_codes/satellite_map/satellite_map.csv" + + +def import_codes(host: str, port: int): + r = redis.Redis(host=host, port=port, db=0) + + # Clear Existing Data + r.flushall() + + # Code Map + for filename in os.listdir(code_conv_list_path): + csvreader = csv.reader( + open(code_conv_list_path + filename, "r", newline="", encoding="utf-8") + ) + + print(f"Importing {filename}") + for row in csvreader: + source_coding_standard = row[0] + source_code = row[1] + destination_coding_standard = row[2] + destination_code = row[3] + + Codes().set_code_mapping_item( + r, + source_coding_standard, + source_code, + destination_coding_standard, + destination_code, + ) + + # Code List + for filename in os.listdir(code_list_path): + csvreader = csv.reader( + open(code_list_path + filename, "r", newline="", encoding="utf-8") + ) + + print(f"Importing {filename}") + for row in csvreader: + coding_standard = row[0] + try: + code = row[1] + except Exception: + print(filename) + print(row) + raise + + if len(row) >= 3: + description: Optional[str] = row[2] + else: + description = None + + if len(row) >= 4: + code_type: Optional[str] = row[3] + else: + code_type = None + + if len(row) >= 5: + units: Optional[str] = row[4] + else: + units = None + + key = "CODE_LIST:" + key += coding_standard + ":" + key += code + + if description: + r.hset(key, "description", description) + else: + r.hset(key, "description", code) + + if code_type: + r.hset(key, "code_type", code_type) + + if units: + r.hset(key, "units", units) + + # Code Exclusions + for filename in os.listdir(code_exclusion_path): + csvreader = csv.reader( + open(code_exclusion_path + filename, "r", newline="", encoding="utf-8") + ) + + for row in csvreader: + + coding_standard = row[0] + code = row[1] + system = row[2] + + Codes().set_code_exclusion(r, coding_standard, code, system) + + # Satellite Map + + csvreader = csv.reader(open(satellite_map_path, "r", newline="", encoding="utf-8")) + + for row in csvreader: + satellite_code = row[0] + main_unit_code = row[1] + + key = "SATELLITE_LIST:" + key += satellite_code + + r.set(key, main_unit_code) + + +if __name__ == "__main__": + + import argparse + + parser = argparse.ArgumentParser() + parser.add_argument("--local", action="store_true") + + local: bool = parser.parse_args().local + + if local: + import_codes("localhost", 6379) + + else: + + fname = os.path.expanduser("~/.config/ukrdc/services/db_conf.json") + print("Configuration File: ", fname) + with open(fname) as fhandle: + params = json.load(fhandle) + + with SSHTunnelForwarder( + (params[UKRDC_INSTANCE]["HOST"], 22), + ssh_password=params[UKRDC_INSTANCE]["PASSWORD"], + ssh_username=params[UKRDC_INSTANCE]["USER"], + remote_bind_address=("localhost", 6379), + # Make an SSH Tunnel to Redis on the chosen App Server + ) as ukrdc_redis_tunnel: + host = "localhost" + port = ukrdc_redis_tunnel.local_bind_port + import_codes(host, port) diff --git a/scripts/run_schema_report.sh b/scripts/run_schema_report.sh deleted file mode 100644 index 631e240..0000000 --- a/scripts/run_schema_report.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh -x -ssh -f -N -M -S /tmp/ukrdc_resources_socket root@10.38.181.121 -L 6000:db.ukrdc.nhs.uk:5432 -source env/bin/activate -pip install ukrdc-services -pip install ukrdc.database -pip install xlwt -pip install lxml -python scripts/schema_report.py -ssh -S /tmp/ukrdc_resources_socket -O exit xxx -exit 0 diff --git a/scripts/schema_report.py b/scripts/schema_report.py deleted file mode 100644 index 7712d05..0000000 --- a/scripts/schema_report.py +++ /dev/null @@ -1,340 +0,0 @@ -"""Produces an XLS Report comparing the UKRDC Schema to -the Repository Database""" - -import csv -import os - -from lxml import etree -import xlwt - -from ukrdc.database import Connection - -# NOTE: This may assume a PostgreSQL DB - - -def get_db_table_list(session): - sqlstring = """ - SELECT DISTINCT - A.table_name - FROM - information_schema.columns A - LEFT JOIN information_schema.tables B - ON A.table_name = B.table_name AND - A.table_schema = B.table_schema - WHERE - A.table_schema = 'extract' AND - B.table_type <> 'VIEW' - """ - - return [row[0] for row in session.execute(sqlstring)] - - -def get_db_column_metadata(session, tablename): - sqlstring = """ - SELECT - tab_columns.column_name, - data_type, - character_maximum_length, - numeric_precision, - is_nullable, - tab_constraints.constraint_type, - col_constraints.constraint_name, - col_check_constraints.check_clause - FROM - information_schema.columns AS tab_columns - LEFT OUTER JOIN - information_schema.constraint_column_usage AS col_constraints ON - tab_columns.table_name = col_constraints.table_name AND - tab_columns.column_name = col_constraints.column_name - LEFT OUTER JOIN - information_schema.table_constraints AS tab_constraints ON - tab_constraints.constraint_name = col_constraints.constraint_name - LEFT OUTER JOIN - information_schema.check_constraints AS col_check_constraints ON - col_check_constraints.constraint_name = tab_constraints.constraint_name - WHERE - tab_columns.table_name = :table_name AND - tab_columns.table_schema = 'extract' - ORDER BY ordinal_position; - """ - - results = session.execute(sqlstring, {"table_name": tablename}) - return results - - -def get_field_contents_stats(session, table_name, column_name): - - # We could add MAX/MIN/AVG here but it wouldn't make much sense - # As ResultValue/ObservationValue will be across all tests - - sql_string = ( - """ - SELECT - COUNT(*) AS ROW_COUNT, - SUM(CASE WHEN """ - + column_name - + """ IS NOT NULL THEN 1 ELSE 0 END) AS VALUE_COUNT, - COUNT(DISTINCT """ - + column_name - + """) AS DISTINCT_VALUE_COUNT - FROM - """ - + table_name - ) - - result = session.execute(sql_string) - return result.fetchone() - - -def get_coded_fields(session): - - sql_string = """ - SELECT - tab_columns.table_name, - tab_columns.column_name - FROM - information_schema.columns AS tab_columns - WHERE - tab_columns.column_name LIKE :column_name_like AND - tab_columns.table_schema = 'extract' - """ - - results = session.execute(sql_string, {"column_name_like": "%codestd"}) - return results - - -def query_coded_fields(session, table_name, column_name): - - # codestd - base_name = column_name[:-7] - - code_std_field = column_name - desc_field = base_name + "desc" - code_field = base_name + "code" - - sql_string = ( - """ - - SELECT - '""" - + table_name - + """', - '""" - + code_std_field - + """', - """ - + code_std_field - + """, - '""" - + code_field - + """', - """ - + code_field - + """, - '""" - + desc_field - + """', - """ - + desc_field - + """, - COUNT(*) - FROM - """ - + table_name - + """ - GROUP BY - """ - + code_std_field - + """, - """ - + code_field - + """, - """ - + desc_field - ) - - results = session.execute(sql_string) - return results - - -class DBMetadata(object): - def __init__(self, session, xsdpath): - self.session = session - self.xsdpath = xsdpath - - def set_db_metadata(self): - - db_metadata = dict() - - session = self.session - table_names = get_db_table_list(session) - - for table_name in table_names: - print(table_name) - db_metadata[table_name] = dict() - for row in get_db_column_metadata(session, table_name): - column_name = row[0] - field_stats = get_field_contents_stats(session, table_name, column_name) - row = list(row) - row.extend(field_stats) - db_metadata[table_name][column_name] = row - - self.db_metadata = db_metadata - - def process_xsd_file(self, fh): - ns = "http://www.w3.org/2001/XMLSchema" - xml_doc = etree.parse(fh) - appinfo_nodes = xml_doc.xpath("//xs:appinfo", namespaces={"xs": ns}) - xml_metadata = self.xml_metadata - for appinfo_node in appinfo_nodes: - appinfo_text = appinfo_node.text - # Assume value in format: - # table_name.column_name - split_appinfo_text = appinfo_text.split(".") - table_name = split_appinfo_text[0] - column_name = split_appinfo_text[1] - - try: - documentation_node = appinfo_node.xpath( - "following-sibling::xs:documentation", namespaces={"xs": ns} - )[-1] - except: # noqa: E722 - print("Error with", table_name, column_name) - continue - - documentation_text = documentation_node.text - - # NOTE: Here we go "up" from the documentation tag looking - # for the first element which doesn't match exclusions - # This may not be necessary and we might just be able to look - # for xs:element nodes. - element_node = appinfo_node.xpath( - "ancestor::*[not(self::xs:annotation)]", namespaces={"xs": ns} - )[-1] - xml_element_name = element_node.attrib["name"] - - xml_element_type = element_node.attrib.get("type", None) - - # If not present minOccurs default is 1 - xml_element_minoccurs = element_node.attrib.get("minOccurs", "1") - - xml_element_maxoccurs = element_node.attrib.get("maxOccurs", None) - - if table_name not in xml_metadata: - xml_metadata[table_name] = dict() - - xml_metadata[table_name][column_name] = ( - xml_element_name, - xml_element_type, - xml_element_minoccurs, - xml_element_maxoccurs, - documentation_text, - ) - - def set_xml_metadata(self): - self.xml_metadata = dict() - for root, dirs, files in os.walk(self.xsdpath, topdown=False): - for name in files: - if not name.endswith(".xsd"): - continue - fp = os.path.join(root, name) - with open(fp) as fh: - self.process_xsd_file(fh) - - def run(self): - self.set_db_metadata() - self.set_xml_metadata() - xml_metadata = self.xml_metadata - db_metadata = self.db_metadata - xml_md_keys = xml_metadata.keys() - for table_name in db_metadata.keys(): - if table_name not in xml_metadata: - continue - xml_md_table_keys = xml_metadata[table_name].keys() - for column_name in db_metadata[table_name].keys(): - extra = all( - (table_name in xml_md_keys, column_name in xml_md_table_keys) - ) - if extra: - # Add the extra XML columns if there's a match - db_column_data = db_metadata[table_name][column_name] - xml_column_data = xml_metadata[table_name][column_name] - db_column_data.extend(xml_column_data) - db_metadata[table_name][column_name] = db_column_data - - -def make_report(db_metadata, filepath): - - work_book = xlwt.Workbook() - fields = ( - "Column Name", - "Data Type", - "Max Length", - "Numeric Precision", - "Is Nullable", - "Constraint Type", - "Constraint Name", - "Check Clause", - "Row Count", - "Value Count", - "Distinct Value Count", - "XML Element Name", - "XML Type", - "XML MinOccurs", - "XML MaxOccurs", - "XML Description", - ) - for table_name in db_metadata.keys(): - work_sheet = work_book.add_sheet(table_name) - row = work_sheet.row(0) - - for x, header in enumerate(fields): - row.write(x, header) - - y = 1 - for column_name in db_metadata[table_name]: - field_row = db_metadata[table_name][column_name] - row = work_sheet.row(y) - for x, value in enumerate(field_row): - row.write(x, value) - y += 1 - work_book.save(filepath) - - -def make_coded_field_report(session, filepath): - - csvwriter = csv.writer(open(filepath, "w", newline="", encoding="utf-8")) - - csvwriter.writerow( - ( - "Table Name", - "Coding Std Field", - "Coding Std Value", - "Code Field", - "Code Value", - "Desc Field", - "Desc", - ) - ) - - coded_fields = get_coded_fields(session) - - for table_name, column_name in coded_fields: - print(table_name, column_name) - results = query_coded_fields(session, table_name, column_name) - for row in results: - csvwriter.writerow(row) - - -def main(): - xsd_path = "schema/ukrdc/" - sessionmaker = Connection.get_sessionmaker_from_file(key="ukrdc_live") - session = sessionmaker() - dbm = DBMetadata(session, xsd_path) - dbm.run() - make_report(dbm.db_metadata, "dataset_report.xls") - make_coded_field_report(session, "coded_field_report.csv") - - -if __name__ == "__main__": - main() diff --git a/xsdata_build/build.sh b/xsdata_build/build.sh index db870fc..2f4d6a0 100755 --- a/xsdata_build/build.sh +++ b/xsdata_build/build.sh @@ -1,3 +1,6 @@ xsdata ../schema/ukrdc/UKRDC.xsd --config .xsdata.xml --package ukrdc_xsdata.ukrdc xsdata ../schema/pv2/PV_2_0.xsd --config .xsdata.xml --package ukrdc_xsdata.pv xsdata ../schema/rrtf/RRTF_4.xsd --config .xsdata.xml --package ukrdc_xsdata.rrtf + +# Add py.typed to top-level package to enable type checking +touch ukrdc_xsdata/py.typed diff --git a/xsdata_build/setup.py b/xsdata_build/setup.py index f774de0..3f33540 100644 --- a/xsdata_build/setup.py +++ b/xsdata_build/setup.py @@ -1,13 +1,13 @@ -from setuptools import setup -from setuptools import find_packages from pathlib import Path +from setuptools import find_packages +from setuptools import setup # Read the contents of the README file long_description = (Path(__file__).parent / "README.md").read_text() setup( name="ukrdc-xsdata", - version="3.3.1", + version="4.2.0", long_description=long_description, long_description_content_type='text/markdown', author="UK Renal Registry",