From 568794c0d43dfcdbe615b60aec107deb89508fee Mon Sep 17 00:00:00 2001 From: An Date: Sun, 19 Sep 2021 21:10:33 -0700 Subject: [PATCH 01/41] set up initial workflow to run UK Biobank terms through mapper --- .github/inputs/terms.txt | 1565 +++++++++++++++++++++++++++++ .github/inputs/test-script.py | 25 + .github/workflows/python-test.yml | 44 + requirements.txt | 4 + 4 files changed, 1638 insertions(+) create mode 100644 .github/inputs/terms.txt create mode 100644 .github/inputs/test-script.py create mode 100644 .github/workflows/python-test.yml create mode 100644 requirements.txt diff --git a/.github/inputs/terms.txt b/.github/inputs/terms.txt new file mode 100644 index 0000000..cab6fe6 --- /dev/null +++ b/.github/inputs/terms.txt @@ -0,0 +1,1565 @@ +Vascular disorders of intestine +Gonarthrosis +Psoriatic and enteropathic arthropathies +Pain associated with micturition +Other mood +Preterm delivery +Injury of nerves at forearm level +Injury of nerves at wrist and hand level +Gastritis and duodenitis +Problems related to physical environment +Pre existing hypertension complicating pregnancy childbirth and the puerperium +Pre existing hypertensive disorder with superimposed proteinuria +Injury of blood vessels at wrist and hand level +Superficial injuries involving multiple body regions +Open wounds involving multiple body regions +Other injuries involving multiple body regions +Effects of air pressure and water pressure +Sequelae of injuries of neck and trunk +Sequelae of injuries involving multiple and unspecified body regions +Sequelae of other effects of external causes +Other injuries of spine and trunk level unspecified +Personal history of malignant neoplasm +Seropositive rheumatoid arthritis +Hypertrophic disorders of skin +Other infestations +Fibrosis and cirrhosis of liver +Polyarthrosis +Supervision of normal pregnancy +Unspecified contracted kidney +Infections of genitourinary tract in pregnancy +Sequelae of cerebrovascular disease +Other acute ischaemic heart diseases +Complications and ill defined descriptions of heart disease +Osteoporosis in diseases classified elsewhere +Mental and behavioural disorders due to use of sedatives or hypnotics +Mental and behavioural disorders due to use of hallucinogens +Mental and behavioural disorders due to use of volatile solvents +Fracture of lumbar spine and pelvis +Hereditary and idiopathic neuropathy +Osteopathies in diseases classified elsewhere +Other extrapyramidal and movement disorders +Other congenital musculoskeletal deformities +Carrier of infectious disease +Premature rupture of membranes +Anogenital herpesviral infection +Postinfective and reactive arthropathies in diseases classified elsewhere +Early syphilis +Sequelae of toxic effects of substances chiefly nonmedicinal as to source +Subclinical iodine deficiency hypothyroidism +Disorders of vitreous body and globe in diseases classified elsewhere +Polyarteritis nodosa and related conditions +Sequelae of inflammatory diseases of CNS +Respiratory tuberculosis not confimed +Disorders of conjunctiva in diseases classified elsewhere +Congenital deformities of hip +Neonatal jaundice from other causes +Urethral stricture +Other specific arthropathies +Conductive and sensorineural hearing loss +other injuries of shoulder and upper arm +Effects of heat and light +Other disorders of middle ear and mastoid +Atypical virus infections of CNS +Female genital prolapse +Dentofacial anomalies +Cleft palate with cleft lip +Congenital malformations of nose +Disorders of refraction and accommodation +Congenital malformations of gallbladder bile ducts and liver +Obstructed labour due to maternal pelvic abnormality +Abnormal findings in specimens from respiratory organs and thorax +Congenital malformations of lung +Other congenital malformations of peripheral vascular system +Varicose veins of lower extremities +Varicose veins of other sites +Acute lymphadenitis +Other abnormal findings in urine +Unspecified abdominal hernia +Unspecified viral hepatitis +Other congenital malformations of digestive system +Other congenital malformations of circulatory system +Other congenital malformations of skin +Pneumoconiosis due to other inorganic dusts +Corns and callosities +Disorders of lacrimal system and orbit in diseases classified elsewhere +Alzheimer s disease +Endocarditis valve unspecified +Family history of other conditions +Unspecified maternal hypertension +Stroke not specified as haemorrhage or infarction +Subarachnoid haemorrhage +Unspecified human immunodeficiency virus +Other endocrine disorders +Other diseases of liver +Primary disorders of muscles +Pervasive developmental disorders +Other cerebrovascular diseases +Other diseases of gallbladder +Pain +Fracture of spine level unspecified +Acute hepatitis B +Abnormalities of heart beat +Scoliosis +Other congenital malformations of heart +Disorders of tooth development and eruption +Intracerebral haemorrhage +Retinal detachments and breaks +Tuberculosis of nervous system +Acute hepatitis A +Hookworm diseases +Female infertility +Sleep disorders +Thiamine deficiency +Viral conjunctivitis +Alcoholic liver disease +Spinal osteochondrosis +Diseases of salivary glands +Gender identity disorders +Status asthmaticus +Cystic kidney disease +Polyp of female genital tract +Persistent mood +Disorders of vitreous body +Ovarian dysfunction +Other coagulation defects +Granulomatous disorders of skin and subcutaneous tissue +Excessive vomiting in pregnancy +Hyperfunction of pituitary gland +Other nutritional deficiencies +Other rheumatic heart diseases +Other helminthiases +Unspecified viral infection of CNS +Diverticular disease of intestine +Premature separation of placenta +Retention of urine +Unspecified urinary incontinence +Isolated proteinuria +Cleft palate +Hydrocephalus +Visual disturbances +Unspecified dementia +Unspecified haematuria +Cholecystitis +Dystonia +Ascites +Iron deficiency anaemia +Acute renal failure +Nonspecific lymphadenitis +Cachexia +Disseminated intravascular coagulation +Senile cataract +Agranulocytosis +Helicobacter pylori +Reduction defects of lower limb +Congenital hydrocephalus +Immunodeficiency with predominantly antibody defects +Congenital malformations of oesophagus +Syndactyly +Other congenital malformations of intestine +Other functional intestinal disorders +Other disorders of peripheral nervous system +Spondylosis +Hypofunction and other disorders of pituitary gland +Other retinal disorders +Arterial embolism and thrombosis +Juvenile osteochondrosis of hip and pelvis +Encephalitis myelitis and encephalomyelitis +Atrial fibrillation and flutter +Dermatopolymyositis +Lack of food +Inflammatory diseases of prostate +Chronic renal failure +Postpolio syndrome +Dementia in Alzheimer s disease +Other disorders of circulatory system in diseases classified elsewhere +Meningitis due to other causes +Gestational hypertension with significant proteinuria +Respiratory disorders in diseases classified elsewhere +Vitamin B12 deficiency anaemia +Unspecified arthropod borne viral fever +HIV disease resulting in infectious and parasitic diseases +Chronic ischaemic heart disease +Mental and behavioural disorders due to use of cocaine +Benign mammary dysplasia +Depressive episode +Recurrent depressive disorder +Mental and behavioural disorders due to use of tobacco +Mental and behavioural disorders due to use of alcohol +Dorsalgia +Disorders of globe +Mental and behavioural disorders due to use of cannabinoids +Osteochondrodysplasia with defects of growth of tubular bones and spine +Mental and behavioural disorders due to use of opioids +Mosquito borne viral encephalitis +Tick borne viral encephalitis +Respiratory tuberculosis confimed +Unspecified lump in breast +Erysipeloid +Rheumatic fever without mention of heart involvement +Pyogenic arthritis +Toxic effect of metals +Staphylococcal scalded skin syndrome +Phobic anxiety disorders +Adult osteomalacia +Functional disorders of polymorphonuclear neutrophils +Encephalocele +Tuberculosis of other organs +Localized adiposity +Atopic dermatitis +Cardiomyopathy +other disorders of circulatory system +Crohn s disease +Unspecified diabetes mellitus +Other specified diabetes mellitus +Epilepsy +Glaucoma +Irritable bowel syndrome +Schizophrenia +Ulcerative colitis +Viral infection of unspecified site +Myositis +Other cataract +Cytomegaloviral disease +Endometriosis +Obesity +Insulin dependent diabetes mellitus +Non insulin dependent diabetes mellitus +Parkinson s disease +Juvenile arthritis +Cellulitis +Cushing s syndrome +Osteomyelitis +Spina bifida +Heart failure +Vitamin D deficiency +Dental caries +Migraine +Pulmonary embolism +Other peripheral vascular diseases +Multiple sclerosis +Acne +Ankylosing spondylitis +Angina pectoris +Atherosclerosis +Gastro oesophageal reflux disease +Sunburn +Cleft lip +Androgenic alopecia +Alopecia areata +Vitiligo +Hypospadias +Otosclerosis +Conduct disorders +Male infertility +Meningococcal infection +Calculus of kidney and ureter +Nephrotic syndrome +Osteonecrosis +Paget s disease of bone +Other anaemias +Gout +Diabetes mellitus in pregnancy +Duodenal ulcer +Cholelithiasis +Leishmaniasis +Eating disorders +Hypotension +Unspecified contact dermatitis +Schizoaffective disorders +Urticaria +Seborrhoeic keratosis +Shigellosis +Other vitamin deficiencies +Zoster +Pyoderma gangrenosum +Decubitus ulcer +Actinomycosis +Amoebiasis +Unspecified appendicitis +Ascariasis +Aspergillosis +Varicella +Cryptococcosis +Echinococcosis +Enterobiasis +Granuloma inguinale +Histoplasmosis +Infectious mononucleosis +Leptospirosis +Listeriosis +Miliary tuberculosis +Myiasis +Optic neuritis +Placenta praevia +Plasmodium falciparum malaria +Plasmodium vivax malaria +Acute poliomyelitis +Scarlet fever +Strongyloidiasis +Suppurative and unspecified otitis media +other syphilis +Toxoplasmosis +Yaws +Status epilepticus +Fracture of femur +Diaphragmatic hernia +Niacin deficiency +Gangrene +Acute myocardial infarction +Subsequent myocardial infarction +Peritonitis +Diseases of spleen +Typhus fever +Other diseases of intestine +Fibroblastic disorders +Unspecified acute lower respiratory infection +Other ill defined and unspecified causes of mortality +Cystitis +Lactose intolerance +Thyroiditis +Acute pancreatitis +Acanthosis nigricans +Allergic contact dermatitis +Cholesteatoma of middle ear +Erythema multiforme +Hyperhidrosis +Impetigo +Irritant contact dermatitis +Lichen planus +Parapsoriasis +Pemphigus +Pityriasis rosea +Rosacea +Seborrhoeic dermatitis +Atrophic disorders of skin +Coxarthrosis +Coalworker s pneumoconiosis +Ascorbic acid deficiency +Bacterial meningitis +Dysplasia of cervix uteri +Habitual aborter +Other rickettsioses +Secondary parkinsonism +Viral meningitis +Vitamin A deficiency +Spontaneous abortion +Phlebitis and thrombophlebitis +Unspecified renal colic +Taeniasis +Synovitis and tenosynovitis +Schistosomiasis +Unspecified abortion +Femoral hernia +Ventral hernia +Amyloidosis +Cicatricial alopecia +Other disorders of nervous system +Polyuria +Pruritus +Nausea and vomiting +Peptic ulcer site unspecified +Erythema nodosum +Oesophagitis +Common variable immunodeficiency +Adrenogenital disorders +Sickle cell disorders +Congenital malformations of great veins +Huntington s disease +Cystic fibrosis +Hypertrichosis +Sarcoidosis +Turner s syndrome +Congenital malformations of great arteries +Hereditary factor VIII deficiency +Hereditary factor IX deficiency +Congenital malformations of cardiac chambers and connections +Acute nephritic syndrome +Keratitis +Conjunctivitis +Hypoparathyroidism +Hyperaldosteronism +Hemiplegia +Gastric ulcer +Disorders of lacrimal system +Exfoliative dermatitis +Apocrine sweat disorders +Spotted fever +Unspecified nephritic syndrome +Facial nerve disorders +Essential primary hypertension +Congenital malformations of uterus and cervix +Abnormal findings in specimens from female genital organs +Other congenital malformations of male genital organs +Abnormal findings in specimens from male genital organs +Congenital lens malformations +Congenital malformations of eyelid lacrimal apparatus and orbit +Enduring personality changes not attributable to brain damage and disease +Congenital malformations of breast +Unspecified jaundice +Iridocyclitis +Abnormalities of gait and mobility +Hypoglycemic coma +Hepatic failure +Umbilical hernia +Polyhydramnios +cardiac arrest +Congenital deformities of feet +Abnormalities of forces of labour +Other assisted single delivery +Multiple delivery +Abnormality of red blood cells +Abnormal leukocyte morphology +Hypothermia +Lymphadenopathy +Abnormal findings in cerebrospinal fluid +Glycosuria +Congenital malformations of posterior segment of eye +Abnormality of aromatic amino acid family metabolism +Abnormality of glycoprotein metabolism +Abnormality of glycosaminoglycan metabolism +Congenital septal defect +Abscess of anal and rectal regions +Abnormalities of breathing +Paroxysmal tachycardia +Congenital malformations of anterior segment of eye +Gynecomastia +Polydactyly +Pilonidal cyst +Congenital obstructive defects of renal pelvis and congenital malformations of ureter +Single delivery by forceps and vacuum extractor +Personality disorder +Mixed and other personality disorders +Acquired pure red cell aplasia +Chorioretinitis +Other congenital malformations of upper alimentary tract +Congenital malformations of larynx +Cervicitis +Portal vein thrombosis +Cutaneous abscess furuncle and carbuncle +Congenital malformations of ear causing impairment of hearing +Other congenital malformations of ear +Abnormality of movement +Calcification and ossification of muscle +Eclampsia +Other mosquito borne viral fevers +Internal derangement of knee +Fistulae involving female genital tract +Multiple gestation +Postpartum haemorrhage +Retained placenta and membranes without haemorrhage +Faecal incontinence +Disturbances of skin sensation +Abnormal results of function studies +Superficial injury of head +Crushing injury of head +Crushing injury of head +Injury of heart +Superficial injury of abdomen lower back and pelvis +Injury of intra abdominal organs +Crushing injury of shoulder and upper arm +Fracture at wrist and hand level +Open wound of hip and thigh +Injury of nerves at hip and thigh level +Injury of nerves at hip and thigh level +Injury of blood vessels at hip and thigh level +Other and specified injuries of hip and thigh +Injury of nerves at lower leg level +Injury of nerves at lower leg level +Fractures involving multiple body regions +Dislocations sprains and strains involving multiple body regions +Dislocations sprains and strains involving multiple body regions +Crushing injuries involving multiple body regions +Fracture of upper limb level unspecified +Other injuries of upper limb level unspecified +Fracture of lower limb level unspecified +Other injuries of lower limb level unspecified +Foreign body in ear +Foreign body in alimentary tract +Burn and corrosion of ankle and foot +Burn and corrosion of ankle and foot +Burns and corrosions of multiple body regions +Burns and corrosions of multiple body regions +Burns classified according to extent of body surface involved +Frostbite involving multiple body regions and unspecified frostbite +Toxic effect of organic solvents +Toxic effect of soaps and detergents +Toxic effect of other gases fumes and vapours +Toxic effect of pesticides +Complications following infusion transfusion and therapeutic injection +Complications of cardiac and vascular prosthetic devices implants and grafts +Complications of genitourinary prosthetic devices implants and grafts +Complications of internal orthopaedic prosthetic devices implants and grafts +Complications of other internal prosthetic devices implants and grafts +Sequelae of injuries of head +Sequelae of injuries of upper limb +Sequelae of injuries of lower limb +Sequelae of burns corrosions and frostbite +Sequelae of burns corrosions and frostbite +Sequelae of burns corrosions and frostbite +Unspecified fall +Routine general health check up of defined subpopulation +Contraceptive management +Supervision of high risk pregnancy +Prophylactic surgery +Other orthopaedic follow up care +Care involving use of rehabilitation procedures +Disorders of mineral metabolism +Other disorders of eye and adnexa in diseases classified elsewhere +Nonrheumatic tricuspid valve disorders +Disorders of sclera and cornea in diseases classified elsewhere +Other disorders of cornea +uremia +Oesophageal varices +Disorders of autonomic nervous system +marasmus +Mononeuropathies of upper limb +Mononeuropathies of lower limb +Other disorders of binocular movement +Inflammatory disease of uterus except cervix +Polyneuropathy in diseases classified elsewhere +Noninflammatory disorders of ovary fallopian tube and broad ligament +Pain and other conditions associated with female genital organs and menstrual cycle +Anuria and oliguria +Multiple valve diseases +Disorders of male genital organs in diseases classified elsewhere +Obstructive and reflux uropathy +Disorders of eyelid in diseases classified elsewhere +Diseases of pulp and periapical tissues +Disorders of trigeminal nerve +Pulmonary valve disorders +Other disorders of tympanic membrane +Other diseases of oesophagus +Nonrheumatic mitral valve disorders +Rheumatic aortic valve diseases +Nonrheumatic aortic valve disorders +Other degenerative diseases of basal ganglia +Other inflammation of eyelid +Otitis externa +Other diseases of biliary tract +Haemorrhoids +Arthrosis of first carpometacarpal joint +Inflammatory polyneuropathy +Congenital malformations of aortic and mitral valves +HIV disease resulting in malignant neoplasms +Anaemia due to enzyme disorders +Other disorders of peritoneum +Intestinal malabsorption +Other headache syndromes +Disorders resulting from impaired renal tubular function +Unspecified intestinal parasitism +Nerve root and plexus disorders +HIV disease resulting in other specified diseases +HIV disease resulting in other conditions +Skin changes due to chronic exposure to nonionizing radiation +Cervical disc disorders +Other diseases of appendix +Small kidney of unknown cause +Perforation of tympanic membrane +Other spirochaetal infections +Disturbances of smell and taste +Other diseases of jaws +Diseases of Bartholin s gland +Soft tissue disorders related to use overuse and pressure +Soft tissue disorders in diseases classified elsewhere +Waist circumference +Hip circumference +Standing height +Pulse rate, automated reading +Sleep duration +Morning/evening person (chronotype) +Sleeplessness / insomnia +Snoring +Alcohol intake frequency. +Mood swings +Irritability +Loneliness, isolation +Frequency of tiredness / lethargy in last 2 weeks +Hearing difficulty/problems with background noise +Chest pain or discomfort +Relative age voice broke +Age when periods started (menarche) +Had menopause +Forced vital capacity (FVC) +Forced expiratory volume in 1-second (FEV1) +Neck/shoulder pain for 3+ months +Hip pain for 3+ months +Back pain for 3+ months +Ever had hysterectomy (womb removed) +Length of menstrual cycle +Stomach/abdominal pain for 3+ months +Headaches for 3+ months +Gestational diabetes only +Diastolic blood pressure, automated reading +Systolic blood pressure, automated reading +Pulse rate +Leg pain on walking +Leg pain when standing still or sitting +Leg pain in calf/calves +Chest pain felt during physical activity +Chest pain felt outside physical activity +Maximum heart rate during fitness test +Fluid intelligence score +Birth weight +Bipolar disorder status +Neuroticism score +Forced expiratory volume in 1-second (FEV1), Best measure +Forced vital capacity (FVC), Best measure +Body mass index (BMI) +Weight +Pulse wave Arterial Stiffness index +hayfever or allergic rhinitis +asthma +emphysema +chronic bronchitis +COPD (chronic obstructive pulmonary disease) +sarcoidosis +bronchiectasis +idiopathic pulmonary fibrosis +tuberculosis +lung cancer (not mesothelioma) +Body fat percentage +Whole body fat mass +Whole body fat-free mass +Basal metabolic rate +Potassium in urine +Sodium in urine +Age at death +lung cancer +breast cancer +skin cancer +cancer of lip/mouth/pharynx/oral cavity +larynx/throat cancer +tongue cancer +oesophageal cancer +stomach cancer +small intestine/small bowel cancer +large bowel cancer/colorectal cancer +colon cancer/sigmoid cancer +rectal cancer +liver/hepatocellular cancer +eye and/or adnexal cancer +brain cancer / primary malignant brain tumour +kidney/renal cell cancer +bladder cancer +ovarian cancer +uterine/endometrial cancer +cervical cancer +prostate cancer +testicular cancer +lymphoma +leukaemia +multiple myeloma +hodgkins lymphoma / hodgkins disease +non-hodgkins lymphoma +chronic lymphocytic +chronic myeloid +malignant melanoma +non-melanoma skin cancer +basal cell carcinoma +squamous cell carcinoma +primary bone cancer +thyroid cancer +malignant lymph node, unspecified +hypertension +heart/cardiac problem +peripheral vascular disease +venous thromboembolic disease +essential hypertension +gestational hypertension/pre-eclampsia +angina +heart attack/myocardial infarction +heart failure/pulmonary odema +heart arrhythmia +cardiomyopathy +stroke +transient ischaemic attack (tia) +subdural haemorrhage/haematoma +subarachnoid haemorrhage +leg claudication/ intermittent claudication +pulmonary embolism +/- dvt +deep venous thrombosis (dvt) +asthma +chronic obstructive airways disease/copd +emphysema/chronic bronchitis +bronchiectasis +interstitial lung disease +asbestosis +pulmonary fibrosis +fibrosing alveolitis/unspecified alveolitis +sleep apnoea +pleurisy +spontaneous pneumothorax/recurrent pneumothorax +gastro-oesophageal reflux (gord) / gastric reflux +oesophagitis/barretts oesophagus +gastric/stomach ulcers +gastritis/gastric erosions +irritable bowel syndrome +hepatitis +infective/viral hepatitis +liver failure/cirrhosis +gall bladder disease +cholelithiasis/gall stones +cholecystitis +pancreatitis +peritonitis +gastrointestinal bleeding +renal/kidney failure +urinary tract infection/kidney infection +kidney stone/ureter stone/bladder stone +ureteric obstruction/hydronephrosis +urinary frequency / incontinence +diabetes +gestational diabetes +type 1 diabetes +type 2 diabetes +hyperthyroidism/thyrotoxicosis +hypothyroidism/myxoedema +parathyroid hyperplasia/adenoma +pituitary adenoma/tumour +encephalitis +bell's palsy/facial nerve palsy +peripheral neuropathy +acute infective polyneuritis/guillain-barre syndrome +multiple sclerosis +parkinsons disease +dementia/alzheimers/cognitive impairment +epilepsy +migraine +spinal injury +eye infection +retinal problem +glaucoma +cataract +retinal detachment +retinal artery/vein occlusion +depression +schizophrenia +deliberate self-harm/suicide attempt +mania/bipolar disorder/manic depression +bone disorder +joint disorder +osteomyelitis +osteoporosis +ankylosing spondylitis +myositis/myopathy +low platelets/platelet disorder +iron deficiency anaemia +pernicious anaemia +thalassaemia +ovarian cyst or cysts +polycystic ovaries/polycystic ovarian syndrome +uterine fibroids +vaginal prolapse/uterine prolapse +fibrocystic disease +breast cysts +sarcoidosis +vasculitis +connective tissue disorder +allergy/hypersensitivity/anaphylaxis +giant cell/temporal arteritis +polymyalgia rheumatica +wegners granulmatosis +systemic lupus erythematosis/sle +sjogren's syndrome/sicca syndrome +scleroderma/systemic sclerosis +allergy or anaphylactic reaction to food +hayfever/allergic rhinitis +pneumonia +peptic ulcer +endometriosis +female infertility +alcohol dependency +ear/vestibular disorder +chronic sinusitis +nasal polyps +otosclerosis +meniere's disease +cerebral aneurysm +myocarditis +polycystic kidney +thyroiditis +hypopituitarism +cerebral palsy +optic neuritis +headaches (not migraine) +myasthenia gravis +polycythaemia vera +hiv/aids +tuberculosis (tb) +malaria +helicobacter pylori +anaemia +neutropenia/lymphopenia +eczema/dermatitis +psoriasis +chronic skin ulcers +malabsorption/coeliac disease +duodenal ulcer +diverticular disease/diverticulitis +colitis/not crohns or ulcerative colitis +rectal or colon adenoma/polyps +inflammatory bowel disease +crohns disease +ulcerative colitis +rheumatoid arthritis +osteoarthritis +gout +post-traumatic stress disorder +anorexia/bulimia/other eating disorder +atrial fibrillation +emphysema +high cholesterol +hiatus hernia +sciatica +psoriatic arthropathy +rheumatic fever +chronic fatigue syndrome +irregular heart beat +brain haemorrhage +varicose veins +lymphoedema +pneumothorax +labyrinthitis +vertigo +pyloric stenosis +appendicitis +anal fissure +haemorrhoids / piles +jaundice (unknown cause) +gastroenteritis/dysentry +dyspepsia / indigestion +abdominal hernia +umbilical hernia +inguinal hernia +cystitis +bph / benign prostatic hypertrophy +prostatitis +erectile dysfunction / impotence +grave's disease +trigemminal neuralgia +benign / essential tremor +polio / poliomyelitis +dry eyes +iritis +post-natal depression +disc degeneration +back pain +scoliosis +spinal stenosis +joint pain +arthritis (nos) +plantar fascitis +carpal tunnel syndrome +fibromyalgia +dupuytren's contracture +acne/acne vulgaris +lichen planus +lichen sclerosis +cervical intra-epithelial neoplasia (cin) / precancerous cells cervix +menorrhagia (unknown cause) +ectopic pregnancy +miscarriage +breast fibroadenoma +raynaud's phenomenon/disease +food intolerance +urticaria +infectious mononucleosis / glandular fever / epstein barr virus (ebv) +measles / morbillivirus +mumps / epidemic parotitis +rubella / german measles +chickenpox +whooping cough / pertussis +shingles +herpes simplex +hepatitis a +hepatitis b +hepatitis c +mitral regurgitation / incompetence +aortic regurgitation / incompetence +hypertrophic cardiomyopathy (hcm / hocm) +pericarditis +respiratory infection +tinnitus / tiniitis +tonsiltis +constipation +rectal prolapse +femoral hernia +incisional hernia +nephritis +thyroid goitre +blepharitis / eyelid infection +obsessive compulsive disorder (ocd) +insomnia +osteopenia +tendonitis / tendinitis / tenosynovitis +bursitis +tennis elbow / lateral epicondylitis +cellulitis +fracture skull / head +fracture radius +fracture ulna +fracture tibia +septicaemia / sepsis +meningioma / benign meningeal tumour +rosacea +vitiligo +cervical erosion +dysmenorrhoea / dysmenorrhea +menopausal symptoms / menopause +alopecia / hair loss +scarlet fever / scarlatina +undescended testicle +Hearing difficulty/problems: Yes +Comparative height size at age 10 +Miserableness +Sensitivity / hurt feelings +Fed-up feelings +Nervous feelings +Guilty feelings +Risk taking +Overall health rating +Number of live births +General pain for 3+ months +Chest pain or discomfort walking normally +Chest pain due to walking ceases when standing still +Chest pain or discomfort when walking uphill or hurrying +Knee pain for 3+ months +Number of spontaneous miscarriages +Heel bone mineral density (BMD) T-score, automated (left) +Heel bone mineral density (BMD) T-score, automated (right) +Pulse wave reflection index +Family relationship satisfaction +Maximum workload during fitness test +Prospective memory result +Cough on most days +Years of cough on most days +liver/biliary/pancreas problem +psychological/psychiatric problem +head injury +gynaecological disorder (not cancer) +peripheral nerve injury +fracture jaw +fracture nose +fracture face / orbit / eye socket +fracture clavicle / collar bone +fracture shoulder / scapula +fracture forearm / wrist +fracture wrist / colles fracture +fracture hand +fracture finger +fracture thumb +fracture rib +fracture pelvis +fracture neck of femur / hip +fracture shaft of femur +fracture patella / knee +fracture lower leg / ankle +fracture fibula +fracture foot +fracture metatarsal +fracture toe +Hair/balding pattern: Pattern 2 +Hair/balding pattern: Pattern 3 +Hair/balding pattern: Pattern 4 +Hand grip strength (left) +Hand grip strength (right) +Heel bone mineral density (BMD) T-score, automated +Age completed full time education +Daytime dozing / sleeping (narcolepsy) +Current tobacco smoking +Past tobacco smoking +Exposure to tobacco smoke at home +Exposure to tobacco smoke outside home +Worrier / anxious feelings +Frequency of depressed mood in last 2 weeks +Frequency of unenthusiasm / disinterest in last 2 weeks +Diabetes diagnosed by doctor +Cancer diagnosed by doctor +Fractured/broken bones in last 5 years +Ever had stillbirth, spontaneous miscarriage or termination +Ever used hormone-replacement therapy (HRT) +Fracture resulting from simple fall +Facial pains for 3+ months +Longest period of depression +Number of depression episodes +Longest period of unenthusiasm / disinterest +Mean time to correctly identify matches +Creatinine (enzymatic) in urine +Handedness (chirality/laterality): Left-handed +Handedness (chirality/laterality): Use both right and left hands equally +sarcoma/fibrosarcoma +cin/pre-cancer cells cervix +rodent ulcer +heart valve problem/heart murmur +pericardial problem +other respiratory problems +oesophageal disorder +stomach disorder +non-infective hepatitis +renal failure requiring dialysis +renal failure not requiring dialysis +parathyroid gland problem (not cancer) +meningitis +chronic/degenerative neurological problem +anxiety/panic attacks +muscle/soft tissue problem +spine arthritis/spondylitis +prolapsed disc/slipped disc +other renal/kidney problem +bronchitis +other joint disorder +diabetic neuropathy/ulcers +cervical spondylosis +svt / supraventricular tachycardia +anal problem +macular degeneration +bowel / intestinal obstruction +stress +fracture upper arm / humerus / elbow +fracture vertebra / crush fracture / vertebral collapse +allergy to house dust mite +benign neuroma +Hearing difficulty/problems: I am completely deaf +Which eye(s) are affected by cataract: Right eye +Which eye(s) are affected by cataract: Left eye +Number of self-reported cancers +Number of self-reported non-cancer illnesses +Number of operations, self-reported +Number of treatments/medications taken +Townsend deprivation index at recruitment +Number of incorrect matches in round +Getting up in morning +Nap during day +Comparative body size at age 10 +Father's age at death +Number of full brothers +Number of full sisters +Tense / 'highly strung' +Worry too long after embarrassment +Suffer from 'nerves' +Seen doctor (GP) for nerves, anxiety, tension or depression +Seen a psychiatrist for nerves, anxiety, tension or depression +Long-standing illness, disability or infirmity +Falls in the last year +Wheeze or whistling in the chest in last year +Relative age of first facial hair +Number of children fathered +Birth weight of first child +Age at first live birth +Age at last live birth +Bilateral oophorectomy (both ovaries removed) +Peak expiratory flow (PEF) +Pace-maker +Hearing aid user +Mother's age at death +Number of stillbirths +Age of primiparous women at birth of child +Pulse wave reflection index +Happiness +Work/job satisfaction +Health satisfaction +Friendships satisfaction +Financial situation satisfaction +Ever depressed for a whole week +Ever unenthusiastic/disinterested for a whole week +Ever manic/hyper for 2 days +Ever highly irritable/argumentative for 2 days +Shortness of breath walking on level ground +Cochlear implant +Tinnitus severity/nuisance +Number of unenthusiastic/disinterested episodes +Surgery on leg arteries (other than for varicose veins) +Length of longest manic/irritable episode +Severity of manic/irritable episodes +Able to walk or cycle unaided for 10 minutes +Target heart rate achieved +Sitting height +Cascot confidence score +Bring up phlegm/sputum/mucus on most days +Whole body water mass +Reported occurrences of cancer +Procreative_management +other abdominal problem +oesophageal stricture +bladder problem (not cancer) +prostate problem (not cancer) +testicular problems (not cancer) +thyroid problem (not cancer) +thyroid radioablation therapy +adrenocortical insufficiency/addison's disease +neurological injury/trauma +eye/eyelid problem +cranial nerve problem/palsy +spinal cord disorder +peripheral nerve disorder +trapped nerve/compressed nerve +diabetic eye disease +eye trauma +nervous breakdown +back problem +uterine polyps +breast disease (not cancer) +allergy or anaphylactic reaction to drug +enlarged prostate +muscle or soft tissue injuries +burns +nasal/sinus disorder +throat or larynx disorder +vocal cord polyp +other neurological problem +clotting disorder/excessive bleeding +hereditary/genetic haematological disorder +blistering/desquamating skin disorder +disc problem +neck problem/injury +cervical polyps +soft tissue inflammation +abnormal smear (cervix) +benign breast lump +Problems_related_to_social_environment +Problems_related_to_life_management_difficulty +Volume_depletion +Spondylopathies_in_diseases_classified_elsewhere +Shoulder_lesions +Maternal_care_for_known_or_suspected_malpresentation_of_fetus +Maternal_care_for_known_or_suspected_disproportion +Maternal_care_for_known_or_suspected_abnormality_of_pelvic_organs +Long_labour +Perineal_laceration_during_delivery +Other_obstetric_trauma +Complications_of_anaesthesia_during_the_puerperium +Intrauterine_hypoxia +Abnormal_serum_enzyme_levels +Injury_of_blood_vessels_at_neck_level injury EFO_0009886 Broad S15 DONE +Injury_of_other_intrathoracic_organs +Injury_of_blood_vessels_at_abdomen_lower_back_and_pelvis_level +Injury_of_blood_vessels_at_shoulder_and_upper_arm_level +Other_fluke_infections +Other_postsurgical_states +Acquired_haemolytic_anaemia +Artificial_opening_status +Persons encountering health services in other circumstances +Persons encountering health services for other counselling and medical advice, not elsewhere classified +Hereditary_ataxia +Mycetoma +Viral_warts +Acquired_absence_of_limb +Convalescence +Pemphigoid +Eccrine_sweat_disorders +Traumatic_amputations_involving_multiple_body_regions +Need_for_immunization_against_certain_single_viral_diseases +Need_for_immunization_against_other_single_viral_diseases +Need_for_immunization_against_other_single_infectious_diseases +Need_for_immunization_against_combinations_of_infectious_diseases +Transplanted_organ_and_tissue_status +Persons encountering health services for specifie procedures, not carried out +Haemorrhage_from_respiratory_passages +Renal_tubulo_interstitial_disorders_in_diseases_classified_elsewhere +Occlusion_and_stenosis_of_cerebral_arteries_notcerebral_infarction +Orchitis_and_epididymitis +Other_disorders_of_nervous_system +Rheumatic_fever_with_heart_involvement +Rapidly_progressive_nephritic_syndrome +Dizziness_and_giddiness +Chlamydia_psittaci_infection +Glomerular_disorders_in_diseases_classified_elsewhere +Hypertensive_renal_disease +Congenital_ichthyosis +Fracture of skull and facial bones +Headache +Fever of unknown origin +Dysphagia +Heartburn +Cough +Urethritis and urethral syndrome +Other arthritis +Systemic lupus erythematosus +Systemic sclerosis +Psoriasis +Follicular cysts of skin and subcutaneous tissue +Other disorders of pigmentation +Ulcer of lower limb, not elsewhere classified +Dyspepsia +Inguinal hernia +Acute sinusitis +Pneumonia due to Streptococcus pneumoniae +Bacterial pneumonia, not elsewhere classified +Pneumonia, organism unspecified +Nasal polyp +Peritonsillar abscess +Emphysema +Other chronic obstructive pulmonary disease +Asthma +Bronchiectasis +Other interstitial pulmonary diseases +Other respiratory disorders +Aortic aneurysm and dissection +Hordeolum and chalazion +Myasthenia gravis and other myoneural disorders +Manic episode +Bipolar affective disorder +Sexual dysfunction, not caused by organic disorder or disease +Other hypothyroidism +Melanoma in situ +Haemangioma and lymphangioma, any site +Leiomyoma of uterus +Benign neoplasm of ovary +Benign neoplasm of other and unspecified female genital organs +Benign neoplasm of brain and other parts of central nervous system +Benign neoplasm of thyroid gland +Polycythaemia vera +Myelodysplastic syndromes +Purpura and other haemorrhagic conditions +Malignant neoplasm of colon +Malignant neoplasm of larynx +Mesothelioma +Secondary and unspecified malignant neoplasm of lymph nodes +Hodgkin's disease +Follicular [nodular] non-Hodgkin's lymphoma +Multiple myeloma and malignant plasma cell neoplasms +Lymphoid leukaemia +Myeloid leukaemia +Fracture of shoulder and upper arm +Elevated blood glucose level +Other necrotising vasculopathies +Other local infections of skin and subcutaneous tissue +Retinal vascular occlusions +Reaction to severe stress, and adjustment disorders +Benign neoplasm of colon, rectum, anus and anal canal +Benign neoplasm of breast +Malignant neoplasm of rectosigmoid junction +Malignant neoplasm of breast +Malignant neoplasm of prostate +Malignant neoplasm of testis +Malignant neoplasm of brain +Failure and rejection of transplanted organs and tissues +Poisoning by diuretics and other and unspecified drugs, medicaments and biological substances +Poisoning by psychotropic drugs, not elsewhere classified +Poisoning by antiepileptic, sedative-hypnotic and anti-Parkinsonism drugs +Poisoning by narcotics and psychodysleptics [hallucinogens] +Poisoning by nonopioid analgesics, antipyretics and antirheumatics +Dislocation, sprain and strain of joints and ligaments at ankle and foot level +Fracture of foot, except ankle +Fracture of forearm +Abdominal and pelvic pain +Medical abortion +Other disorders of bladder +Hydrocele and spermatocele +Redundant prepuce, phimosis and paraphimosis +Salpingitis and oophoritis +Other inflammation of vagina and vulva +Other rheumatoid arthritis +Other joint disorders, not elsewhere classified +Osteoporosis without pathological fracture +Lichen simplex chronicus and prurigo +Other disorders of skin and subcutaneous tissue, not elsewhere classified +Acute appendicitis +Chronic sinusitis +Pneumothorax +Acute pericarditis +Other nontraumatic intracranial haemorrhage +Cerebral infarction +Other aneurysm +Other hearing loss +Transient cerebral ischaemic attacks and related syndromes +Acute and transient psychotic disorders +Other anxiety disorders +Mental disorder, not otherwise specified +Other disorders of thyroid +Hyperparathyroidism and other disorders of parathyroid gland +Carcinoma in situ of skin +Carcinoma in situ of breast +Carcinoma in situ of cervix uteri +Benign neoplasm of mouth and pharynx +Benign neoplasm of major salivary glands +Other benign neoplasms of uterus +Neoplasm of uncertain or unknown behaviour of female genital organs +Neoplasm of uncertain or unknown behaviour of endocrine glands +Malignant neoplasm of other and unspecified parts of tongue +Malignant neoplasm of tonsil +Malignant neoplasm of oesophagus +Malignant neoplasm of stomach +Malignant neoplasm of rectum +Malignant neoplasm of anus and anal canal +Malignant neoplasm of liver and intrahepatic bile ducts +Malignant neoplasm of pancreas +Malignant neoplasm of bronchus and lung +Malignant melanoma of skin +Malignant neoplasm of cervix uteri +Malignant neoplasm of corpus uteri +Malignant neoplasm of ovary +Malignant neoplasm of kidney, except renal pelvis +Malignant neoplasm of bladder +Malignant neoplasm of eye and adnexa +Malignant neoplasm of thyroid gland +Diffuse non-Hodgkin's lymphoma +Chronic viral hepatitis +Diarrhoea and gastro-enteritis of presumed infectious origin +Other septicaemia +Personal history of other diseases and conditions +Family history of malignant neoplasm +Other medical care +Fitting and adjustment of other devices +Adjustment and management of implanted device +Donors of organs and tissues +Fitting and adjustment of external prosthetic device +Other surgical follow-up care +Attention to artificial openings +Postpartum care and examination +Antenatal screening +Certain early complications of trauma, not elsewhere classified +Follow-up care involving plastic surgery +Procedures for purposes other than remedying health state +Abnormal findings on diagnostic imaging of other body structures +Symptoms and signs concerning food and fluid intake +Pregnancy examination and test +Special screening examination for other diseases and disorders +Special screening examination for neoplasms +Special screening examination for infectious and parasitic diseases +Follow-up examination after treatment for conditions other than malignant neoplasms +Follow-up examination after treatment for malignant neoplasm +Examination and observation for other reasons +Medical observation and evaluation for suspected diseases and conditions +Other special examinations and investigations of persons without complaint or reported diagnosis +General examination and investigation of persons without complaint or reported diagnosis +Other complications of surgical and medical care, not elsewhere classified +Complications peculiar to reattachment and amputation +Complications of procedures, not elsewhere classified +Certain early complications of trauma, not elsewhere classified +Adverse effects, not elsewhere classified +Foreign body in respiratory tract +Injury of unspecified body region +Open wound of ankle and foot +Other and unspecified injuries of lower leg +Injury of muscle and tendon at lower leg level +Dislocation, sprain and strain of joints and ligaments of knee +Fracture of lower leg, including ankle +Open wound of lower leg +Superficial injury of lower leg +Injury of muscle and tendon at hip and thigh level +Other and unspecified injuries of wrist and hand +Traumatic amputation of wrist and hand +Crushing injury of wrist and hand +Injury of muscle and tendon at wrist and hand level +Dislocation, sprain and strain of joints and ligaments at wrist and hand level +Open wound of wrist and hand +Superficial injury of wrist and hand +Injury of muscle and tendon at forearm level +Open wound of forearm +Injury of muscle and tendon at shoulder and upper arm level +Dislocation, sprain and strain of joints and ligaments of shoulder girdle +Other and unspecified injuries of abdomen, lower back and pelvis +Open wound of abdomen, lower back and pelvis +Fracture of rib(s), sternum and thoracic spine +Superficial injury of thorax +Dislocation, sprain and strain of joints and ligaments at neck level +Fracture of neck +Other and unspecified injuries of head +Intracranial injury +Injury of eye and orbit +Open wound of head +Other abnormal products of conception +Abnormal findings on diagnostic imaging of lung +Abnormal findings on diagnostic imaging of central nervous system +Other abnormal findings of blood chemistry +Other abnormal immunological findings in serum +Unknown and unspecified causes of morbidity +Other general symptoms and signs +Maternal care for other conditions predominantly related to pregnancy +Oedema, not elsewhere classified +Convulsions, not elsewhere classified +Syncope and collapse +Senility +Malaise and fatigue +Voice disturbances +Speech disturbances, not elsewhere classified +Other symptoms and signs involving cognitive functions and awareness +Somnolence, stupor and coma +Other symptoms and signs involving the urinary system +Other symptoms and signs involving the nervous and musculoskeletal systems +Other skin changes +Localised swelling, mass and lump of skin and subcutaneous tissue +Rash and other nonspecific skin eruption +Other symptoms and signs involving the digestive system and abdomen +Flatulence and related conditions +Other symptoms and signs involving the circulatory and respiratory systems +Pain in throat and chest +Other congenital malformations of tongue, mouth and pharynx +Other congenital malformations of face and neck +Ectopic pregnancy +Maternal care for known or suspected foetal abnormality and damage +Gestational [pregnancy-induced] hypertension without significant proteinuria +Haemorrhage in early pregnancy +Maternal care for other known or suspected foetal problems +Other deforming dorsopathies +Other inflammatory spondylopathies +Other disorders of amniotic fluid and membranes +Antepartum haemorrhage, not elsewhere classified +False labour +Prolonged pregnancy +Obstructed labour due to malposition and malpresentation of foetus +Other obstructed labour +Labour and delivery complicated by foetal stress [distress] +Labour and delivery complicated by umbilical cord complications +Other complications of labour and delivery, not elsewhere classified +Single spontaneous delivery +Single delivery by Caesarean section +Complications of the puerperium, not elsewhere classified +Other maternal diseases classifiable elsewhere but complicating pregnancy, childbirth and the puerperium +Recurrent and persistent haematuria +Acute tubulo-interstitial nephritis +Tubulo-interstitial nephritis, not specified as acute or chronic +Calculus of lower urinary tract +Other disorders of kidney and ureter, not elsewhere classified +Neuromuscular dysfunction of bladder, not elsewhere classified +Other disorders of urethra +Other disorders of urinary system +Hyperplasia of prostate +Other disorders of prostate +Other disorders of penis +Inflammatory disorders of male genital organs, not elsewhere classified +Other disorders of male genital organs +Inflammatory disorders of breast +Other disorders of breast +Other female pelvic inflammatory diseases +Other noninflammatory disorders of uterus, except cervix +Erosion and ectropion of cervix uteri +Other noninflammatory disorders of cervix uteri +Other noninflammatory disorders of vagina +Other noninflammatory disorders of vulva and perineum +Excessive, frequent and irregular menstruation +Other abnormal uterine and vaginal bleeding +Menopausal and other perimenopausal disorders +Postprocedural disorders of genito-urinary system, not elsewhere classified +Other arthrosis +Acquired deformities of fingers and toes +Other acquired deformities of limbs +Disorders of patella +Other specific joint derangements +Other systemic involvement of connective tissue +Other spondylopathies +Other dorsopathies, not elsewhere classified +Other spondylopathies +Other intervertebral disk disorders +Other dorsopathies, not elsewhere classified +Other disorders of muscle +Spontaneous rupture of synovium and tendon +Other disorders of synovium and tendon +Other bursopathies +Enthesopathies of lower limb, excluding foot +Other enthesopathies +Other soft tissue disorders, not elsewhere classified +Osteoporosis with pathological fracture +Disorders of continuity of bone +Other disorders of bone density and structure +Other disorders of bone +Other disorders of cartilage +Other acquired deformities of musculoskeletal system and connective tissue +Postprocedural musculoskeletal disorders, not elsewhere classified +Dermatitis due to substances taken internally +Other dermatitis +Other erythematous conditions +Nail disorders +Other follicular disorders +Other epidermal thickening +Embedded and impacted teeth +Gingivitis and periodontal diseases +Other disorders of gingiva and edentulous alveolar ridge +Other disorders of teeth and supporting structures +Cysts of oral region, not elsewhere classified +Stomatitis and related lesions +Other diseases of lip and oral mucosa +Diseases of tongue +Other diseases of stomach and duodenum +Other non-infective gastro-enteritis and colitis +Paralytic ileus and intestinal obstruction without hernia +Fissure and fistula of anal and rectal regions +Other diseases of anus and rectum +Other inflammatory liver diseases +Other diseases of pancreas +Postprocedural disorders of digestive system, not elsewhere classified +Other diseases of digestive system +Acute pharyngitis +Acute tonsillitis +Acute upper respiratory infections of multiple and unspecified sites +Chronic rhinitis, nasopharyngitis and pharyngitis +Other disorders of nose and nasal sinuses +Chronic diseases of tonsils and adenoids +Diseases of vocal cords and larynx, not elsewhere classified +Other diseases of upper respiratory tract +Bronchitis, not specified as acute or chronic +Pyothorax +Pleural effusion, not elsewhere classified +Respiratory failure, not elsewhere classified +Rheumatic mitral valve diseases +Other diseases of pericardium +Acute and subacute endocarditis +Atrioventricular and left bundle-branch block +Other conduction disorders +Other cardiac arrhythmias +Occlusion and stenosis of precerebral arteries, not resulting in cerebral infarction +Other disorders of arteries and arterioles +Diseases of capillaries +Other venous embolism and thrombosis +Other disorders of veins +Other non-infective disorders of lymphatic vessels and lymph nodes +Other disorders of eyelid +Disorders of orbit +Other disorders of conjunctiva +Other disorders of lens +Paralytic strabismus +Other strabismus +Other disorders of eye and adnexa +Postprocedural disorders of eye and adnexa, not elsewhere classified +Other disorders of external ear +Nonsuppurative otitis media +Other disorders of Eustachian tube +Disorders of vestibular function +Other diseases of inner ear +Otalgia and effusion of ear +Other disorders of ear, not elsewhere classified +Other demyelinating diseases of central nervous system +Other mononeuropathies +Other polyneuropathies +Paraplegia and tetraplegia +Other disorders of brain +Other diseases of spinal cord +Somatoform disorders +Other non-toxic goitre +Thyrotoxicosis [hyperthyroidism] +Other disorders of pancreatic internal secretion +Other disorders of fluid, electrolyte and acid-base balance +Carcinoma in situ of other and unspecified genital organs +Carcinoma in situ of other and unspecified sites +Benign neoplasm of other and ill-defined parts of digestive system +Benign neoplasm of middle ear and respiratory system +Benign neoplasm of bone and articular cartilage +Benign lipomatous neoplasm +Other benign neoplasms of connective and other soft tissue +Melanocytic naevi +Other benign neoplasms of skin +Benign neoplasm of urinary organs +Benign neoplasm of meninges +Benign neoplasm of other and unspecified endocrine glands +Benign neoplasm of other and unspecified sites +Neoplasm of uncertain or unknown behaviour of oral cavity and digestive organs +Neoplasm of uncertain or unknown behaviour of middle ear and respiratory and intrathoracic organs +Neoplasm of uncertain or unknown behaviour of urinary organs +Other neoplasms of uncertain or unknown behaviour of lymphoid, haematopoietic and related tissue +Neoplasm of uncertain or unknown behaviour of other and unspecified sites +Other aplastic anaemias +Other diseases of blood and blood-forming organs +Other disorders involving the immune mechanism, not elsewhere classified +Other malignant neoplasms of skin +Malignant neoplasm of other connective and soft tissue +Secondary malignant neoplasm of respiratory and digestive organs +Secondary malignant neoplasm of other sites +Malignant neoplasm without specification of site +Other and unspecified types of non-Hodgkin's lymphoma +Candidiasis +Other bacterial intestinal infections +Viral and other specified intestinal infections +Other predominantly sexually transmitted diseases, not elsewhere classified +Other disorders of adrenal gland \ No newline at end of file diff --git a/.github/inputs/test-script.py b/.github/inputs/test-script.py new file mode 100644 index 0000000..6617584 --- /dev/null +++ b/.github/inputs/test-script.py @@ -0,0 +1,25 @@ +import pandas as pd + + +def extractTerms( + goldStandard="https://raw.githubusercontent.com/EBISPOT/EFO-UKB-mappings/master/UK_Biobank_master_file.tsv", + columnName="ZOOMA QUERY", + fileName="./terms.txt", +): + """ + extracts the terms in the column columnName of the goldStandard .tsv file + and saves them + """ + biobank = pd.read_csv( + goldStandard, + sep="\t", + header=0, + ) + + terms = "" + for term in biobank[columnName]: + terms += term + "\n" + terms = terms[:-1] # remove trailing newline + + with open(fileName, "w") as f: + f.write(terms) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml new file mode 100644 index 0000000..b4e5bda --- /dev/null +++ b/.github/workflows/python-test.yml @@ -0,0 +1,44 @@ +# This workflow will install Python dependencies, run tests and lint with a single version of Python +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: Python application + +on: + push: + branches: [task5-workflow] + pull_request: + branches: [task5-workflow] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.9 + uses: actions/setup-python@v2 + with: + python-version: 3.9 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install flake8 pytest + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Run mapper on Biobank source terms + run: | + python3 t2t.py -s ./.github/inputs/terms.txt + -t https://github.com/EBISPOT/efo/releases/download/current/efo.owl + - name: Archive mapping output + uses: actions/upload-artifact@v2 + with: + name: mapping-output + path: t2t-out-*.csv + # - name: Lint with flake8 + # run: | + # # stop the build if there are Python syntax errors or undefined names + # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + # - name: Test with pytest + # run: | + # pytest diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..277681a --- /dev/null +++ b/requirements.txt @@ -0,0 +1,4 @@ +pandas +sparse-dot-topn +sklearn +owlready2 From f3ba66e436715ff9cd5e4196fc0352829bfb38d8 Mon Sep 17 00:00:00 2001 From: An Date: Sun, 19 Sep 2021 21:20:01 -0700 Subject: [PATCH 02/41] update workflow to have correct command for calling mapper --- .github/workflows/python-test.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index b4e5bda..ba96fdf 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -26,8 +26,7 @@ jobs: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Run mapper on Biobank source terms run: | - python3 t2t.py -s ./.github/inputs/terms.txt - -t https://github.com/EBISPOT/efo/releases/download/current/efo.owl + python3 t2t.py -s ./.github/inputs/terms.txt -t https://github.com/EBISPOT/efo/releases/download/current/efo.owl - name: Archive mapping output uses: actions/upload-artifact@v2 with: From af959023f13bae1b88317cb538068ba56122ca48 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 2 Oct 2021 20:03:12 -0700 Subject: [PATCH 03/41] try adding link to test repo --- .github/workflows/python-test.yml | 30 +++++++++++++++++++++--------- 1 file changed, 21 insertions(+), 9 deletions(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index ba96fdf..c93815b 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -32,12 +32,24 @@ jobs: with: name: mapping-output path: t2t-out-*.csv - # - name: Lint with flake8 - # run: | - # # stop the build if there are Python syntax errors or undefined names - # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - # - name: Test with pytest - # run: | - # pytest + test: + steps: + - uses: actions/checkout@v2 + name: Checkout test repository + with: + repository: "ccb-hms/ontology-mapper-tests" + persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. + fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. + - name: Download a single artifact + uses: actions/download-artifact@v2 + with: + name: mapping-output + - name: Commit files + run: | + git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" + git config --local user.name "github-actions[bot]" + git commit -m "Add file" -a + - name: Push changes + uses: ad-m/github-push-action@master + with: + repository: "ccb-hms/ontology-mapper-tests" From 3bdc0fe28d2c9aaba0e4446917b9569fcb38cabe Mon Sep 17 00:00:00 2001 From: An Date: Sat, 2 Oct 2021 20:05:14 -0700 Subject: [PATCH 04/41] add runs-on to new test job --- .github/workflows/python-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index c93815b..12c4405 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -33,12 +33,13 @@ jobs: name: mapping-output path: t2t-out-*.csv test: + runs-on: ubuntu-latest + steps: - uses: actions/checkout@v2 name: Checkout test repository with: repository: "ccb-hms/ontology-mapper-tests" - persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - name: Download a single artifact uses: actions/download-artifact@v2 From f0a43ce27b6d74e666e857eb09fffac87d1b7faf Mon Sep 17 00:00:00 2001 From: An Date: Sat, 2 Oct 2021 20:09:36 -0700 Subject: [PATCH 05/41] update job dependencies, enabled github authentication for private repo --- .github/workflows/python-test.yml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index 12c4405..ab3102f 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -10,9 +10,9 @@ on: branches: [task5-workflow] jobs: - build: + run_mapper: runs-on: ubuntu-latest - + name: Run Mapper steps: - uses: actions/checkout@v2 - name: Set up Python 3.9 @@ -32,14 +32,16 @@ jobs: with: name: mapping-output path: t2t-out-*.csv - test: + save_to_test: runs-on: ubuntu-latest - + name: Save Output to Test Repo + needs: run_mapper steps: - uses: actions/checkout@v2 name: Checkout test repository with: repository: "ccb-hms/ontology-mapper-tests" + persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - name: Download a single artifact uses: actions/download-artifact@v2 @@ -54,3 +56,4 @@ jobs: uses: ad-m/github-push-action@master with: repository: "ccb-hms/ontology-mapper-tests" + github_token: ${{ secrets.GITHUB_TOKEN }} From 5181db2a36e11ae2e60b871f9c733d282c09e9e3 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 2 Oct 2021 20:27:17 -0700 Subject: [PATCH 06/41] explicitly git add file --- .github/workflows/python-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index ab3102f..fa4baa7 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -41,7 +41,6 @@ jobs: name: Checkout test repository with: repository: "ccb-hms/ontology-mapper-tests" - persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - name: Download a single artifact uses: actions/download-artifact@v2 @@ -51,7 +50,8 @@ jobs: run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" - git commit -m "Add file" -a + git add t2t-out-*.csv + git commit -m "Add file" - name: Push changes uses: ad-m/github-push-action@master with: From 92bbd52233608dda2a939f13428782e857cad47c Mon Sep 17 00:00:00 2001 From: An Date: Mon, 4 Oct 2021 15:09:16 -0700 Subject: [PATCH 07/41] update workflow to use MAPPER_SECRET token --- .github/workflows/python-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index fa4baa7..133250c 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -41,6 +41,7 @@ jobs: name: Checkout test repository with: repository: "ccb-hms/ontology-mapper-tests" + token: ${{ secrets.MAPPER_TESTING }} fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - name: Download a single artifact uses: actions/download-artifact@v2 @@ -56,4 +57,4 @@ jobs: uses: ad-m/github-push-action@master with: repository: "ccb-hms/ontology-mapper-tests" - github_token: ${{ secrets.GITHUB_TOKEN }} + github_token: ${{ secrets.MAPPER_TESTING }} From f98812b030e4bbc4d73934c1580e5fe1486cf429 Mon Sep 17 00:00:00 2001 From: An Date: Mon, 4 Oct 2021 15:19:39 -0700 Subject: [PATCH 08/41] condense workflow to only test accessing the repository --- .github/workflows/python-test.yml | 56 +++++++++++++++++-------------- 1 file changed, 31 insertions(+), 25 deletions(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index 133250c..21e0f61 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -10,28 +10,28 @@ on: branches: [task5-workflow] jobs: - run_mapper: - runs-on: ubuntu-latest - name: Run Mapper - steps: - - uses: actions/checkout@v2 - - name: Set up Python 3.9 - uses: actions/setup-python@v2 - with: - python-version: 3.9 - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Run mapper on Biobank source terms - run: | - python3 t2t.py -s ./.github/inputs/terms.txt -t https://github.com/EBISPOT/efo/releases/download/current/efo.owl - - name: Archive mapping output - uses: actions/upload-artifact@v2 - with: - name: mapping-output - path: t2t-out-*.csv + # run_mapper: + # runs-on: ubuntu-latest + # name: Run Mapper + # steps: + # - uses: actions/checkout@v2 + # - name: Set up Python 3.9 + # uses: actions/setup-python@v2 + # with: + # python-version: 3.9 + # - name: Install dependencies + # run: | + # python -m pip install --upgrade pip + # pip install flake8 pytest + # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + # - name: Run mapper on Biobank source terms + # run: | + # python3 t2t.py -s ./.github/inputs/terms.txt -t https://github.com/EBISPOT/efo/releases/download/current/efo.owl + # - name: Archive mapping output + # uses: actions/upload-artifact@v2 + # with: + # name: mapping-output + # path: t2t-out-*.csv save_to_test: runs-on: ubuntu-latest name: Save Output to Test Repo @@ -41,7 +41,7 @@ jobs: name: Checkout test repository with: repository: "ccb-hms/ontology-mapper-tests" - token: ${{ secrets.MAPPER_TESTING }} + token: ${{ secrets.ACCESS_TOKEN }} fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - name: Download a single artifact uses: actions/download-artifact@v2 @@ -51,10 +51,16 @@ jobs: run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" - git add t2t-out-*.csv + touch test.txt + git add test.txt git commit -m "Add file" + # run: | + # git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" + # git config --local user.name "github-actions[bot]" + # git add t2t-out-*.csv + # git commit -m "Add file" - name: Push changes uses: ad-m/github-push-action@master with: repository: "ccb-hms/ontology-mapper-tests" - github_token: ${{ secrets.MAPPER_TESTING }} + github_token: ${{ secrets.ACCESS_TOKEN }} From dc8a7defbf1a338e679df00b26738d7432e46a7e Mon Sep 17 00:00:00 2001 From: An Date: Mon, 4 Oct 2021 15:20:37 -0700 Subject: [PATCH 09/41] temporarily remove dependency --- .github/workflows/python-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index 21e0f61..2cc7a62 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -35,7 +35,7 @@ jobs: save_to_test: runs-on: ubuntu-latest name: Save Output to Test Repo - needs: run_mapper + # needs: run_mapper steps: - uses: actions/checkout@v2 name: Checkout test repository From 02cbc501d7c047cebf398157e79a2d69b5a7c9ae Mon Sep 17 00:00:00 2001 From: An Date: Mon, 4 Oct 2021 15:23:02 -0700 Subject: [PATCH 10/41] restore full workflow --- .github/workflows/python-test.yml | 59 ++++++++++++++----------------- 1 file changed, 26 insertions(+), 33 deletions(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index 2cc7a62..84c4f72 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -10,57 +10,50 @@ on: branches: [task5-workflow] jobs: - # run_mapper: - # runs-on: ubuntu-latest - # name: Run Mapper - # steps: - # - uses: actions/checkout@v2 - # - name: Set up Python 3.9 - # uses: actions/setup-python@v2 - # with: - # python-version: 3.9 - # - name: Install dependencies - # run: | - # python -m pip install --upgrade pip - # pip install flake8 pytest - # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - # - name: Run mapper on Biobank source terms - # run: | - # python3 t2t.py -s ./.github/inputs/terms.txt -t https://github.com/EBISPOT/efo/releases/download/current/efo.owl - # - name: Archive mapping output - # uses: actions/upload-artifact@v2 - # with: - # name: mapping-output - # path: t2t-out-*.csv + run_mapper: + runs-on: ubuntu-latest + name: Run Mapper + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.9 + uses: actions/setup-python@v2 + with: + python-version: 3.9 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install flake8 pytest + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Run mapper on Biobank source terms + run: | + python3 t2t.py -s ./.github/inputs/terms.txt -t https://github.com/EBISPOT/efo/releases/download/current/efo.owl + - name: Archive mapping output + uses: actions/upload-artifact@v2 + with: + name: mapping-output + path: t2t-out-*.csv save_to_test: runs-on: ubuntu-latest name: Save Output to Test Repo - # needs: run_mapper + needs: run_mapper steps: - uses: actions/checkout@v2 name: Checkout test repository with: repository: "ccb-hms/ontology-mapper-tests" - token: ${{ secrets.ACCESS_TOKEN }} + token: ${{ secrets.MAPPER_TESTING }} fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - name: Download a single artifact uses: actions/download-artifact@v2 with: name: mapping-output - - name: Commit files run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" - touch test.txt - git add test.txt + git add t2t-out-*.csv git commit -m "Add file" - # run: | - # git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" - # git config --local user.name "github-actions[bot]" - # git add t2t-out-*.csv - # git commit -m "Add file" - name: Push changes uses: ad-m/github-push-action@master with: repository: "ccb-hms/ontology-mapper-tests" - github_token: ${{ secrets.ACCESS_TOKEN }} + github_token: ${{ secrets.MAPPER_TESTING }} From 7f0d0ec58915b576e3f70988a2cd169bd4a66a06 Mon Sep 17 00:00:00 2001 From: An Date: Mon, 4 Oct 2021 15:24:14 -0700 Subject: [PATCH 11/41] fix nesting --- .github/workflows/python-test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index 84c4f72..133250c 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -47,6 +47,7 @@ jobs: uses: actions/download-artifact@v2 with: name: mapping-output + - name: Commit files run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" From 066ad04284d5b1921377af2b19d205e294ffe7f8 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 21:42:18 -0700 Subject: [PATCH 12/41] update workflow; remove unnecessary files --- .github/inputs/terms.txt | 1565 ----------------- .github/inputs/test-script.py | 25 - .../{python-test.yml => mapper-test.yml} | 58 +- 3 files changed, 31 insertions(+), 1617 deletions(-) delete mode 100644 .github/inputs/terms.txt delete mode 100644 .github/inputs/test-script.py rename .github/workflows/{python-test.yml => mapper-test.yml} (59%) diff --git a/.github/inputs/terms.txt b/.github/inputs/terms.txt deleted file mode 100644 index cab6fe6..0000000 --- a/.github/inputs/terms.txt +++ /dev/null @@ -1,1565 +0,0 @@ -Vascular disorders of intestine -Gonarthrosis -Psoriatic and enteropathic arthropathies -Pain associated with micturition -Other mood -Preterm delivery -Injury of nerves at forearm level -Injury of nerves at wrist and hand level -Gastritis and duodenitis -Problems related to physical environment -Pre existing hypertension complicating pregnancy childbirth and the puerperium -Pre existing hypertensive disorder with superimposed proteinuria -Injury of blood vessels at wrist and hand level -Superficial injuries involving multiple body regions -Open wounds involving multiple body regions -Other injuries involving multiple body regions -Effects of air pressure and water pressure -Sequelae of injuries of neck and trunk -Sequelae of injuries involving multiple and unspecified body regions -Sequelae of other effects of external causes -Other injuries of spine and trunk level unspecified -Personal history of malignant neoplasm -Seropositive rheumatoid arthritis -Hypertrophic disorders of skin -Other infestations -Fibrosis and cirrhosis of liver -Polyarthrosis -Supervision of normal pregnancy -Unspecified contracted kidney -Infections of genitourinary tract in pregnancy -Sequelae of cerebrovascular disease -Other acute ischaemic heart diseases -Complications and ill defined descriptions of heart disease -Osteoporosis in diseases classified elsewhere -Mental and behavioural disorders due to use of sedatives or hypnotics -Mental and behavioural disorders due to use of hallucinogens -Mental and behavioural disorders due to use of volatile solvents -Fracture of lumbar spine and pelvis -Hereditary and idiopathic neuropathy -Osteopathies in diseases classified elsewhere -Other extrapyramidal and movement disorders -Other congenital musculoskeletal deformities -Carrier of infectious disease -Premature rupture of membranes -Anogenital herpesviral infection -Postinfective and reactive arthropathies in diseases classified elsewhere -Early syphilis -Sequelae of toxic effects of substances chiefly nonmedicinal as to source -Subclinical iodine deficiency hypothyroidism -Disorders of vitreous body and globe in diseases classified elsewhere -Polyarteritis nodosa and related conditions -Sequelae of inflammatory diseases of CNS -Respiratory tuberculosis not confimed -Disorders of conjunctiva in diseases classified elsewhere -Congenital deformities of hip -Neonatal jaundice from other causes -Urethral stricture -Other specific arthropathies -Conductive and sensorineural hearing loss -other injuries of shoulder and upper arm -Effects of heat and light -Other disorders of middle ear and mastoid -Atypical virus infections of CNS -Female genital prolapse -Dentofacial anomalies -Cleft palate with cleft lip -Congenital malformations of nose -Disorders of refraction and accommodation -Congenital malformations of gallbladder bile ducts and liver -Obstructed labour due to maternal pelvic abnormality -Abnormal findings in specimens from respiratory organs and thorax -Congenital malformations of lung -Other congenital malformations of peripheral vascular system -Varicose veins of lower extremities -Varicose veins of other sites -Acute lymphadenitis -Other abnormal findings in urine -Unspecified abdominal hernia -Unspecified viral hepatitis -Other congenital malformations of digestive system -Other congenital malformations of circulatory system -Other congenital malformations of skin -Pneumoconiosis due to other inorganic dusts -Corns and callosities -Disorders of lacrimal system and orbit in diseases classified elsewhere -Alzheimer s disease -Endocarditis valve unspecified -Family history of other conditions -Unspecified maternal hypertension -Stroke not specified as haemorrhage or infarction -Subarachnoid haemorrhage -Unspecified human immunodeficiency virus -Other endocrine disorders -Other diseases of liver -Primary disorders of muscles -Pervasive developmental disorders -Other cerebrovascular diseases -Other diseases of gallbladder -Pain -Fracture of spine level unspecified -Acute hepatitis B -Abnormalities of heart beat -Scoliosis -Other congenital malformations of heart -Disorders of tooth development and eruption -Intracerebral haemorrhage -Retinal detachments and breaks -Tuberculosis of nervous system -Acute hepatitis A -Hookworm diseases -Female infertility -Sleep disorders -Thiamine deficiency -Viral conjunctivitis -Alcoholic liver disease -Spinal osteochondrosis -Diseases of salivary glands -Gender identity disorders -Status asthmaticus -Cystic kidney disease -Polyp of female genital tract -Persistent mood -Disorders of vitreous body -Ovarian dysfunction -Other coagulation defects -Granulomatous disorders of skin and subcutaneous tissue -Excessive vomiting in pregnancy -Hyperfunction of pituitary gland -Other nutritional deficiencies -Other rheumatic heart diseases -Other helminthiases -Unspecified viral infection of CNS -Diverticular disease of intestine -Premature separation of placenta -Retention of urine -Unspecified urinary incontinence -Isolated proteinuria -Cleft palate -Hydrocephalus -Visual disturbances -Unspecified dementia -Unspecified haematuria -Cholecystitis -Dystonia -Ascites -Iron deficiency anaemia -Acute renal failure -Nonspecific lymphadenitis -Cachexia -Disseminated intravascular coagulation -Senile cataract -Agranulocytosis -Helicobacter pylori -Reduction defects of lower limb -Congenital hydrocephalus -Immunodeficiency with predominantly antibody defects -Congenital malformations of oesophagus -Syndactyly -Other congenital malformations of intestine -Other functional intestinal disorders -Other disorders of peripheral nervous system -Spondylosis -Hypofunction and other disorders of pituitary gland -Other retinal disorders -Arterial embolism and thrombosis -Juvenile osteochondrosis of hip and pelvis -Encephalitis myelitis and encephalomyelitis -Atrial fibrillation and flutter -Dermatopolymyositis -Lack of food -Inflammatory diseases of prostate -Chronic renal failure -Postpolio syndrome -Dementia in Alzheimer s disease -Other disorders of circulatory system in diseases classified elsewhere -Meningitis due to other causes -Gestational hypertension with significant proteinuria -Respiratory disorders in diseases classified elsewhere -Vitamin B12 deficiency anaemia -Unspecified arthropod borne viral fever -HIV disease resulting in infectious and parasitic diseases -Chronic ischaemic heart disease -Mental and behavioural disorders due to use of cocaine -Benign mammary dysplasia -Depressive episode -Recurrent depressive disorder -Mental and behavioural disorders due to use of tobacco -Mental and behavioural disorders due to use of alcohol -Dorsalgia -Disorders of globe -Mental and behavioural disorders due to use of cannabinoids -Osteochondrodysplasia with defects of growth of tubular bones and spine -Mental and behavioural disorders due to use of opioids -Mosquito borne viral encephalitis -Tick borne viral encephalitis -Respiratory tuberculosis confimed -Unspecified lump in breast -Erysipeloid -Rheumatic fever without mention of heart involvement -Pyogenic arthritis -Toxic effect of metals -Staphylococcal scalded skin syndrome -Phobic anxiety disorders -Adult osteomalacia -Functional disorders of polymorphonuclear neutrophils -Encephalocele -Tuberculosis of other organs -Localized adiposity -Atopic dermatitis -Cardiomyopathy -other disorders of circulatory system -Crohn s disease -Unspecified diabetes mellitus -Other specified diabetes mellitus -Epilepsy -Glaucoma -Irritable bowel syndrome -Schizophrenia -Ulcerative colitis -Viral infection of unspecified site -Myositis -Other cataract -Cytomegaloviral disease -Endometriosis -Obesity -Insulin dependent diabetes mellitus -Non insulin dependent diabetes mellitus -Parkinson s disease -Juvenile arthritis -Cellulitis -Cushing s syndrome -Osteomyelitis -Spina bifida -Heart failure -Vitamin D deficiency -Dental caries -Migraine -Pulmonary embolism -Other peripheral vascular diseases -Multiple sclerosis -Acne -Ankylosing spondylitis -Angina pectoris -Atherosclerosis -Gastro oesophageal reflux disease -Sunburn -Cleft lip -Androgenic alopecia -Alopecia areata -Vitiligo -Hypospadias -Otosclerosis -Conduct disorders -Male infertility -Meningococcal infection -Calculus of kidney and ureter -Nephrotic syndrome -Osteonecrosis -Paget s disease of bone -Other anaemias -Gout -Diabetes mellitus in pregnancy -Duodenal ulcer -Cholelithiasis -Leishmaniasis -Eating disorders -Hypotension -Unspecified contact dermatitis -Schizoaffective disorders -Urticaria -Seborrhoeic keratosis -Shigellosis -Other vitamin deficiencies -Zoster -Pyoderma gangrenosum -Decubitus ulcer -Actinomycosis -Amoebiasis -Unspecified appendicitis -Ascariasis -Aspergillosis -Varicella -Cryptococcosis -Echinococcosis -Enterobiasis -Granuloma inguinale -Histoplasmosis -Infectious mononucleosis -Leptospirosis -Listeriosis -Miliary tuberculosis -Myiasis -Optic neuritis -Placenta praevia -Plasmodium falciparum malaria -Plasmodium vivax malaria -Acute poliomyelitis -Scarlet fever -Strongyloidiasis -Suppurative and unspecified otitis media -other syphilis -Toxoplasmosis -Yaws -Status epilepticus -Fracture of femur -Diaphragmatic hernia -Niacin deficiency -Gangrene -Acute myocardial infarction -Subsequent myocardial infarction -Peritonitis -Diseases of spleen -Typhus fever -Other diseases of intestine -Fibroblastic disorders -Unspecified acute lower respiratory infection -Other ill defined and unspecified causes of mortality -Cystitis -Lactose intolerance -Thyroiditis -Acute pancreatitis -Acanthosis nigricans -Allergic contact dermatitis -Cholesteatoma of middle ear -Erythema multiforme -Hyperhidrosis -Impetigo -Irritant contact dermatitis -Lichen planus -Parapsoriasis -Pemphigus -Pityriasis rosea -Rosacea -Seborrhoeic dermatitis -Atrophic disorders of skin -Coxarthrosis -Coalworker s pneumoconiosis -Ascorbic acid deficiency -Bacterial meningitis -Dysplasia of cervix uteri -Habitual aborter -Other rickettsioses -Secondary parkinsonism -Viral meningitis -Vitamin A deficiency -Spontaneous abortion -Phlebitis and thrombophlebitis -Unspecified renal colic -Taeniasis -Synovitis and tenosynovitis -Schistosomiasis -Unspecified abortion -Femoral hernia -Ventral hernia -Amyloidosis -Cicatricial alopecia -Other disorders of nervous system -Polyuria -Pruritus -Nausea and vomiting -Peptic ulcer site unspecified -Erythema nodosum -Oesophagitis -Common variable immunodeficiency -Adrenogenital disorders -Sickle cell disorders -Congenital malformations of great veins -Huntington s disease -Cystic fibrosis -Hypertrichosis -Sarcoidosis -Turner s syndrome -Congenital malformations of great arteries -Hereditary factor VIII deficiency -Hereditary factor IX deficiency -Congenital malformations of cardiac chambers and connections -Acute nephritic syndrome -Keratitis -Conjunctivitis -Hypoparathyroidism -Hyperaldosteronism -Hemiplegia -Gastric ulcer -Disorders of lacrimal system -Exfoliative dermatitis -Apocrine sweat disorders -Spotted fever -Unspecified nephritic syndrome -Facial nerve disorders -Essential primary hypertension -Congenital malformations of uterus and cervix -Abnormal findings in specimens from female genital organs -Other congenital malformations of male genital organs -Abnormal findings in specimens from male genital organs -Congenital lens malformations -Congenital malformations of eyelid lacrimal apparatus and orbit -Enduring personality changes not attributable to brain damage and disease -Congenital malformations of breast -Unspecified jaundice -Iridocyclitis -Abnormalities of gait and mobility -Hypoglycemic coma -Hepatic failure -Umbilical hernia -Polyhydramnios -cardiac arrest -Congenital deformities of feet -Abnormalities of forces of labour -Other assisted single delivery -Multiple delivery -Abnormality of red blood cells -Abnormal leukocyte morphology -Hypothermia -Lymphadenopathy -Abnormal findings in cerebrospinal fluid -Glycosuria -Congenital malformations of posterior segment of eye -Abnormality of aromatic amino acid family metabolism -Abnormality of glycoprotein metabolism -Abnormality of glycosaminoglycan metabolism -Congenital septal defect -Abscess of anal and rectal regions -Abnormalities of breathing -Paroxysmal tachycardia -Congenital malformations of anterior segment of eye -Gynecomastia -Polydactyly -Pilonidal cyst -Congenital obstructive defects of renal pelvis and congenital malformations of ureter -Single delivery by forceps and vacuum extractor -Personality disorder -Mixed and other personality disorders -Acquired pure red cell aplasia -Chorioretinitis -Other congenital malformations of upper alimentary tract -Congenital malformations of larynx -Cervicitis -Portal vein thrombosis -Cutaneous abscess furuncle and carbuncle -Congenital malformations of ear causing impairment of hearing -Other congenital malformations of ear -Abnormality of movement -Calcification and ossification of muscle -Eclampsia -Other mosquito borne viral fevers -Internal derangement of knee -Fistulae involving female genital tract -Multiple gestation -Postpartum haemorrhage -Retained placenta and membranes without haemorrhage -Faecal incontinence -Disturbances of skin sensation -Abnormal results of function studies -Superficial injury of head -Crushing injury of head -Crushing injury of head -Injury of heart -Superficial injury of abdomen lower back and pelvis -Injury of intra abdominal organs -Crushing injury of shoulder and upper arm -Fracture at wrist and hand level -Open wound of hip and thigh -Injury of nerves at hip and thigh level -Injury of nerves at hip and thigh level -Injury of blood vessels at hip and thigh level -Other and specified injuries of hip and thigh -Injury of nerves at lower leg level -Injury of nerves at lower leg level -Fractures involving multiple body regions -Dislocations sprains and strains involving multiple body regions -Dislocations sprains and strains involving multiple body regions -Crushing injuries involving multiple body regions -Fracture of upper limb level unspecified -Other injuries of upper limb level unspecified -Fracture of lower limb level unspecified -Other injuries of lower limb level unspecified -Foreign body in ear -Foreign body in alimentary tract -Burn and corrosion of ankle and foot -Burn and corrosion of ankle and foot -Burns and corrosions of multiple body regions -Burns and corrosions of multiple body regions -Burns classified according to extent of body surface involved -Frostbite involving multiple body regions and unspecified frostbite -Toxic effect of organic solvents -Toxic effect of soaps and detergents -Toxic effect of other gases fumes and vapours -Toxic effect of pesticides -Complications following infusion transfusion and therapeutic injection -Complications of cardiac and vascular prosthetic devices implants and grafts -Complications of genitourinary prosthetic devices implants and grafts -Complications of internal orthopaedic prosthetic devices implants and grafts -Complications of other internal prosthetic devices implants and grafts -Sequelae of injuries of head -Sequelae of injuries of upper limb -Sequelae of injuries of lower limb -Sequelae of burns corrosions and frostbite -Sequelae of burns corrosions and frostbite -Sequelae of burns corrosions and frostbite -Unspecified fall -Routine general health check up of defined subpopulation -Contraceptive management -Supervision of high risk pregnancy -Prophylactic surgery -Other orthopaedic follow up care -Care involving use of rehabilitation procedures -Disorders of mineral metabolism -Other disorders of eye and adnexa in diseases classified elsewhere -Nonrheumatic tricuspid valve disorders -Disorders of sclera and cornea in diseases classified elsewhere -Other disorders of cornea -uremia -Oesophageal varices -Disorders of autonomic nervous system -marasmus -Mononeuropathies of upper limb -Mononeuropathies of lower limb -Other disorders of binocular movement -Inflammatory disease of uterus except cervix -Polyneuropathy in diseases classified elsewhere -Noninflammatory disorders of ovary fallopian tube and broad ligament -Pain and other conditions associated with female genital organs and menstrual cycle -Anuria and oliguria -Multiple valve diseases -Disorders of male genital organs in diseases classified elsewhere -Obstructive and reflux uropathy -Disorders of eyelid in diseases classified elsewhere -Diseases of pulp and periapical tissues -Disorders of trigeminal nerve -Pulmonary valve disorders -Other disorders of tympanic membrane -Other diseases of oesophagus -Nonrheumatic mitral valve disorders -Rheumatic aortic valve diseases -Nonrheumatic aortic valve disorders -Other degenerative diseases of basal ganglia -Other inflammation of eyelid -Otitis externa -Other diseases of biliary tract -Haemorrhoids -Arthrosis of first carpometacarpal joint -Inflammatory polyneuropathy -Congenital malformations of aortic and mitral valves -HIV disease resulting in malignant neoplasms -Anaemia due to enzyme disorders -Other disorders of peritoneum -Intestinal malabsorption -Other headache syndromes -Disorders resulting from impaired renal tubular function -Unspecified intestinal parasitism -Nerve root and plexus disorders -HIV disease resulting in other specified diseases -HIV disease resulting in other conditions -Skin changes due to chronic exposure to nonionizing radiation -Cervical disc disorders -Other diseases of appendix -Small kidney of unknown cause -Perforation of tympanic membrane -Other spirochaetal infections -Disturbances of smell and taste -Other diseases of jaws -Diseases of Bartholin s gland -Soft tissue disorders related to use overuse and pressure -Soft tissue disorders in diseases classified elsewhere -Waist circumference -Hip circumference -Standing height -Pulse rate, automated reading -Sleep duration -Morning/evening person (chronotype) -Sleeplessness / insomnia -Snoring -Alcohol intake frequency. -Mood swings -Irritability -Loneliness, isolation -Frequency of tiredness / lethargy in last 2 weeks -Hearing difficulty/problems with background noise -Chest pain or discomfort -Relative age voice broke -Age when periods started (menarche) -Had menopause -Forced vital capacity (FVC) -Forced expiratory volume in 1-second (FEV1) -Neck/shoulder pain for 3+ months -Hip pain for 3+ months -Back pain for 3+ months -Ever had hysterectomy (womb removed) -Length of menstrual cycle -Stomach/abdominal pain for 3+ months -Headaches for 3+ months -Gestational diabetes only -Diastolic blood pressure, automated reading -Systolic blood pressure, automated reading -Pulse rate -Leg pain on walking -Leg pain when standing still or sitting -Leg pain in calf/calves -Chest pain felt during physical activity -Chest pain felt outside physical activity -Maximum heart rate during fitness test -Fluid intelligence score -Birth weight -Bipolar disorder status -Neuroticism score -Forced expiratory volume in 1-second (FEV1), Best measure -Forced vital capacity (FVC), Best measure -Body mass index (BMI) -Weight -Pulse wave Arterial Stiffness index -hayfever or allergic rhinitis -asthma -emphysema -chronic bronchitis -COPD (chronic obstructive pulmonary disease) -sarcoidosis -bronchiectasis -idiopathic pulmonary fibrosis -tuberculosis -lung cancer (not mesothelioma) -Body fat percentage -Whole body fat mass -Whole body fat-free mass -Basal metabolic rate -Potassium in urine -Sodium in urine -Age at death -lung cancer -breast cancer -skin cancer -cancer of lip/mouth/pharynx/oral cavity -larynx/throat cancer -tongue cancer -oesophageal cancer -stomach cancer -small intestine/small bowel cancer -large bowel cancer/colorectal cancer -colon cancer/sigmoid cancer -rectal cancer -liver/hepatocellular cancer -eye and/or adnexal cancer -brain cancer / primary malignant brain tumour -kidney/renal cell cancer -bladder cancer -ovarian cancer -uterine/endometrial cancer -cervical cancer -prostate cancer -testicular cancer -lymphoma -leukaemia -multiple myeloma -hodgkins lymphoma / hodgkins disease -non-hodgkins lymphoma -chronic lymphocytic -chronic myeloid -malignant melanoma -non-melanoma skin cancer -basal cell carcinoma -squamous cell carcinoma -primary bone cancer -thyroid cancer -malignant lymph node, unspecified -hypertension -heart/cardiac problem -peripheral vascular disease -venous thromboembolic disease -essential hypertension -gestational hypertension/pre-eclampsia -angina -heart attack/myocardial infarction -heart failure/pulmonary odema -heart arrhythmia -cardiomyopathy -stroke -transient ischaemic attack (tia) -subdural haemorrhage/haematoma -subarachnoid haemorrhage -leg claudication/ intermittent claudication -pulmonary embolism +/- dvt -deep venous thrombosis (dvt) -asthma -chronic obstructive airways disease/copd -emphysema/chronic bronchitis -bronchiectasis -interstitial lung disease -asbestosis -pulmonary fibrosis -fibrosing alveolitis/unspecified alveolitis -sleep apnoea -pleurisy -spontaneous pneumothorax/recurrent pneumothorax -gastro-oesophageal reflux (gord) / gastric reflux -oesophagitis/barretts oesophagus -gastric/stomach ulcers -gastritis/gastric erosions -irritable bowel syndrome -hepatitis -infective/viral hepatitis -liver failure/cirrhosis -gall bladder disease -cholelithiasis/gall stones -cholecystitis -pancreatitis -peritonitis -gastrointestinal bleeding -renal/kidney failure -urinary tract infection/kidney infection -kidney stone/ureter stone/bladder stone -ureteric obstruction/hydronephrosis -urinary frequency / incontinence -diabetes -gestational diabetes -type 1 diabetes -type 2 diabetes -hyperthyroidism/thyrotoxicosis -hypothyroidism/myxoedema -parathyroid hyperplasia/adenoma -pituitary adenoma/tumour -encephalitis -bell's palsy/facial nerve palsy -peripheral neuropathy -acute infective polyneuritis/guillain-barre syndrome -multiple sclerosis -parkinsons disease -dementia/alzheimers/cognitive impairment -epilepsy -migraine -spinal injury -eye infection -retinal problem -glaucoma -cataract -retinal detachment -retinal artery/vein occlusion -depression -schizophrenia -deliberate self-harm/suicide attempt -mania/bipolar disorder/manic depression -bone disorder -joint disorder -osteomyelitis -osteoporosis -ankylosing spondylitis -myositis/myopathy -low platelets/platelet disorder -iron deficiency anaemia -pernicious anaemia -thalassaemia -ovarian cyst or cysts -polycystic ovaries/polycystic ovarian syndrome -uterine fibroids -vaginal prolapse/uterine prolapse -fibrocystic disease -breast cysts -sarcoidosis -vasculitis -connective tissue disorder -allergy/hypersensitivity/anaphylaxis -giant cell/temporal arteritis -polymyalgia rheumatica -wegners granulmatosis -systemic lupus erythematosis/sle -sjogren's syndrome/sicca syndrome -scleroderma/systemic sclerosis -allergy or anaphylactic reaction to food -hayfever/allergic rhinitis -pneumonia -peptic ulcer -endometriosis -female infertility -alcohol dependency -ear/vestibular disorder -chronic sinusitis -nasal polyps -otosclerosis -meniere's disease -cerebral aneurysm -myocarditis -polycystic kidney -thyroiditis -hypopituitarism -cerebral palsy -optic neuritis -headaches (not migraine) -myasthenia gravis -polycythaemia vera -hiv/aids -tuberculosis (tb) -malaria -helicobacter pylori -anaemia -neutropenia/lymphopenia -eczema/dermatitis -psoriasis -chronic skin ulcers -malabsorption/coeliac disease -duodenal ulcer -diverticular disease/diverticulitis -colitis/not crohns or ulcerative colitis -rectal or colon adenoma/polyps -inflammatory bowel disease -crohns disease -ulcerative colitis -rheumatoid arthritis -osteoarthritis -gout -post-traumatic stress disorder -anorexia/bulimia/other eating disorder -atrial fibrillation -emphysema -high cholesterol -hiatus hernia -sciatica -psoriatic arthropathy -rheumatic fever -chronic fatigue syndrome -irregular heart beat -brain haemorrhage -varicose veins -lymphoedema -pneumothorax -labyrinthitis -vertigo -pyloric stenosis -appendicitis -anal fissure -haemorrhoids / piles -jaundice (unknown cause) -gastroenteritis/dysentry -dyspepsia / indigestion -abdominal hernia -umbilical hernia -inguinal hernia -cystitis -bph / benign prostatic hypertrophy -prostatitis -erectile dysfunction / impotence -grave's disease -trigemminal neuralgia -benign / essential tremor -polio / poliomyelitis -dry eyes -iritis -post-natal depression -disc degeneration -back pain -scoliosis -spinal stenosis -joint pain -arthritis (nos) -plantar fascitis -carpal tunnel syndrome -fibromyalgia -dupuytren's contracture -acne/acne vulgaris -lichen planus -lichen sclerosis -cervical intra-epithelial neoplasia (cin) / precancerous cells cervix -menorrhagia (unknown cause) -ectopic pregnancy -miscarriage -breast fibroadenoma -raynaud's phenomenon/disease -food intolerance -urticaria -infectious mononucleosis / glandular fever / epstein barr virus (ebv) -measles / morbillivirus -mumps / epidemic parotitis -rubella / german measles -chickenpox -whooping cough / pertussis -shingles -herpes simplex -hepatitis a -hepatitis b -hepatitis c -mitral regurgitation / incompetence -aortic regurgitation / incompetence -hypertrophic cardiomyopathy (hcm / hocm) -pericarditis -respiratory infection -tinnitus / tiniitis -tonsiltis -constipation -rectal prolapse -femoral hernia -incisional hernia -nephritis -thyroid goitre -blepharitis / eyelid infection -obsessive compulsive disorder (ocd) -insomnia -osteopenia -tendonitis / tendinitis / tenosynovitis -bursitis -tennis elbow / lateral epicondylitis -cellulitis -fracture skull / head -fracture radius -fracture ulna -fracture tibia -septicaemia / sepsis -meningioma / benign meningeal tumour -rosacea -vitiligo -cervical erosion -dysmenorrhoea / dysmenorrhea -menopausal symptoms / menopause -alopecia / hair loss -scarlet fever / scarlatina -undescended testicle -Hearing difficulty/problems: Yes -Comparative height size at age 10 -Miserableness -Sensitivity / hurt feelings -Fed-up feelings -Nervous feelings -Guilty feelings -Risk taking -Overall health rating -Number of live births -General pain for 3+ months -Chest pain or discomfort walking normally -Chest pain due to walking ceases when standing still -Chest pain or discomfort when walking uphill or hurrying -Knee pain for 3+ months -Number of spontaneous miscarriages -Heel bone mineral density (BMD) T-score, automated (left) -Heel bone mineral density (BMD) T-score, automated (right) -Pulse wave reflection index -Family relationship satisfaction -Maximum workload during fitness test -Prospective memory result -Cough on most days -Years of cough on most days -liver/biliary/pancreas problem -psychological/psychiatric problem -head injury -gynaecological disorder (not cancer) -peripheral nerve injury -fracture jaw -fracture nose -fracture face / orbit / eye socket -fracture clavicle / collar bone -fracture shoulder / scapula -fracture forearm / wrist -fracture wrist / colles fracture -fracture hand -fracture finger -fracture thumb -fracture rib -fracture pelvis -fracture neck of femur / hip -fracture shaft of femur -fracture patella / knee -fracture lower leg / ankle -fracture fibula -fracture foot -fracture metatarsal -fracture toe -Hair/balding pattern: Pattern 2 -Hair/balding pattern: Pattern 3 -Hair/balding pattern: Pattern 4 -Hand grip strength (left) -Hand grip strength (right) -Heel bone mineral density (BMD) T-score, automated -Age completed full time education -Daytime dozing / sleeping (narcolepsy) -Current tobacco smoking -Past tobacco smoking -Exposure to tobacco smoke at home -Exposure to tobacco smoke outside home -Worrier / anxious feelings -Frequency of depressed mood in last 2 weeks -Frequency of unenthusiasm / disinterest in last 2 weeks -Diabetes diagnosed by doctor -Cancer diagnosed by doctor -Fractured/broken bones in last 5 years -Ever had stillbirth, spontaneous miscarriage or termination -Ever used hormone-replacement therapy (HRT) -Fracture resulting from simple fall -Facial pains for 3+ months -Longest period of depression -Number of depression episodes -Longest period of unenthusiasm / disinterest -Mean time to correctly identify matches -Creatinine (enzymatic) in urine -Handedness (chirality/laterality): Left-handed -Handedness (chirality/laterality): Use both right and left hands equally -sarcoma/fibrosarcoma -cin/pre-cancer cells cervix -rodent ulcer -heart valve problem/heart murmur -pericardial problem -other respiratory problems -oesophageal disorder -stomach disorder -non-infective hepatitis -renal failure requiring dialysis -renal failure not requiring dialysis -parathyroid gland problem (not cancer) -meningitis -chronic/degenerative neurological problem -anxiety/panic attacks -muscle/soft tissue problem -spine arthritis/spondylitis -prolapsed disc/slipped disc -other renal/kidney problem -bronchitis -other joint disorder -diabetic neuropathy/ulcers -cervical spondylosis -svt / supraventricular tachycardia -anal problem -macular degeneration -bowel / intestinal obstruction -stress -fracture upper arm / humerus / elbow -fracture vertebra / crush fracture / vertebral collapse -allergy to house dust mite -benign neuroma -Hearing difficulty/problems: I am completely deaf -Which eye(s) are affected by cataract: Right eye -Which eye(s) are affected by cataract: Left eye -Number of self-reported cancers -Number of self-reported non-cancer illnesses -Number of operations, self-reported -Number of treatments/medications taken -Townsend deprivation index at recruitment -Number of incorrect matches in round -Getting up in morning -Nap during day -Comparative body size at age 10 -Father's age at death -Number of full brothers -Number of full sisters -Tense / 'highly strung' -Worry too long after embarrassment -Suffer from 'nerves' -Seen doctor (GP) for nerves, anxiety, tension or depression -Seen a psychiatrist for nerves, anxiety, tension or depression -Long-standing illness, disability or infirmity -Falls in the last year -Wheeze or whistling in the chest in last year -Relative age of first facial hair -Number of children fathered -Birth weight of first child -Age at first live birth -Age at last live birth -Bilateral oophorectomy (both ovaries removed) -Peak expiratory flow (PEF) -Pace-maker -Hearing aid user -Mother's age at death -Number of stillbirths -Age of primiparous women at birth of child -Pulse wave reflection index -Happiness -Work/job satisfaction -Health satisfaction -Friendships satisfaction -Financial situation satisfaction -Ever depressed for a whole week -Ever unenthusiastic/disinterested for a whole week -Ever manic/hyper for 2 days -Ever highly irritable/argumentative for 2 days -Shortness of breath walking on level ground -Cochlear implant -Tinnitus severity/nuisance -Number of unenthusiastic/disinterested episodes -Surgery on leg arteries (other than for varicose veins) -Length of longest manic/irritable episode -Severity of manic/irritable episodes -Able to walk or cycle unaided for 10 minutes -Target heart rate achieved -Sitting height -Cascot confidence score -Bring up phlegm/sputum/mucus on most days -Whole body water mass -Reported occurrences of cancer -Procreative_management -other abdominal problem -oesophageal stricture -bladder problem (not cancer) -prostate problem (not cancer) -testicular problems (not cancer) -thyroid problem (not cancer) -thyroid radioablation therapy -adrenocortical insufficiency/addison's disease -neurological injury/trauma -eye/eyelid problem -cranial nerve problem/palsy -spinal cord disorder -peripheral nerve disorder -trapped nerve/compressed nerve -diabetic eye disease -eye trauma -nervous breakdown -back problem -uterine polyps -breast disease (not cancer) -allergy or anaphylactic reaction to drug -enlarged prostate -muscle or soft tissue injuries -burns -nasal/sinus disorder -throat or larynx disorder -vocal cord polyp -other neurological problem -clotting disorder/excessive bleeding -hereditary/genetic haematological disorder -blistering/desquamating skin disorder -disc problem -neck problem/injury -cervical polyps -soft tissue inflammation -abnormal smear (cervix) -benign breast lump -Problems_related_to_social_environment -Problems_related_to_life_management_difficulty -Volume_depletion -Spondylopathies_in_diseases_classified_elsewhere -Shoulder_lesions -Maternal_care_for_known_or_suspected_malpresentation_of_fetus -Maternal_care_for_known_or_suspected_disproportion -Maternal_care_for_known_or_suspected_abnormality_of_pelvic_organs -Long_labour -Perineal_laceration_during_delivery -Other_obstetric_trauma -Complications_of_anaesthesia_during_the_puerperium -Intrauterine_hypoxia -Abnormal_serum_enzyme_levels -Injury_of_blood_vessels_at_neck_level injury EFO_0009886 Broad S15 DONE -Injury_of_other_intrathoracic_organs -Injury_of_blood_vessels_at_abdomen_lower_back_and_pelvis_level -Injury_of_blood_vessels_at_shoulder_and_upper_arm_level -Other_fluke_infections -Other_postsurgical_states -Acquired_haemolytic_anaemia -Artificial_opening_status -Persons encountering health services in other circumstances -Persons encountering health services for other counselling and medical advice, not elsewhere classified -Hereditary_ataxia -Mycetoma -Viral_warts -Acquired_absence_of_limb -Convalescence -Pemphigoid -Eccrine_sweat_disorders -Traumatic_amputations_involving_multiple_body_regions -Need_for_immunization_against_certain_single_viral_diseases -Need_for_immunization_against_other_single_viral_diseases -Need_for_immunization_against_other_single_infectious_diseases -Need_for_immunization_against_combinations_of_infectious_diseases -Transplanted_organ_and_tissue_status -Persons encountering health services for specifie procedures, not carried out -Haemorrhage_from_respiratory_passages -Renal_tubulo_interstitial_disorders_in_diseases_classified_elsewhere -Occlusion_and_stenosis_of_cerebral_arteries_notcerebral_infarction -Orchitis_and_epididymitis -Other_disorders_of_nervous_system -Rheumatic_fever_with_heart_involvement -Rapidly_progressive_nephritic_syndrome -Dizziness_and_giddiness -Chlamydia_psittaci_infection -Glomerular_disorders_in_diseases_classified_elsewhere -Hypertensive_renal_disease -Congenital_ichthyosis -Fracture of skull and facial bones -Headache -Fever of unknown origin -Dysphagia -Heartburn -Cough -Urethritis and urethral syndrome -Other arthritis -Systemic lupus erythematosus -Systemic sclerosis -Psoriasis -Follicular cysts of skin and subcutaneous tissue -Other disorders of pigmentation -Ulcer of lower limb, not elsewhere classified -Dyspepsia -Inguinal hernia -Acute sinusitis -Pneumonia due to Streptococcus pneumoniae -Bacterial pneumonia, not elsewhere classified -Pneumonia, organism unspecified -Nasal polyp -Peritonsillar abscess -Emphysema -Other chronic obstructive pulmonary disease -Asthma -Bronchiectasis -Other interstitial pulmonary diseases -Other respiratory disorders -Aortic aneurysm and dissection -Hordeolum and chalazion -Myasthenia gravis and other myoneural disorders -Manic episode -Bipolar affective disorder -Sexual dysfunction, not caused by organic disorder or disease -Other hypothyroidism -Melanoma in situ -Haemangioma and lymphangioma, any site -Leiomyoma of uterus -Benign neoplasm of ovary -Benign neoplasm of other and unspecified female genital organs -Benign neoplasm of brain and other parts of central nervous system -Benign neoplasm of thyroid gland -Polycythaemia vera -Myelodysplastic syndromes -Purpura and other haemorrhagic conditions -Malignant neoplasm of colon -Malignant neoplasm of larynx -Mesothelioma -Secondary and unspecified malignant neoplasm of lymph nodes -Hodgkin's disease -Follicular [nodular] non-Hodgkin's lymphoma -Multiple myeloma and malignant plasma cell neoplasms -Lymphoid leukaemia -Myeloid leukaemia -Fracture of shoulder and upper arm -Elevated blood glucose level -Other necrotising vasculopathies -Other local infections of skin and subcutaneous tissue -Retinal vascular occlusions -Reaction to severe stress, and adjustment disorders -Benign neoplasm of colon, rectum, anus and anal canal -Benign neoplasm of breast -Malignant neoplasm of rectosigmoid junction -Malignant neoplasm of breast -Malignant neoplasm of prostate -Malignant neoplasm of testis -Malignant neoplasm of brain -Failure and rejection of transplanted organs and tissues -Poisoning by diuretics and other and unspecified drugs, medicaments and biological substances -Poisoning by psychotropic drugs, not elsewhere classified -Poisoning by antiepileptic, sedative-hypnotic and anti-Parkinsonism drugs -Poisoning by narcotics and psychodysleptics [hallucinogens] -Poisoning by nonopioid analgesics, antipyretics and antirheumatics -Dislocation, sprain and strain of joints and ligaments at ankle and foot level -Fracture of foot, except ankle -Fracture of forearm -Abdominal and pelvic pain -Medical abortion -Other disorders of bladder -Hydrocele and spermatocele -Redundant prepuce, phimosis and paraphimosis -Salpingitis and oophoritis -Other inflammation of vagina and vulva -Other rheumatoid arthritis -Other joint disorders, not elsewhere classified -Osteoporosis without pathological fracture -Lichen simplex chronicus and prurigo -Other disorders of skin and subcutaneous tissue, not elsewhere classified -Acute appendicitis -Chronic sinusitis -Pneumothorax -Acute pericarditis -Other nontraumatic intracranial haemorrhage -Cerebral infarction -Other aneurysm -Other hearing loss -Transient cerebral ischaemic attacks and related syndromes -Acute and transient psychotic disorders -Other anxiety disorders -Mental disorder, not otherwise specified -Other disorders of thyroid -Hyperparathyroidism and other disorders of parathyroid gland -Carcinoma in situ of skin -Carcinoma in situ of breast -Carcinoma in situ of cervix uteri -Benign neoplasm of mouth and pharynx -Benign neoplasm of major salivary glands -Other benign neoplasms of uterus -Neoplasm of uncertain or unknown behaviour of female genital organs -Neoplasm of uncertain or unknown behaviour of endocrine glands -Malignant neoplasm of other and unspecified parts of tongue -Malignant neoplasm of tonsil -Malignant neoplasm of oesophagus -Malignant neoplasm of stomach -Malignant neoplasm of rectum -Malignant neoplasm of anus and anal canal -Malignant neoplasm of liver and intrahepatic bile ducts -Malignant neoplasm of pancreas -Malignant neoplasm of bronchus and lung -Malignant melanoma of skin -Malignant neoplasm of cervix uteri -Malignant neoplasm of corpus uteri -Malignant neoplasm of ovary -Malignant neoplasm of kidney, except renal pelvis -Malignant neoplasm of bladder -Malignant neoplasm of eye and adnexa -Malignant neoplasm of thyroid gland -Diffuse non-Hodgkin's lymphoma -Chronic viral hepatitis -Diarrhoea and gastro-enteritis of presumed infectious origin -Other septicaemia -Personal history of other diseases and conditions -Family history of malignant neoplasm -Other medical care -Fitting and adjustment of other devices -Adjustment and management of implanted device -Donors of organs and tissues -Fitting and adjustment of external prosthetic device -Other surgical follow-up care -Attention to artificial openings -Postpartum care and examination -Antenatal screening -Certain early complications of trauma, not elsewhere classified -Follow-up care involving plastic surgery -Procedures for purposes other than remedying health state -Abnormal findings on diagnostic imaging of other body structures -Symptoms and signs concerning food and fluid intake -Pregnancy examination and test -Special screening examination for other diseases and disorders -Special screening examination for neoplasms -Special screening examination for infectious and parasitic diseases -Follow-up examination after treatment for conditions other than malignant neoplasms -Follow-up examination after treatment for malignant neoplasm -Examination and observation for other reasons -Medical observation and evaluation for suspected diseases and conditions -Other special examinations and investigations of persons without complaint or reported diagnosis -General examination and investigation of persons without complaint or reported diagnosis -Other complications of surgical and medical care, not elsewhere classified -Complications peculiar to reattachment and amputation -Complications of procedures, not elsewhere classified -Certain early complications of trauma, not elsewhere classified -Adverse effects, not elsewhere classified -Foreign body in respiratory tract -Injury of unspecified body region -Open wound of ankle and foot -Other and unspecified injuries of lower leg -Injury of muscle and tendon at lower leg level -Dislocation, sprain and strain of joints and ligaments of knee -Fracture of lower leg, including ankle -Open wound of lower leg -Superficial injury of lower leg -Injury of muscle and tendon at hip and thigh level -Other and unspecified injuries of wrist and hand -Traumatic amputation of wrist and hand -Crushing injury of wrist and hand -Injury of muscle and tendon at wrist and hand level -Dislocation, sprain and strain of joints and ligaments at wrist and hand level -Open wound of wrist and hand -Superficial injury of wrist and hand -Injury of muscle and tendon at forearm level -Open wound of forearm -Injury of muscle and tendon at shoulder and upper arm level -Dislocation, sprain and strain of joints and ligaments of shoulder girdle -Other and unspecified injuries of abdomen, lower back and pelvis -Open wound of abdomen, lower back and pelvis -Fracture of rib(s), sternum and thoracic spine -Superficial injury of thorax -Dislocation, sprain and strain of joints and ligaments at neck level -Fracture of neck -Other and unspecified injuries of head -Intracranial injury -Injury of eye and orbit -Open wound of head -Other abnormal products of conception -Abnormal findings on diagnostic imaging of lung -Abnormal findings on diagnostic imaging of central nervous system -Other abnormal findings of blood chemistry -Other abnormal immunological findings in serum -Unknown and unspecified causes of morbidity -Other general symptoms and signs -Maternal care for other conditions predominantly related to pregnancy -Oedema, not elsewhere classified -Convulsions, not elsewhere classified -Syncope and collapse -Senility -Malaise and fatigue -Voice disturbances -Speech disturbances, not elsewhere classified -Other symptoms and signs involving cognitive functions and awareness -Somnolence, stupor and coma -Other symptoms and signs involving the urinary system -Other symptoms and signs involving the nervous and musculoskeletal systems -Other skin changes -Localised swelling, mass and lump of skin and subcutaneous tissue -Rash and other nonspecific skin eruption -Other symptoms and signs involving the digestive system and abdomen -Flatulence and related conditions -Other symptoms and signs involving the circulatory and respiratory systems -Pain in throat and chest -Other congenital malformations of tongue, mouth and pharynx -Other congenital malformations of face and neck -Ectopic pregnancy -Maternal care for known or suspected foetal abnormality and damage -Gestational [pregnancy-induced] hypertension without significant proteinuria -Haemorrhage in early pregnancy -Maternal care for other known or suspected foetal problems -Other deforming dorsopathies -Other inflammatory spondylopathies -Other disorders of amniotic fluid and membranes -Antepartum haemorrhage, not elsewhere classified -False labour -Prolonged pregnancy -Obstructed labour due to malposition and malpresentation of foetus -Other obstructed labour -Labour and delivery complicated by foetal stress [distress] -Labour and delivery complicated by umbilical cord complications -Other complications of labour and delivery, not elsewhere classified -Single spontaneous delivery -Single delivery by Caesarean section -Complications of the puerperium, not elsewhere classified -Other maternal diseases classifiable elsewhere but complicating pregnancy, childbirth and the puerperium -Recurrent and persistent haematuria -Acute tubulo-interstitial nephritis -Tubulo-interstitial nephritis, not specified as acute or chronic -Calculus of lower urinary tract -Other disorders of kidney and ureter, not elsewhere classified -Neuromuscular dysfunction of bladder, not elsewhere classified -Other disorders of urethra -Other disorders of urinary system -Hyperplasia of prostate -Other disorders of prostate -Other disorders of penis -Inflammatory disorders of male genital organs, not elsewhere classified -Other disorders of male genital organs -Inflammatory disorders of breast -Other disorders of breast -Other female pelvic inflammatory diseases -Other noninflammatory disorders of uterus, except cervix -Erosion and ectropion of cervix uteri -Other noninflammatory disorders of cervix uteri -Other noninflammatory disorders of vagina -Other noninflammatory disorders of vulva and perineum -Excessive, frequent and irregular menstruation -Other abnormal uterine and vaginal bleeding -Menopausal and other perimenopausal disorders -Postprocedural disorders of genito-urinary system, not elsewhere classified -Other arthrosis -Acquired deformities of fingers and toes -Other acquired deformities of limbs -Disorders of patella -Other specific joint derangements -Other systemic involvement of connective tissue -Other spondylopathies -Other dorsopathies, not elsewhere classified -Other spondylopathies -Other intervertebral disk disorders -Other dorsopathies, not elsewhere classified -Other disorders of muscle -Spontaneous rupture of synovium and tendon -Other disorders of synovium and tendon -Other bursopathies -Enthesopathies of lower limb, excluding foot -Other enthesopathies -Other soft tissue disorders, not elsewhere classified -Osteoporosis with pathological fracture -Disorders of continuity of bone -Other disorders of bone density and structure -Other disorders of bone -Other disorders of cartilage -Other acquired deformities of musculoskeletal system and connective tissue -Postprocedural musculoskeletal disorders, not elsewhere classified -Dermatitis due to substances taken internally -Other dermatitis -Other erythematous conditions -Nail disorders -Other follicular disorders -Other epidermal thickening -Embedded and impacted teeth -Gingivitis and periodontal diseases -Other disorders of gingiva and edentulous alveolar ridge -Other disorders of teeth and supporting structures -Cysts of oral region, not elsewhere classified -Stomatitis and related lesions -Other diseases of lip and oral mucosa -Diseases of tongue -Other diseases of stomach and duodenum -Other non-infective gastro-enteritis and colitis -Paralytic ileus and intestinal obstruction without hernia -Fissure and fistula of anal and rectal regions -Other diseases of anus and rectum -Other inflammatory liver diseases -Other diseases of pancreas -Postprocedural disorders of digestive system, not elsewhere classified -Other diseases of digestive system -Acute pharyngitis -Acute tonsillitis -Acute upper respiratory infections of multiple and unspecified sites -Chronic rhinitis, nasopharyngitis and pharyngitis -Other disorders of nose and nasal sinuses -Chronic diseases of tonsils and adenoids -Diseases of vocal cords and larynx, not elsewhere classified -Other diseases of upper respiratory tract -Bronchitis, not specified as acute or chronic -Pyothorax -Pleural effusion, not elsewhere classified -Respiratory failure, not elsewhere classified -Rheumatic mitral valve diseases -Other diseases of pericardium -Acute and subacute endocarditis -Atrioventricular and left bundle-branch block -Other conduction disorders -Other cardiac arrhythmias -Occlusion and stenosis of precerebral arteries, not resulting in cerebral infarction -Other disorders of arteries and arterioles -Diseases of capillaries -Other venous embolism and thrombosis -Other disorders of veins -Other non-infective disorders of lymphatic vessels and lymph nodes -Other disorders of eyelid -Disorders of orbit -Other disorders of conjunctiva -Other disorders of lens -Paralytic strabismus -Other strabismus -Other disorders of eye and adnexa -Postprocedural disorders of eye and adnexa, not elsewhere classified -Other disorders of external ear -Nonsuppurative otitis media -Other disorders of Eustachian tube -Disorders of vestibular function -Other diseases of inner ear -Otalgia and effusion of ear -Other disorders of ear, not elsewhere classified -Other demyelinating diseases of central nervous system -Other mononeuropathies -Other polyneuropathies -Paraplegia and tetraplegia -Other disorders of brain -Other diseases of spinal cord -Somatoform disorders -Other non-toxic goitre -Thyrotoxicosis [hyperthyroidism] -Other disorders of pancreatic internal secretion -Other disorders of fluid, electrolyte and acid-base balance -Carcinoma in situ of other and unspecified genital organs -Carcinoma in situ of other and unspecified sites -Benign neoplasm of other and ill-defined parts of digestive system -Benign neoplasm of middle ear and respiratory system -Benign neoplasm of bone and articular cartilage -Benign lipomatous neoplasm -Other benign neoplasms of connective and other soft tissue -Melanocytic naevi -Other benign neoplasms of skin -Benign neoplasm of urinary organs -Benign neoplasm of meninges -Benign neoplasm of other and unspecified endocrine glands -Benign neoplasm of other and unspecified sites -Neoplasm of uncertain or unknown behaviour of oral cavity and digestive organs -Neoplasm of uncertain or unknown behaviour of middle ear and respiratory and intrathoracic organs -Neoplasm of uncertain or unknown behaviour of urinary organs -Other neoplasms of uncertain or unknown behaviour of lymphoid, haematopoietic and related tissue -Neoplasm of uncertain or unknown behaviour of other and unspecified sites -Other aplastic anaemias -Other diseases of blood and blood-forming organs -Other disorders involving the immune mechanism, not elsewhere classified -Other malignant neoplasms of skin -Malignant neoplasm of other connective and soft tissue -Secondary malignant neoplasm of respiratory and digestive organs -Secondary malignant neoplasm of other sites -Malignant neoplasm without specification of site -Other and unspecified types of non-Hodgkin's lymphoma -Candidiasis -Other bacterial intestinal infections -Viral and other specified intestinal infections -Other predominantly sexually transmitted diseases, not elsewhere classified -Other disorders of adrenal gland \ No newline at end of file diff --git a/.github/inputs/test-script.py b/.github/inputs/test-script.py deleted file mode 100644 index 6617584..0000000 --- a/.github/inputs/test-script.py +++ /dev/null @@ -1,25 +0,0 @@ -import pandas as pd - - -def extractTerms( - goldStandard="https://raw.githubusercontent.com/EBISPOT/EFO-UKB-mappings/master/UK_Biobank_master_file.tsv", - columnName="ZOOMA QUERY", - fileName="./terms.txt", -): - """ - extracts the terms in the column columnName of the goldStandard .tsv file - and saves them - """ - biobank = pd.read_csv( - goldStandard, - sep="\t", - header=0, - ) - - terms = "" - for term in biobank[columnName]: - terms += term + "\n" - terms = terms[:-1] # remove trailing newline - - with open(fileName, "w") as f: - f.write(terms) diff --git a/.github/workflows/python-test.yml b/.github/workflows/mapper-test.yml similarity index 59% rename from .github/workflows/python-test.yml rename to .github/workflows/mapper-test.yml index 133250c..be112f2 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/mapper-test.yml @@ -1,7 +1,7 @@ # This workflow will install Python dependencies, run tests and lint with a single version of Python # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions -name: Python application +name: Mapper Test on: push: @@ -12,9 +12,22 @@ on: jobs: run_mapper: runs-on: ubuntu-latest - name: Run Mapper + name: Run Tests steps: - uses: actions/checkout@v2 + name: Checkout out mapper repository + with: + path: mapper + - uses: actions/checkout@v2 + name: Checkout test repository + with: + path: tests + repository: "ccb-hms/ontology-mapper-tests" + token: ${{ secrets.MAPPER_TESTING }} + fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. + - name: Go into mapper repository and set up local variables + run: | + cd mapper - name: Set up Python 3.9 uses: actions/setup-python@v2 with: @@ -24,35 +37,26 @@ jobs: python -m pip install --upgrade pip pip install flake8 pytest if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Run mapper on Biobank source terms + - name: Run mapper on UK Biobank source terms run: | - python3 t2t.py -s ./.github/inputs/terms.txt -t https://github.com/EBISPOT/efo/releases/download/current/efo.owl - - name: Archive mapping output - uses: actions/upload-artifact@v2 - with: - name: mapping-output - path: t2t-out-*.csv - save_to_test: - runs-on: ubuntu-latest - name: Save Output to Test Repo - needs: run_mapper - steps: - - uses: actions/checkout@v2 - name: Checkout test repository - with: - repository: "ccb-hms/ontology-mapper-tests" - token: ${{ secrets.MAPPER_TESTING }} - fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - - name: Download a single artifact - uses: actions/download-artifact@v2 - with: - name: mapping-output - - name: Commit files + python3 t2t.py -s $source_path -t $target_path -o $output_path + env: + source_path: ../tests/data/ukb-efo/terms.txt + target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl + output_path: ../tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv + - name: Setup summary spreadsheet row + run: | + echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> summary_path + env: + sumamry_path: "../tests/summary.csv" + - name: Commit changes to tests repo run: | + cd ../tests git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" - git add t2t-out-*.csv - git commit -m "Add file" + git add ./mapper-outputs/* + git add ./summary.csv + git commit -m "Add files" - name: Push changes uses: ad-m/github-push-action@master with: From 9b302f3ee2c12f87698502a8670d722517276400 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 21:45:15 -0700 Subject: [PATCH 13/41] update workflow so repos are nested rather than side-by-side --- .github/workflows/mapper-test.yml | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index be112f2..3494d87 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -16,8 +16,6 @@ jobs: steps: - uses: actions/checkout@v2 name: Checkout out mapper repository - with: - path: mapper - uses: actions/checkout@v2 name: Checkout test repository with: @@ -25,9 +23,6 @@ jobs: repository: "ccb-hms/ontology-mapper-tests" token: ${{ secrets.MAPPER_TESTING }} fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - - name: Go into mapper repository and set up local variables - run: | - cd mapper - name: Set up Python 3.9 uses: actions/setup-python@v2 with: @@ -41,17 +36,17 @@ jobs: run: | python3 t2t.py -s $source_path -t $target_path -o $output_path env: - source_path: ../tests/data/ukb-efo/terms.txt + source_path: ./tests/data/ukb-efo/terms.txt target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl - output_path: ../tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv + output_path: ./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv - name: Setup summary spreadsheet row run: | echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> summary_path env: - sumamry_path: "../tests/summary.csv" + sumamry_path: "./tests/summary.csv" - name: Commit changes to tests repo run: | - cd ../tests + cd ./tests git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" git add ./mapper-outputs/* From 35670be6b014ba43e64103888a37285175574f62 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 21:53:31 -0700 Subject: [PATCH 14/41] change reference to test repo and add debug 'ls' --- .github/workflows/mapper-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 3494d87..26f1e9c 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -46,7 +46,7 @@ jobs: sumamry_path: "./tests/summary.csv" - name: Commit changes to tests repo run: | - cd ./tests + cd tests git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" git add ./mapper-outputs/* From 3afdc7fed6565af1711f06a4538b000ef07dea80 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 21:59:45 -0700 Subject: [PATCH 15/41] make moving into the tests repo a separate step --- .github/workflows/mapper-test.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 26f1e9c..3675037 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -39,14 +39,17 @@ jobs: source_path: ./tests/data/ukb-efo/terms.txt target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl output_path: ./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv + - name: Move to tests repo + - run: | + cd tests + ls - name: Setup summary spreadsheet row run: | echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> summary_path env: - sumamry_path: "./tests/summary.csv" + sumamry_path: "./summary.csv" - name: Commit changes to tests repo run: | - cd tests git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" git add ./mapper-outputs/* From 5486413b0414a80804abac07b45e45518f6a464a Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 22:00:33 -0700 Subject: [PATCH 16/41] fix typo --- .github/workflows/mapper-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 3675037..62489c4 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -40,7 +40,7 @@ jobs: target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl output_path: ./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv - name: Move to tests repo - - run: | + run: | cd tests ls - name: Setup summary spreadsheet row From aa2c0fac12278c2da44b9bc2aab05e8a6154ac53 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 22:07:25 -0700 Subject: [PATCH 17/41] update paths --- .github/workflows/mapper-test.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 62489c4..a0a6ec7 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -43,17 +43,18 @@ jobs: run: | cd tests ls + ls mapper-outputs/ukb-efo - name: Setup summary spreadsheet row run: | echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> summary_path env: - sumamry_path: "./summary.csv" + sumamry_path: ./summary.csv - name: Commit changes to tests repo run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" - git add ./mapper-outputs/* - git add ./summary.csv + git add mapper-outputs/* + git add summary.csv git commit -m "Add files" - name: Push changes uses: ad-m/github-push-action@master From dc8dd5b3391f6d16f36b72c59cf384fb4dc69251 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 22:18:19 -0700 Subject: [PATCH 18/41] don't use relative path for output --- .github/workflows/mapper-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index a0a6ec7..7bc8299 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -38,7 +38,7 @@ jobs: env: source_path: ./tests/data/ukb-efo/terms.txt target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl - output_path: ./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv + output_path: tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv - name: Move to tests repo run: | cd tests From e79a3d35d147e9b99ebab48f714253a51e9a1e56 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 22:22:58 -0700 Subject: [PATCH 19/41] update output file reference --- .github/workflows/mapper-test.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 7bc8299..74f0465 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -34,16 +34,13 @@ jobs: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Run mapper on UK Biobank source terms run: | - python3 t2t.py -s $source_path -t $target_path -o $output_path + python3 t2t.py -s $source_path -t $target_path -o tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv env: source_path: ./tests/data/ukb-efo/terms.txt target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl - output_path: tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv - name: Move to tests repo run: | cd tests - ls - ls mapper-outputs/ukb-efo - name: Setup summary spreadsheet row run: | echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> summary_path From 869ea952d48aa7ed1905ade4e2ae652ec71ad10b Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 22:29:02 -0700 Subject: [PATCH 20/41] wrap output path in quotes --- .github/workflows/mapper-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 74f0465..e8238d4 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -34,7 +34,7 @@ jobs: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Run mapper on UK Biobank source terms run: | - python3 t2t.py -s $source_path -t $target_path -o tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv + python3 t2t.py -s $source_path -t $target_path -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" env: source_path: ./tests/data/ukb-efo/terms.txt target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl @@ -50,7 +50,7 @@ jobs: run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" - git add mapper-outputs/* + git add mapper-outputs/*/*.csv git add summary.csv git commit -m "Add files" - name: Push changes From 5a09805ad9e80649ca999c6d7f202343f23878d1 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 22:33:25 -0700 Subject: [PATCH 21/41] add debug 'ls', refactor git add --- .github/workflows/mapper-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index e8238d4..abf5665 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -41,6 +41,7 @@ jobs: - name: Move to tests repo run: | cd tests + ls mapper-outputs/ukb-efo - name: Setup summary spreadsheet row run: | echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> summary_path @@ -50,8 +51,7 @@ jobs: run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" - git add mapper-outputs/*/*.csv - git add summary.csv + git add . git commit -m "Add files" - name: Push changes uses: ad-m/github-push-action@master From c4536b1061b13e1c23d3b4db6ceae702480ad5e5 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 22:38:55 -0700 Subject: [PATCH 22/41] fix summary path typo --- .github/workflows/mapper-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index abf5665..f506748 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -41,10 +41,10 @@ jobs: - name: Move to tests repo run: | cd tests - ls mapper-outputs/ukb-efo - name: Setup summary spreadsheet row run: | - echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> summary_path + ls + echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path env: sumamry_path: ./summary.csv - name: Commit changes to tests repo From 8f9ef889685b6c8d5767007a1846b0e109e79b23 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 22:44:07 -0700 Subject: [PATCH 23/41] update to use working-directory attribute --- .github/workflows/mapper-test.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index f506748..a88b240 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -38,23 +38,23 @@ jobs: env: source_path: ./tests/data/ukb-efo/terms.txt target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl - - name: Move to tests repo - run: | - cd tests - name: Setup summary spreadsheet row run: | - ls echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path + working-directory: tests env: sumamry_path: ./summary.csv - name: Commit changes to tests repo run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" git config --local user.name "github-actions[bot]" - git add . + git add mapper-outputs/* + git add summary.csv git commit -m "Add files" + working-directory: tests - name: Push changes uses: ad-m/github-push-action@master with: repository: "ccb-hms/ontology-mapper-tests" github_token: ${{ secrets.MAPPER_TESTING }} + directory: "tests" From a217bf4365d2826c8b9c7bd38608e1297d118709 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 22:51:18 -0700 Subject: [PATCH 24/41] correct typo in sumamry_path var name --- .github/workflows/mapper-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index a88b240..e942b21 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -43,7 +43,7 @@ jobs: echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path working-directory: tests env: - sumamry_path: ./summary.csv + summary_path: summary.csv - name: Commit changes to tests repo run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" From b3e4b0600c3d92f07e60d920314274184c6055ba Mon Sep 17 00:00:00 2001 From: An Date: Sat, 9 Oct 2021 23:15:13 -0700 Subject: [PATCH 25/41] fix formatting on start of row --- .github/workflows/mapper-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index e942b21..cb2cd07 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -40,7 +40,7 @@ jobs: target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl - name: Setup summary spreadsheet row run: | - echo "\n${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path + echo -n "${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path working-directory: tests env: summary_path: summary.csv From 38dfcd200cb7c347e187843e78fea608fab37890 Mon Sep 17 00:00:00 2001 From: An Date: Thu, 4 Nov 2021 13:14:25 -0700 Subject: [PATCH 26/41] set minimum score for mapper tool to 0 --- .github/workflows/mapper-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index cb2cd07..5a1830b 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -34,7 +34,7 @@ jobs: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Run mapper on UK Biobank source terms run: | - python3 t2t.py -s $source_path -t $target_path -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" + python3 t2t.py -s $source_path -t $target_path -min 0 -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" env: source_path: ./tests/data/ukb-efo/terms.txt target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl From 1fccdff5e7e6b156bf419a868093eda6f8c5b8a6 Mon Sep 17 00:00:00 2001 From: An Date: Sun, 6 Feb 2022 22:22:06 -0800 Subject: [PATCH 27/41] update numpy version --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index e2a3a7f..7162637 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ Owlready2~=0.31 argparse~=1.4.0 pandas~=1.2.4 -numpy~=1.19.5 +numpy>=1.20.0 gensim~=4.0.1 scipy~=1.6.3 sklearn~=0.0 From 7cf3a436d870d28882a0960b6a4f044b6b7078e9 Mon Sep 17 00:00:00 2001 From: An Date: Sun, 6 Feb 2022 22:50:41 -0800 Subject: [PATCH 28/41] update testing script to run coverage error script --- .github/workflows/mapper-test.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 5a1830b..00d1ab6 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -44,6 +44,11 @@ jobs: working-directory: tests env: summary_path: summary.csv + - name: Run coverage_error script + run: | + python3 t2t.py $script_path + env: + script_path: ./tests/compare-scripts/coverage_error.py - name: Commit changes to tests repo run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" From 4843594463ab483d1e2600916a580e1e3d17e20f Mon Sep 17 00:00:00 2001 From: An Date: Sun, 6 Feb 2022 22:54:23 -0800 Subject: [PATCH 29/41] t2t.py -> text2term.py --- .github/workflows/mapper-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 00d1ab6..21869be 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -34,7 +34,7 @@ jobs: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Run mapper on UK Biobank source terms run: | - python3 t2t.py -s $source_path -t $target_path -min 0 -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" + python3 text2term.py -s $source_path -t $target_path -min 0 -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" env: source_path: ./tests/data/ukb-efo/terms.txt target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl From 27540e11ebf19cba5675560255a7ca44402c68e6 Mon Sep 17 00:00:00 2001 From: An Date: Sun, 6 Feb 2022 23:11:43 -0800 Subject: [PATCH 30/41] fix typo in coverage-script running --- .github/workflows/mapper-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 21869be..516df3a 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -46,7 +46,7 @@ jobs: summary_path: summary.csv - name: Run coverage_error script run: | - python3 t2t.py $script_path + python3 $script_path env: script_path: ./tests/compare-scripts/coverage_error.py - name: Commit changes to tests repo From e424d4482e9f306833dce70054b74726d38fe2a6 Mon Sep 17 00:00:00 2001 From: An Date: Sun, 6 Feb 2022 23:36:53 -0800 Subject: [PATCH 31/41] test summary.csv --- .github/workflows/mapper-test.yml | 40 +++++++++++++++---------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 516df3a..f8ef3f6 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -23,32 +23,32 @@ jobs: repository: "ccb-hms/ontology-mapper-tests" token: ${{ secrets.MAPPER_TESTING }} fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - - name: Set up Python 3.9 - uses: actions/setup-python@v2 - with: - python-version: 3.9 - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Run mapper on UK Biobank source terms - run: | - python3 text2term.py -s $source_path -t $target_path -min 0 -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" - env: - source_path: ./tests/data/ukb-efo/terms.txt - target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl + # - name: Set up Python 3.9 + # uses: actions/setup-python@v2 + # with: + # python-version: 3.9 + # - name: Install dependencies + # run: | + # python -m pip install --upgrade pip + # pip install flake8 pytest + # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + # - name: Run mapper on UK Biobank source terms + # run: | + # python3 text2term.py -s $source_path -t $target_path -min 0 -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" + # env: + # source_path: ./tests/data/ukb-efo/terms.txt + # target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl - name: Setup summary spreadsheet row run: | echo -n "${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path working-directory: tests env: summary_path: summary.csv - - name: Run coverage_error script - run: | - python3 $script_path - env: - script_path: ./tests/compare-scripts/coverage_error.py + # - name: Run coverage_error script + # run: | + # python3 $script_path + # env: + # script_path: ./tests/compare-scripts/coverage_error.py - name: Commit changes to tests repo run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" From 20505a18cc9af776a51501a72868fac708fe06c8 Mon Sep 17 00:00:00 2001 From: An Date: Sun, 6 Feb 2022 23:40:38 -0800 Subject: [PATCH 32/41] adjust working directory for coverage-erro script --- .github/workflows/mapper-test.yml | 41 ++++++++++++++++--------------- 1 file changed, 21 insertions(+), 20 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index f8ef3f6..2840227 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -23,32 +23,33 @@ jobs: repository: "ccb-hms/ontology-mapper-tests" token: ${{ secrets.MAPPER_TESTING }} fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - # - name: Set up Python 3.9 - # uses: actions/setup-python@v2 - # with: - # python-version: 3.9 - # - name: Install dependencies - # run: | - # python -m pip install --upgrade pip - # pip install flake8 pytest - # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - # - name: Run mapper on UK Biobank source terms - # run: | - # python3 text2term.py -s $source_path -t $target_path -min 0 -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" - # env: - # source_path: ./tests/data/ukb-efo/terms.txt - # target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl + - name: Set up Python 3.9 + uses: actions/setup-python@v2 + with: + python-version: 3.9 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install flake8 pytest + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Run mapper on UK Biobank source terms + run: | + python3 text2term.py -s $source_path -t $target_path -min 0 -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" + env: + source_path: ./tests/data/ukb-efo/terms.txt + target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl - name: Setup summary spreadsheet row run: | echo -n "${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path working-directory: tests env: summary_path: summary.csv - # - name: Run coverage_error script - # run: | - # python3 $script_path - # env: - # script_path: ./tests/compare-scripts/coverage_error.py + - name: Run coverage_error script + run: | + python3 $script_path + working-directory: tests/compare-scripts + env: + script_path: coverage_error.py - name: Commit changes to tests repo run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" From 3c282d6a1510e0d52ddb2e24360dbf8b96e09d1f Mon Sep 17 00:00:00 2001 From: An Date: Mon, 7 Feb 2022 00:06:42 -0800 Subject: [PATCH 33/41] update output path --- .github/workflows/mapper-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 2840227..90d4d83 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -34,7 +34,7 @@ jobs: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Run mapper on UK Biobank source terms run: | - python3 text2term.py -s $source_path -t $target_path -min 0 -o "tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" + python3 text2term.py -s $source_path -t $target_path -min 0 -o "./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" env: source_path: ./tests/data/ukb-efo/terms.txt target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl From 90d96b65a1a7d826daf533750f7511b1b1ae9fa5 Mon Sep 17 00:00:00 2001 From: An Date: Mon, 7 Feb 2022 00:32:24 -0800 Subject: [PATCH 34/41] debug coverage_error script run error --- .github/workflows/mapper-test.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 90d4d83..2f572a8 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -44,12 +44,12 @@ jobs: working-directory: tests env: summary_path: summary.csv - - name: Run coverage_error script - run: | - python3 $script_path - working-directory: tests/compare-scripts - env: - script_path: coverage_error.py + # - name: Run coverage_error script + # run: | + # python3 $script_path + # working-directory: tests/compare-scripts + # env: + # script_path: coverage_error.py - name: Commit changes to tests repo run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" From b36a996f5351be919fa36bd7a31545fef85500e8 Mon Sep 17 00:00:00 2001 From: An Date: Mon, 7 Feb 2022 11:14:08 -0800 Subject: [PATCH 35/41] update coverage_error script to use new column names --- .github/workflows/mapper-test.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 2f572a8..90d4d83 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -44,12 +44,12 @@ jobs: working-directory: tests env: summary_path: summary.csv - # - name: Run coverage_error script - # run: | - # python3 $script_path - # working-directory: tests/compare-scripts - # env: - # script_path: coverage_error.py + - name: Run coverage_error script + run: | + python3 $script_path + working-directory: tests/compare-scripts + env: + script_path: coverage_error.py - name: Commit changes to tests repo run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" From ae4e50d06064313158610b2a65a14d1ba53af911 Mon Sep 17 00:00:00 2001 From: An Date: Thu, 10 Feb 2022 13:28:27 -0800 Subject: [PATCH 36/41] add UK Biobank EFO owl version and one error and commit message --- .github/workflows/mapper-test.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 90d4d83..c07132e 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -37,10 +37,14 @@ jobs: python3 text2term.py -s $source_path -t $target_path -min 0 -o "./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" env: source_path: ./tests/data/ukb-efo/terms.txt - target_path: https://github.com/EBISPOT/efo/releases/download/current/efo.owl + # https://github.com/EBISPOT/efo/releases/tag/v2019-03-18 + # 2019-03-18 EFO 2.106, as referenced by: + # https://github.com/EBISPOT/EFO-UKB-mappings/blob/master/ISMB_Mapping_UK_Biobank_to_EFO.pdf + # page 2, footnote 9 + target_path: ./tests/data/ukb-efo/efo-v2019-03-18.owl - name: Setup summary spreadsheet row run: | - echo -n "${GITHUB_REF},${GITHUB_SHA},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path + echo -n "${GITHUB_REF},${GITHUB_SHA},${{ github.event.head_commit.message }},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path working-directory: tests env: summary_path: summary.csv From 803db571f8e9819f166a4eb6908b0a9c07dbdf95 Mon Sep 17 00:00:00 2001 From: An Date: Thu, 10 Feb 2022 20:08:01 -0800 Subject: [PATCH 37/41] switch to coverage_one_error script --- .github/workflows/mapper-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index c07132e..a2062d8 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -48,12 +48,12 @@ jobs: working-directory: tests env: summary_path: summary.csv - - name: Run coverage_error script + - name: Run coverage__one_error script run: | python3 $script_path working-directory: tests/compare-scripts env: - script_path: coverage_error.py + script_path: coverage_one_error.py - name: Commit changes to tests repo run: | git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" From 741c28b48a6c1cb4a9083639c245445b2bd7973f Mon Sep 17 00:00:00 2001 From: An Date: Sat, 19 Feb 2022 22:13:33 -0800 Subject: [PATCH 38/41] test, escaping commas --- .github/workflows/mapper-test.yml | 127 +++++++++++++++++------------- 1 file changed, 73 insertions(+), 54 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index a2062d8..d75a4ee 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -10,61 +10,80 @@ on: branches: [task5-workflow] jobs: - run_mapper: + test_bash_script: runs-on: ubuntu-latest - name: Run Tests + name: Test script steps: - - uses: actions/checkout@v2 - name: Checkout out mapper repository - - uses: actions/checkout@v2 - name: Checkout test repository - with: - path: tests - repository: "ccb-hms/ontology-mapper-tests" - token: ${{ secrets.MAPPER_TESTING }} - fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - - name: Set up Python 3.9 - uses: actions/setup-python@v2 - with: - python-version: 3.9 - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Run mapper on UK Biobank source terms - run: | - python3 text2term.py -s $source_path -t $target_path -min 0 -o "./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" - env: - source_path: ./tests/data/ukb-efo/terms.txt - # https://github.com/EBISPOT/efo/releases/tag/v2019-03-18 - # 2019-03-18 EFO 2.106, as referenced by: - # https://github.com/EBISPOT/EFO-UKB-mappings/blob/master/ISMB_Mapping_UK_Biobank_to_EFO.pdf - # page 2, footnote 9 - target_path: ./tests/data/ukb-efo/efo-v2019-03-18.owl - name: Setup summary spreadsheet row run: | - echo -n "${GITHUB_REF},${GITHUB_SHA},${{ github.event.head_commit.message }},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path - working-directory: tests - env: - summary_path: summary.csv - - name: Run coverage__one_error script - run: | - python3 $script_path - working-directory: tests/compare-scripts - env: - script_path: coverage_one_error.py - - name: Commit changes to tests repo - run: | - git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" - git config --local user.name "github-actions[bot]" - git add mapper-outputs/* - git add summary.csv - git commit -m "Add files" - working-directory: tests - - name: Push changes - uses: ad-m/github-push-action@master - with: - repository: "ccb-hms/ontology-mapper-tests" - github_token: ${{ secrets.MAPPER_TESTING }} - directory: "tests" + if grep -q "," <<< "${{ github.event.head_commit.message }}" + then + TEST=\"${MSG}\" + else + TEST=${MSG} + fi + echo -n "${GITHUB_REF},${GITHUB_SHA},${{ github.event.head_commit.message }},ukb-efo/${GITHUB_SHA}.csv," + # run_mapper: + # runs-on: ubuntu-latest + # name: Run Tests + # steps: + # - uses: actions/checkout@v2 + # name: Checkout out mapper repository + # - uses: actions/checkout@v2 + # name: Checkout test repository + # with: + # path: tests + # repository: "ccb-hms/ontology-mapper-tests" + # token: ${{ secrets.MAPPER_TESTING }} + # fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. + # - name: Set up Python 3.9 + # uses: actions/setup-python@v2 + # with: + # python-version: 3.9 + # - name: Install dependencies + # run: | + # python -m pip install --upgrade pip + # pip install flake8 pytest + # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + # - name: Run mapper on UK Biobank source terms + # run: | + # python3 text2term.py -s $source_path -t $target_path -min 0 -o "./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" + # env: + # source_path: ./tests/data/ukb-efo/terms.txt + # # https://github.com/EBISPOT/efo/releases/tag/v2019-03-18 + # # 2019-03-18 EFO 2.106, as referenced by: + # # https://github.com/EBISPOT/EFO-UKB-mappings/blob/master/ISMB_Mapping_UK_Biobank_to_EFO.pdf + # # page 2, footnote 9 + # target_path: ./tests/data/ukb-efo/efo-v2019-03-18.owl + # - name: Setup summary spreadsheet row + # run: | + # if grep -q "," <<< "${{ github.event.head_commit.message }}" + # then + # TEST=\"${MSG}\" + # else + # TEST=${MSG} + # fi + # echo -n "${GITHUB_REF},${GITHUB_SHA},${{ github.event.head_commit.message }},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path + # working-directory: tests + # env: + # summary_path: summary.csv + # - name: Run coverage__one_error script + # run: | + # python3 $script_path + # working-directory: tests/compare-scripts + # env: + # script_path: coverage_one_error.py + # - name: Commit changes to tests repo + # run: | + # git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" + # git config --local user.name "github-actions[bot]" + # git add mapper-outputs/* + # git add summary.csv + # git commit -m "Add files" + # working-directory: tests + # - name: Push changes + # uses: ad-m/github-push-action@master + # with: + # repository: "ccb-hms/ontology-mapper-tests" + # github_token: ${{ secrets.MAPPER_TESTING }} + # directory: "tests" From 6f21f0bad5e1156ecf690a6c59307242b12abf51 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 19 Feb 2022 22:15:25 -0800 Subject: [PATCH 39/41] test 2, now with fixed variable names --- .github/workflows/mapper-test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index d75a4ee..d0b5c73 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -18,11 +18,11 @@ jobs: run: | if grep -q "," <<< "${{ github.event.head_commit.message }}" then - TEST=\"${MSG}\" + MSG=\"${{ github.event.head_commit.message }}\" else - TEST=${MSG} + MSG=${{ github.event.head_commit.message }} fi - echo -n "${GITHUB_REF},${GITHUB_SHA},${{ github.event.head_commit.message }},ukb-efo/${GITHUB_SHA}.csv," + echo -n "${GITHUB_REF},${GITHUB_SHA},${MSG},ukb-efo/${GITHUB_SHA}.csv," # run_mapper: # runs-on: ubuntu-latest # name: Run Tests From ea3e12461caf29c01abe25810aa9043db5e711e4 Mon Sep 17 00:00:00 2001 From: An Date: Sat, 19 Feb 2022 22:18:02 -0800 Subject: [PATCH 40/41] test 3, with more quote marks --- .github/workflows/mapper-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index d0b5c73..3239c48 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -18,9 +18,9 @@ jobs: run: | if grep -q "," <<< "${{ github.event.head_commit.message }}" then - MSG=\"${{ github.event.head_commit.message }}\" + MSG='"${{ github.event.head_commit.message }}"' else - MSG=${{ github.event.head_commit.message }} + MSG='${{ github.event.head_commit.message }}' fi echo -n "${GITHUB_REF},${GITHUB_SHA},${MSG},ukb-efo/${GITHUB_SHA}.csv," # run_mapper: From da9ddc66c2bb32aa6f84110b4d522d8bc24b6e8d Mon Sep 17 00:00:00 2001 From: An Date: Sat, 19 Feb 2022 22:21:05 -0800 Subject: [PATCH 41/41] add escaping, full pipeline --- .github/workflows/mapper-test.yml | 121 +++++++++++++----------------- 1 file changed, 54 insertions(+), 67 deletions(-) diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml index 3239c48..bedb94b 100644 --- a/.github/workflows/mapper-test.yml +++ b/.github/workflows/mapper-test.yml @@ -10,10 +10,38 @@ on: branches: [task5-workflow] jobs: - test_bash_script: + run_mapper: runs-on: ubuntu-latest - name: Test script + name: Run Tests steps: + - uses: actions/checkout@v2 + name: Checkout out mapper repository + - uses: actions/checkout@v2 + name: Checkout test repository + with: + path: tests + repository: "ccb-hms/ontology-mapper-tests" + token: ${{ secrets.MAPPER_TESTING }} + fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. + - name: Set up Python 3.9 + uses: actions/setup-python@v2 + with: + python-version: 3.9 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install flake8 pytest + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Run mapper on UK Biobank source terms + run: | + python3 text2term.py -s $source_path -t $target_path -min 0 -o "./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" + env: + source_path: ./tests/data/ukb-efo/terms.txt + # https://github.com/EBISPOT/efo/releases/tag/v2019-03-18 + # 2019-03-18 EFO 2.106, as referenced by: + # https://github.com/EBISPOT/EFO-UKB-mappings/blob/master/ISMB_Mapping_UK_Biobank_to_EFO.pdf + # page 2, footnote 9 + target_path: ./tests/data/ukb-efo/efo-v2019-03-18.owl - name: Setup summary spreadsheet row run: | if grep -q "," <<< "${{ github.event.head_commit.message }}" @@ -22,68 +50,27 @@ jobs: else MSG='${{ github.event.head_commit.message }}' fi - echo -n "${GITHUB_REF},${GITHUB_SHA},${MSG},ukb-efo/${GITHUB_SHA}.csv," - # run_mapper: - # runs-on: ubuntu-latest - # name: Run Tests - # steps: - # - uses: actions/checkout@v2 - # name: Checkout out mapper repository - # - uses: actions/checkout@v2 - # name: Checkout test repository - # with: - # path: tests - # repository: "ccb-hms/ontology-mapper-tests" - # token: ${{ secrets.MAPPER_TESTING }} - # fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository. - # - name: Set up Python 3.9 - # uses: actions/setup-python@v2 - # with: - # python-version: 3.9 - # - name: Install dependencies - # run: | - # python -m pip install --upgrade pip - # pip install flake8 pytest - # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - # - name: Run mapper on UK Biobank source terms - # run: | - # python3 text2term.py -s $source_path -t $target_path -min 0 -o "./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv" - # env: - # source_path: ./tests/data/ukb-efo/terms.txt - # # https://github.com/EBISPOT/efo/releases/tag/v2019-03-18 - # # 2019-03-18 EFO 2.106, as referenced by: - # # https://github.com/EBISPOT/EFO-UKB-mappings/blob/master/ISMB_Mapping_UK_Biobank_to_EFO.pdf - # # page 2, footnote 9 - # target_path: ./tests/data/ukb-efo/efo-v2019-03-18.owl - # - name: Setup summary spreadsheet row - # run: | - # if grep -q "," <<< "${{ github.event.head_commit.message }}" - # then - # TEST=\"${MSG}\" - # else - # TEST=${MSG} - # fi - # echo -n "${GITHUB_REF},${GITHUB_SHA},${{ github.event.head_commit.message }},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path - # working-directory: tests - # env: - # summary_path: summary.csv - # - name: Run coverage__one_error script - # run: | - # python3 $script_path - # working-directory: tests/compare-scripts - # env: - # script_path: coverage_one_error.py - # - name: Commit changes to tests repo - # run: | - # git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" - # git config --local user.name "github-actions[bot]" - # git add mapper-outputs/* - # git add summary.csv - # git commit -m "Add files" - # working-directory: tests - # - name: Push changes - # uses: ad-m/github-push-action@master - # with: - # repository: "ccb-hms/ontology-mapper-tests" - # github_token: ${{ secrets.MAPPER_TESTING }} - # directory: "tests" + echo -n "${GITHUB_REF},${GITHUB_SHA},${MSG},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path + working-directory: tests + env: + summary_path: summary.csv + - name: Run coverage__one_error script + run: | + python3 $script_path + working-directory: tests/compare-scripts + env: + script_path: coverage_one_error.py + - name: Commit changes to tests repo + run: | + git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" + git config --local user.name "github-actions[bot]" + git add mapper-outputs/* + git add summary.csv + git commit -m "Add files" + working-directory: tests + - name: Push changes + uses: ad-m/github-push-action@master + with: + repository: "ccb-hms/ontology-mapper-tests" + github_token: ${{ secrets.MAPPER_TESTING }} + directory: "tests"