From cf500999b439032254b2b1fd0c26b31be45936aa Mon Sep 17 00:00:00 2001 From: shawa Date: Sun, 26 Mar 2017 20:29:24 +0100 Subject: [PATCH 01/16] Use sha hashing, add agonism --- asclepius/asclepius/enrich.py | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/asclepius/asclepius/enrich.py b/asclepius/asclepius/enrich.py index 69c26d42..47c07e8b 100644 --- a/asclepius/asclepius/enrich.py +++ b/asclepius/asclepius/enrich.py @@ -1,8 +1,24 @@ -def enrich(ddis): - def _enrich(ddi): - result = {'harmful': bool(hash(ddi['uri']) % 2), - 'spacing': abs(hash(ddi['uri']))%14 + 1} - result.update(ddi) - return result +from functools import lru_cache +from hashlib import sha224 + + +def _sha_int(string): + return int(sha224(string.encode()).hexdigest()[-8:], 16) + +@lru_cache() +def _enrich(ddi): + uri = ddi['uri'] + result = { + 'harmful': bool(_sha_int(uri) % 2), + 'spacing': _sha_int(uri) % 14 + 1, + + # we want them to be a bit different + 'agonism': bool(_sha_int(''.join(sorted(uri))) % 2), + } + + result.update(ddi) + return result + +def enrich(ddis): return [_enrich(ddi) for ddi in ddis] From 7ff90b61466a92784fee224562bf26129f0b1983 Mon Sep 17 00:00:00 2001 From: shawa Date: Sat, 1 Apr 2017 17:41:58 +0100 Subject: [PATCH 02/16] Add CSV exporting to `enrich.py` --- asclepius/README.md | 23 ++++++++++++++++++----- asclepius/asclepius/dinto.py | 15 ++++++++++++--- asclepius/asclepius/enrich.py | 24 ++++++++++++++++++++---- asclepius/requirements.txt | 3 +++ 4 files changed, 53 insertions(+), 12 deletions(-) diff --git a/asclepius/README.md b/asclepius/README.md index 8a8e9fc2..0d7cdebd 100644 --- a/asclepius/README.md +++ b/asclepius/README.md @@ -5,8 +5,15 @@ Flask endpoint for querying DINTO. Supports querying for all drugs listed, as we This application acts as an adaptor to Chiron - an instance of Apache Fuseki, Chiron must be running before any queries can be served. -Endpoints ---------- +CSV File Exporting +------------------ + +When run as a program, the `enrich` module will export DDIs, along with mock timing and agonism/harmfulness information. + +Run as `python3 enrich.py > outfile.csv` to export to a CSV file. + +HTTP Endpoints +------------- ### `/all_drugs` @@ -59,15 +66,21 @@ Endpoints [ { "label": "torasemide/trandolapril DDI", - "uri": "http://purl.obolibrary.org/obo/DINTO_11031" + "uri": "http://purl.obolibrary.org/obo/DINTO_11031", + "drug_a": "torasemide", + "drug_b": "trandolapril" }, { "label": "cimetidine/heroin DDI", - "uri": "http://purl.obolibrary.org/obo/DINTO_02733" + "uri": "http://purl.obolibrary.org/obo/DINTO_02733", + "drug_a": "cimetidine", + "drug_b": "heroin" }, { "label": "methylergonovine/telithromycin DDI", - "uri": "http://purl.obolibrary.org/obo/DINTO_10154" + "uri": "http://purl.obolibrary.org/obo/DINTO_10154", + "drug_a": "methylergonovine", + "drug_b": "telithromycin" } ] ``` diff --git a/asclepius/asclepius/dinto.py b/asclepius/asclepius/dinto.py index 53b51592..31c0f3c5 100644 --- a/asclepius/asclepius/dinto.py +++ b/asclepius/asclepius/dinto.py @@ -83,10 +83,19 @@ def drugs(labels=None): def all_ddis(): return f''' {PREFIXES} - SELECT ?uri ?label + SELECT ?drug_a ?drug_b ?uri ?label WHERE {{ - ?uri rdfs:subClassOf {DDI}. - ?uri rdfs:label ?label + ?drug_a_uri rdfs:label ?drug_a. + ?drug_b_uri rdfs:label ?drug_b. + ?uri rdfs:label ?label. + ?uri rdfs:subClassOf {DDI} . + ?uri owl:equivalentClass ?equivalance . + ?equivalance owl:intersectionOf ?restrictions . + ?restrictions rdf:first ?drug1Restriction . + ?restrictions rdf:rest ?tail . + ?tail rdf:first ?drug2Restriction . + ?drug1Restriction owl:someValuesFrom ?drug_a_uri . + ?drug2Restriction owl:someValuesFrom ?drug_b_uri . }} ''' diff --git a/asclepius/asclepius/enrich.py b/asclepius/asclepius/enrich.py index 47c07e8b..6aac111d 100644 --- a/asclepius/asclepius/enrich.py +++ b/asclepius/asclepius/enrich.py @@ -1,12 +1,13 @@ -from functools import lru_cache from hashlib import sha224 - +import csv +import sys +import dinto +import clize +from clize.parameters import one_of def _sha_int(string): return int(sha224(string.encode()).hexdigest()[-8:], 16) - -@lru_cache() def _enrich(ddi): uri = ddi['uri'] result = { @@ -22,3 +23,18 @@ def _enrich(ddi): def enrich(ddis): return [_enrich(ddi) for ddi in ddis] + + +def main(flavour:one_of('harmful', 'agonism')): + fieldnames = ('drug_a', 'drug_b', flavour, 'time', 'unit') + + writer = csv.DictWriter(sys.stdout, fieldnames=fieldnames) + writer.writeheader() + + for ddi in enrich(dinto.all_ddis()): + ddi.update({'time': ddi['spacing'], 'unit': 'hr'}) + writer.writerow({k: ddi[k] for k in fieldnames}) + + +if __name__ == '__main__': + clize.run(main) diff --git a/asclepius/requirements.txt b/asclepius/requirements.txt index 4eab383b..aed334eb 100644 --- a/asclepius/requirements.txt +++ b/asclepius/requirements.txt @@ -11,3 +11,6 @@ py==1.4.32 pytest==3.0.6 requests==2.13.0 Werkzeug==0.11.15 +clize==3.1.0 +sigtools==2.0.1 +six==1.10.0 From 8778f53b1476a48b634bf4829ad9854155091e53 Mon Sep 17 00:00:00 2001 From: shawa Date: Sun, 2 Apr 2017 20:27:10 +0100 Subject: [PATCH 03/16] use sha1 over weirdo 224 --- asclepius/asclepius/enrich.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/asclepius/asclepius/enrich.py b/asclepius/asclepius/enrich.py index 6aac111d..5cc77329 100644 --- a/asclepius/asclepius/enrich.py +++ b/asclepius/asclepius/enrich.py @@ -1,4 +1,4 @@ -from hashlib import sha224 +from hashlib import sha1 import csv import sys import dinto @@ -6,7 +6,7 @@ from clize.parameters import one_of def _sha_int(string): - return int(sha224(string.encode()).hexdigest()[-8:], 16) + return int(sha1(string.encode()).hexdigest()[-8:], 16) def _enrich(ddi): uri = ddi['uri'] From 8c3dd5348d6d0ad29f03840184aa382142019d6d Mon Sep 17 00:00:00 2001 From: shawa Date: Sun, 2 Apr 2017 21:09:11 +0100 Subject: [PATCH 04/16] Add mock ddi exportation --- export-mock-ddi-data.sh | 60 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100755 export-mock-ddi-data.sh diff --git a/export-mock-ddi-data.sh b/export-mock-ddi-data.sh new file mode 100755 index 00000000..e56e7f3d --- /dev/null +++ b/export-mock-ddi-data.sh @@ -0,0 +1,60 @@ +#!/bin/bash +usage() { +cat < + +Resultant CSV file is of the format: + drug_a, drug_b, {agonism or harmful}, time, unit + +Usage: + $0 +EOF +} + + +loading() { + echo 'Exporting' + while true; do + printf "\r | " + sleep 0.125 + printf "\r / " + sleep 0.125 + printf "\r - " + sleep 0.125 + printf "\r \\ " + sleep 0.125 + done +} + + +main() { + if [ $# -ne 2 ]; then + usage + exit 2 + fi + + local readonly flavour="$1"; shift + local readonly outfile="$1"; shift + case "$flavour" in + harmful|agonism) + loading & + local readonly LOAD_PID="$!"; + trap "kill $LOAD_PID 2>&1 > /dev/null; exit" SIGTERM SIGKILL SIGINT + disown + docker-compose --file docker-compose.dev.yml \ + run --rm asclepius python3 asclepius/enrich.py "$flavour" \ + > "$outfile" + kill "$LOAD_PID"; + exit 1 + ;; + + *) + usage + exit 2 + ;; + esac +} + +main "$@" From 62477a5ea7af9618291ac953e0f4050998e9652d Mon Sep 17 00:00:00 2001 From: shawa Date: Sun, 2 Apr 2017 22:00:41 +0100 Subject: [PATCH 05/16] Add privilege escalation prompt, clarifiy PID name, fix exit statuses --- asclepius/asclepius/enrich.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/asclepius/asclepius/enrich.py b/asclepius/asclepius/enrich.py index 5cc77329..361114f6 100644 --- a/asclepius/asclepius/enrich.py +++ b/asclepius/asclepius/enrich.py @@ -5,15 +5,18 @@ import clize from clize.parameters import one_of +UNITS = ('hr', 'day') + def _sha_int(string): return int(sha1(string.encode()).hexdigest()[-8:], 16) def _enrich(ddi): uri = ddi['uri'] + sha = _sha_int(uri) result = { - 'harmful': bool(_sha_int(uri) % 2), - 'spacing': _sha_int(uri) % 14 + 1, - + 'harmful': bool(sha % 2), + 'spacing': sha % 14 + 1, + 'unit': UNITS[sha % len(UNITS)], # we want them to be a bit different 'agonism': bool(_sha_int(''.join(sorted(uri))) % 2), } @@ -32,7 +35,7 @@ def main(flavour:one_of('harmful', 'agonism')): writer.writeheader() for ddi in enrich(dinto.all_ddis()): - ddi.update({'time': ddi['spacing'], 'unit': 'hr'}) + ddi.update({'time': ddi['spacing']}) writer.writerow({k: ddi[k] for k in fieldnames}) From 4ab1aaba7e571aea1228462cd96004de3cc27369 Mon Sep 17 00:00:00 2001 From: shawa Date: Sun, 2 Apr 2017 22:01:58 +0100 Subject: [PATCH 06/16] Drop shifts, clarify spinner PID, sudo everything, privilege escalator --- export-mock-ddi-data.sh | 31 +++++++++++++++++++++---------- 1 file changed, 21 insertions(+), 10 deletions(-) diff --git a/export-mock-ddi-data.sh b/export-mock-ddi-data.sh index e56e7f3d..91e7a308 100755 --- a/export-mock-ddi-data.sh +++ b/export-mock-ddi-data.sh @@ -32,29 +32,40 @@ loading() { main() { if [ $# -ne 2 ]; then usage - exit 2 + exit 1 fi - local readonly flavour="$1"; shift - local readonly outfile="$1"; shift + local readonly flavour="$1" + local readonly outfile="$2" + case "$flavour" in harmful|agonism) loading & - local readonly LOAD_PID="$!"; - trap "kill $LOAD_PID 2>&1 > /dev/null; exit" SIGTERM SIGKILL SIGINT + local readonly LOADING_SPINNER_PID="$!"; + trap "kill $LOADING_SPINNER_PID 2>&1 > /dev/null; exit" SIGTERM SIGKILL SIGINT disown - docker-compose --file docker-compose.dev.yml \ - run --rm asclepius python3 asclepius/enrich.py "$flavour" \ + + sudo docker-compose \ + -p export_ddis run \ + --rm asclepius python3 asclepius/enrich.py "$flavour" \ > "$outfile" - kill "$LOAD_PID"; - exit 1 + + sudo docker-compose -p export_ddis down + + kill "$LOADING_SPINNER_PID"; + exit 0 ;; *) usage - exit 2 + exit 1 ;; esac } +if [ $EUID != 0 ]; then + sudo "$0" "$@" + exit $? +fi + main "$@" From 9a691bae3ab9bfddd68f346861281482ababb6fd Mon Sep 17 00:00:00 2001 From: shawa Date: Sun, 2 Apr 2017 22:03:55 +0100 Subject: [PATCH 07/16] rm --rm --- export-mock-ddi-data.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/export-mock-ddi-data.sh b/export-mock-ddi-data.sh index 91e7a308..8f597e72 100755 --- a/export-mock-ddi-data.sh +++ b/export-mock-ddi-data.sh @@ -46,8 +46,8 @@ main() { disown sudo docker-compose \ - -p export_ddis run \ - --rm asclepius python3 asclepius/enrich.py "$flavour" \ + -p export_ddis \ + run asclepius python3 asclepius/enrich.py "$flavour" \ > "$outfile" sudo docker-compose -p export_ddis down From 61603c8848a15f38278dfd968763424ef6c66a56 Mon Sep 17 00:00:00 2001 From: shawa Date: Mon, 3 Apr 2017 12:02:02 +0100 Subject: [PATCH 08/16] Can't trap sigkill m80 --- export-mock-ddi-data.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/export-mock-ddi-data.sh b/export-mock-ddi-data.sh index 8f597e72..3ac10a35 100755 --- a/export-mock-ddi-data.sh +++ b/export-mock-ddi-data.sh @@ -42,7 +42,7 @@ main() { harmful|agonism) loading & local readonly LOADING_SPINNER_PID="$!"; - trap "kill $LOADING_SPINNER_PID 2>&1 > /dev/null; exit" SIGTERM SIGKILL SIGINT + trap "kill $LOADING_SPINNER_PID 2>&1 > /dev/null; exit" SIGTERM SIGINT disown sudo docker-compose \ From d79ab6c69da521e4611fc8674e11ad212e4a6eba Mon Sep 17 00:00:00 2001 From: shawa Date: Wed, 5 Apr 2017 12:12:00 +0100 Subject: [PATCH 09/16] Add units and more correc time intervals to mock DDIs Include a block until chiron becomes available Export data into mock-enriched-ddis dir for ease Remove the spinner --- asclepius/asclepius/enrich.py | 55 +- export-mock-ddi-data.sh | 40 +- mock-enriched-ddis/agonism.csv | 11576 +++++++++++++++++++++++++++++++ mock-enriched-ddis/harmful.csv | 11576 +++++++++++++++++++++++++++++++ 4 files changed, 23203 insertions(+), 44 deletions(-) create mode 100644 mock-enriched-ddis/agonism.csv create mode 100644 mock-enriched-ddis/harmful.csv diff --git a/asclepius/asclepius/enrich.py b/asclepius/asclepius/enrich.py index 361114f6..2adf0d15 100644 --- a/asclepius/asclepius/enrich.py +++ b/asclepius/asclepius/enrich.py @@ -3,41 +3,80 @@ import sys import dinto import clize +import socket +import time from clize.parameters import one_of -UNITS = ('hr', 'day') +UNITS_INTERVAL = { + 'sec': 60, + 'min': 60, + 'hr': 24, + 'day': 7, + 'week': 52, + 'yr': 5, +} + def _sha_int(string): return int(sha1(string.encode()).hexdigest()[-8:], 16) + def _enrich(ddi): uri = ddi['uri'] sha = _sha_int(uri) + unit = tuple(UNITS_INTERVAL.keys())[sha % len(UNITS_INTERVAL)] result = { 'harmful': bool(sha % 2), - 'spacing': sha % 14 + 1, - 'unit': UNITS[sha % len(UNITS)], - # we want them to be a bit different + 'spacing': sha % UNITS_INTERVAL[unit] + 1, + 'unit': unit, 'agonism': bool(_sha_int(''.join(sorted(uri))) % 2), } result.update(ddi) return result + def enrich(ddis): return [_enrich(ddi) for ddi in ddis] -def main(flavour:one_of('harmful', 'agonism')): - fieldnames = ('drug_a', 'drug_b', flavour, 'time', 'unit') +def main(flavour: one_of('harmful', 'agonism')): + fieldnames = ('Drug 1', 'Drug 2', 'DDI Type', 'Time', 'Unit') - writer = csv.DictWriter(sys.stdout, fieldnames=fieldnames) + writer = csv.DictWriter(sys.stdout, fieldnames=fieldnames, + lineterminator='\n') writer.writeheader() for ddi in enrich(dinto.all_ddis()): - ddi.update({'time': ddi['spacing']}) + ddi['Drug 1'] = ddi['drug_a'] + ddi['Drug 2'] = ddi['drug_b'] + ddi['Time'] = ddi['spacing'] + ddi['Unit'] = ddi['unit'] + + if flavour == 'harmful': + ddi['DDI Type'] = 'bad' if ddi[flavour] else 'good' + if flavour == 'agonism': + ddi['DDI Type'] = 'agonism' if ddi[flavour] else 'antagonism' + writer.writerow({k: ddi[k] for k in fieldnames}) +def block_until_chiron(): + goes = 10 + while goes: + try: + sock = socket.socket() + time.sleep(1) + sock.connect(('chiron', 3030)) + except Exception: + goes -= 1 + continue + else: + return + + sys.exit(1) + + if __name__ == '__main__': + block_until_chiron() clize.run(main) diff --git a/export-mock-ddi-data.sh b/export-mock-ddi-data.sh index 3ac10a35..e0283cad 100755 --- a/export-mock-ddi-data.sh +++ b/export-mock-ddi-data.sh @@ -3,32 +3,16 @@ usage() { cat < +Writes mock enriched DDI data out to Resultant CSV file is of the format: - drug_a, drug_b, {agonism or harmful}, time, unit + Drug 1, Drug 2, DDI Type, Time, Unit Usage: $0 EOF } - -loading() { - echo 'Exporting' - while true; do - printf "\r | " - sleep 0.125 - printf "\r / " - sleep 0.125 - printf "\r - " - sleep 0.125 - printf "\r \\ " - sleep 0.125 - done -} - - main() { if [ $# -ne 2 ]; then usage @@ -40,19 +24,8 @@ main() { case "$flavour" in harmful|agonism) - loading & - local readonly LOADING_SPINNER_PID="$!"; - trap "kill $LOADING_SPINNER_PID 2>&1 > /dev/null; exit" SIGTERM SIGINT - disown - - sudo docker-compose \ - -p export_ddis \ - run asclepius python3 asclepius/enrich.py "$flavour" \ - > "$outfile" - - sudo docker-compose -p export_ddis down - - kill "$LOADING_SPINNER_PID"; + sudo docker-compose -p export run asclepius python3 asclepius/enrich.py "$flavour" > "$outfile" + sudo docker-compose -p export down exit 0 ;; @@ -63,9 +36,4 @@ main() { esac } -if [ $EUID != 0 ]; then - sudo "$0" "$@" - exit $? -fi - main "$@" diff --git a/mock-enriched-ddis/agonism.csv b/mock-enriched-ddis/agonism.csv new file mode 100644 index 00000000..9224e80f --- /dev/null +++ b/mock-enriched-ddis/agonism.csv @@ -0,0 +1,11576 @@ +Drug 1,Drug 2,DDI Type,Time,Unit +nalidixic acid,acenocoumarol,antagonism,4,yr +nalidixic acid,anisindione,antagonism,2,day +nalidixic acid,calcium acetate,agonism,3,yr +nalidixic acid,dicoumarol,agonism,9,hr +nalidixic acid,warfarin,antagonism,21,hr +ciprofloxacin,acenocoumarol,antagonism,3,day +ciprofloxacin,aluminium,antagonism,7,day +ciprofloxacin,aminophylline,antagonism,25,sec +ciprofloxacin,anisindione,antagonism,2,min +ciprofloxacin,caffeine,antagonism,25,sec +ciprofloxacin,calcium,agonism,43,sec +ciprofloxacin,calcium acetate,agonism,55,sec +ciprofloxacin,clozapine,antagonism,39,week +ciprofloxacin,cyclosporin A,antagonism,29,week +ciprofloxacin,dicoumarol,agonism,7,day +ciprofloxacin,dihydroxyaluminium,antagonism,2,day +ciprofloxacin,duloxetine,agonism,38,min +ciprofloxacin,dyphylline,antagonism,14,min +ciprofloxacin,eltrombopag,agonism,4,day +ciprofloxacin,ethotoin,agonism,3,hr +ciprofloxacin,phosphonoformic acid,antagonism,3,yr +ciprofloxacin,iron,agonism,1,day +ciprofloxacin,iron dextran,antagonism,8,min +ciprofloxacin,lomitapide,antagonism,5,yr +ciprofloxacin,magnesium,antagonism,23,week +ciprofloxacin,magnesium oxide,antagonism,1,yr +ciprofloxacin,mephenytoin,antagonism,9,hr +ciprofloxacin,methotrexate,antagonism,41,week +ciprofloxacin,oxtriphylline,agonism,21,hr +ciprofloxacin,phenytoin,antagonism,4,day +ciprofloxacin,procainamide,agonism,2,yr +ciprofloxacin,ramelteon,antagonism,7,sec +ciprofloxacin,rasagiline,agonism,19,sec +ciprofloxacin,ropinirole,antagonism,2,day +ciprofloxacin,sevelamer,agonism,7,sec +ciprofloxacin,sildenafil,antagonism,5,day +ciprofloxacin,sucralfate,antagonism,44,min +ciprofloxacin,tacrine,antagonism,19,sec +ciprofloxacin,theophylline,agonism,1,day +ciprofloxacin,thiothixene,agonism,7,week +ciprofloxacin,tizanidine,antagonism,44,min +ciprofloxacin,warfarin,antagonism,55,sec +ciprofloxacin,zinc,antagonism,3,hr +norfloxacin,acenocoumarol,antagonism,15,week +norfloxacin,aluminium,antagonism,7,day +norfloxacin,aminophylline,antagonism,9,hr +norfloxacin,anisindione,antagonism,2,yr +norfloxacin,artemether,antagonism,3,day +norfloxacin,caffeine,antagonism,20,min +norfloxacin,calcium,antagonism,31,sec +norfloxacin,calcium acetate,agonism,3,day +norfloxacin,clozapine,agonism,27,week +norfloxacin,cyclosporin A,agonism,1,day +norfloxacin,dicoumarol,antagonism,55,sec +norfloxacin,dyphylline,agonism,38,min +norfloxacin,phosphonoformic acid,agonism,9,hr +norfloxacin,iron,agonism,1,day +norfloxacin,iron dextran,antagonism,15,hr +norfloxacin,lumefantrine,antagonism,20,min +norfloxacin,magnesium,antagonism,5,yr +norfloxacin,magnesium oxide,agonism,21,hr +norfloxacin,oxtriphylline,agonism,8,min +norfloxacin,sucralfate,antagonism,38,min +norfloxacin,tacrine,antagonism,1,yr +norfloxacin,tacrolimus (anhydrous),agonism,2,yr +norfloxacin,tamsulosin,antagonism,21,hr +norfloxacin,theophylline,agonism,21,hr +norfloxacin,thiothixene,antagonism,13,sec +norfloxacin,tizanidine,antagonism,11,week +norfloxacin,tolterodine,agonism,6,day +norfloxacin,toremifene,agonism,7,sec +norfloxacin,tramadol hydrochloride,agonism,5,day +norfloxacin,trazodone,agonism,7,week +norfloxacin,trimipramine,antagonism,2,min +norfloxacin,voriconazole,antagonism,9,week +norfloxacin,vorinostat,agonism,1,day 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b/mock-enriched-ddis/harmful.csv @@ -0,0 +1,11576 @@ +Drug 1,Drug 2,DDI Type,Time,Unit +nalidixic acid,acenocoumarol,bad,4,yr +nalidixic acid,anisindione,bad,2,day +nalidixic acid,calcium acetate,bad,3,yr +nalidixic acid,dicoumarol,good,9,hr +nalidixic acid,warfarin,good,21,hr +ciprofloxacin,acenocoumarol,bad,3,day +ciprofloxacin,aluminium,bad,7,day +ciprofloxacin,aminophylline,good,25,sec +ciprofloxacin,anisindione,bad,2,min +ciprofloxacin,caffeine,good,25,sec +ciprofloxacin,calcium,good,43,sec +ciprofloxacin,calcium acetate,good,55,sec +ciprofloxacin,clozapine,good,39,week +ciprofloxacin,cyclosporin A,good,29,week +ciprofloxacin,dicoumarol,bad,7,day +ciprofloxacin,dihydroxyaluminium,bad,2,day +ciprofloxacin,duloxetine,bad,38,min +ciprofloxacin,dyphylline,bad,14,min +ciprofloxacin,eltrombopag,bad,4,day +ciprofloxacin,ethotoin,good,3,hr +ciprofloxacin,phosphonoformic acid,bad,3,yr +ciprofloxacin,iron,bad,1,day +ciprofloxacin,iron dextran,bad,8,min +ciprofloxacin,lomitapide,bad,5,yr 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A,sulfinpyrazone,good,9,hr +cyclosporin A,sulindac,bad,3,yr +cyclosporin A,tacrolimus (anhydrous),good,3,hr +cyclosporin A,talbutal,good,27,week +cyclosporin A,tamsulosin,bad,2,min +cyclosporin A,telaprevir,good,51,week +cyclosporin A,telithromycin,good,21,hr +cyclosporin A,tenoxicam,good,19,sec +cyclosporin A,terbinafine,good,31,week +cyclosporin A,testolactone,bad,5,day +cyclosporin A,testosterone,bad,4,yr +cyclosporin A,testosterone propionate,good,3,hr +cyclosporin A,ticlopidine,good,25,week +cyclosporin A,tipranavir,bad,32,min +cyclosporin A,tobramycin,good,43,sec +cyclosporin A,tolmetin sodium dihydrate,bad,38,min +cyclosporin A,tolterodine,good,1,week +cyclosporin A,topotecan,bad,3,yr +tramadol hydrochloride,cyclosporin A,bad,3,day +cyclosporin A,trandolapril,bad,2,yr +cyclosporin A,trastuzumab,bad,5,yr +cyclosporin A,trazodone,good,3,hr +cyclosporin A,troglitazone,good,21,hr +cyclosporin A,troleandomycin,bad,6,day +cyclosporin A,ursodeoxycholic acid,bad,2,yr +cyclosporin A,verapamil,bad,14,min +cyclosporin A,voriconazole,good,3,hr +cyproheptadine,donepezil,bad,44,min +cyproheptadine,fluoxetine,bad,3,yr +cyproheptadine,galanthamine,good,15,hr +cyproheptadine,metyrapone,good,31,sec +cyproheptadine,rivastigmine,good,19,sec +cyproheptadine,tacrine,good,3,week +cyproheptadine,triprolidine,good,31,week +cyproheptadine,trospium,good,43,sec +dexamethasone,acenocoumarol,bad,7,day +dexamethasone,ambenonium,bad,1,day +dexamethasone,amobarbital,bad,5,day +dexamethasone,aprepitant,good,9,hr +dexamethasone,aprobarbital,good,41,week +dexamethasone,butabarbital,bad,4,yr +dexamethasone,butethal,bad,3,day +dexamethasone,dabigatran etexilate,good,3,hr +dexamethasone,dicoumarol,bad,3,yr +dexamethasone,dihydroquinidine barbiturate,good,5,week +dexamethasone,estradiol valerate/dienogest,bad,5,yr +dexamethasone,ethotoin,bad,32,min +dexamethasone,fosphenytoin,bad,32,min +dexamethasone,heptabarbital,good,49,week +dexamethasone,hexobarbital,good,55,sec +dexamethasone,imatinib,bad,56,min +dexamethasone,lurasidone,good,9,hr +dexamethasone,magnesium salicylate,bad,6,day +dexamethasone,mephenytoin,good,7,week +dexamethasone,mephobarbital,bad,5,yr +dexamethasone,midodrine,good,15,hr +dexamethasone,neostigmine,good,31,week +dexamethasone,pentobarbital,bad,2,day +dexamethasone,phenobarbital,good,43,sec +dexamethasone,phenytoin,bad,4,yr +dexamethasone,primidone,good,33,week +dexamethasone,pyridostigmine,good,31,sec +dexamethasone,quinidine barbiturate,bad,38,min +dexamethasone,rilpivirine,bad,2,yr +dexamethasone,roflumilast,good,9,hr +dexamethasone,salsalate,good,55,sec +dexamethasone,secobarbital,bad,3,yr +dexamethasone,tacrine,good,55,sec +dexamethasone,talbutal,bad,44,min +dexamethasone,telithromycin,bad,1,yr +dexamethasone,temsirolimus,good,31,sec +dexamethasone,thalidomide,good,17,week +tramadol hydrochloride,dexamethasone,good,45,week +dexamethasone,trastuzumab,bad,32,min +dexamethasone,trazodone,good,15,hr +dexamethasone,vandetanib,bad,3,yr +dexamethasone,vecuronium,good,21,hr +dexamethasone,voriconazole,bad,38,min +dacarbazine,thiabendazole,bad,2,day +dacarbazine,trastuzumab,bad,3,yr +danazol,acenocoumarol,good,37,sec +danazol,dicoumarol,good,25,sec +danazol,tacrolimus (anhydrous),good,55,sec +dantrolene,conivaptan,good,55,sec +dantrolene,fosamprenavir,good,31,sec +dantrolene,imatinib,bad,1,day +dantrolene,indinavir,good,43,sec +dantrolene,isoniazid,good,37,sec +dantrolene,itraconazole,bad,44,min +dantrolene,ketoconazole,good,25,sec +dantrolene,lopinavir,bad,2,yr +dantrolene,methotrimeprazine,good,37,sec +dantrolene,nefazodone,bad,4,day +dantrolene,nelfinavir,bad,4,day +dantrolene,nicardipine,bad,50,min +dantrolene,posaconazole,good,37,week +dantrolene,ritonavir,bad,7,day +dantrolene,saquinavir,good,9,hr +dantrolene,telithromycin,good,31,sec +dantrolene,triprolidine,bad,2,day +dantrolene,voriconazole,bad,5,day +dapsone,aluminium,good,23,week +dapsone,calcium,bad,14,min 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+demeclocycline,dicoumarol,good,1,sec +demeclocycline,ethinyl estradiol,good,37,sec +demeclocycline,etretinate,good,29,week +demeclocycline,flucloxacillin,bad,3,day +demeclocycline,hetacillin,good,49,sec +demeclocycline,iron,good,1,week +demeclocycline,iron dextran,good,37,sec +demeclocycline,isotretinoin,bad,4,yr +demeclocycline,magnesium,good,51,week +demeclocycline,mestranol,good,19,sec +demeclocycline,methoxyflurane,good,1,week +demeclocycline,methicillin,good,55,sec +demeclocycline,mezlocillin,good,23,week +demeclocycline,nafcillin,bad,56,min +demeclocycline,oxacillin,good,21,hr +demeclocycline,penicillin v,bad,2,yr +demeclocycline,piperacillin,good,27,week +demeclocycline,pivampicillin,good,9,hr +demeclocycline,pivmecillinam,good,21,hr +demeclocycline,tazobactam,good,9,hr +demeclocycline,ticarcillin,good,9,hr +demeclocycline,zinc,good,3,hr +(S)-fenfluramine,fluoxetine,bad,3,day +(S)-fenfluramine,fluphenazine,bad,56,min +(S)-fenfluramine,fluvoxamine,bad,4,day +(S)-fenfluramine,guanethidine,bad,2,day +(S)-fenfluramine,insulin aspart,bad,1,yr +(S)-fenfluramine,insulin detemir,bad,3,day +(S)-fenfluramine,insulin glulisine,bad,1,yr +(S)-fenfluramine,isocarboxazid,bad,26,min +(S)-fenfluramine,mesoridazine,bad,5,day +(S)-fenfluramine,methdilazine,good,45,week +(S)-fenfluramine,methotrimeprazine,bad,3,yr +(S)-fenfluramine,paroxetine,bad,7,day +(S)-fenfluramine,perphenazine,good,19,sec +(S)-fenfluramine,phenelzine,bad,3,yr +(S)-fenfluramine,prochlorperazine,bad,2,day +(S)-fenfluramine,promazine,bad,2,yr +(S)-fenfluramine,promethazine,good,47,week +(S)-fenfluramine,propiomazine,good,9,hr +(S)-fenfluramine,rasagiline,bad,5,day +(S)-fenfluramine,thiethylperazine,good,9,hr +(S)-fenfluramine,thioridazine,bad,6,day +(S)-fenfluramine,tranylcypromine,good,21,hr +(S)-fenfluramine,trifluoperazine,bad,4,day +(S)-fenfluramine,triflupromazine,bad,20,min +(S)-fenfluramine,trimeprazine,good,31,sec +(S)-fenfluramine,venlafaxine,good,35,week +desogestrel,bexarotene,bad,5,day +desogestrel,colesevelam,good,49,week +desogestrel,lamotrigine,good,25,sec +dexmedetomidine,tranylcypromine,bad,56,min +dexmedetomidine,treprostinil,bad,7,day +dexmedetomidine,trimipramine,good,51,week +(S)-amphetamine,fluoxetine,bad,1,yr +(S)-amphetamine,fluphenazine,good,49,sec +(S)-amphetamine,fluvoxamine,bad,26,min +(S)-amphetamine,guanethidine,good,33,week +(S)-amphetamine,isocarboxazid,bad,4,yr +(S)-amphetamine,mesoridazine,good,1,week +(S)-amphetamine,methotrimeprazine,good,29,week +(S)-amphetamine,paroxetine,bad,6,day +(S)-amphetamine,perphenazine,bad,2,day +(S)-amphetamine,phenelzine,bad,26,min +(S)-amphetamine,prochlorperazine,bad,50,min +(S)-amphetamine,promethazine,good,55,sec +(S)-amphetamine,rasagiline,bad,8,min +(S)-amphetamine,thioridazine,bad,20,min +tramadol hydrochloride,(S)-amphetamine,bad,3,yr +(S)-amphetamine,trandolapril,good,37,sec +(S)-amphetamine,tranylcypromine,good,21,hr +(S)-amphetamine,trifluoperazine,bad,3,yr +(S)-amphetamine,triprolidine,bad,2,day +dezocine,alvimopan,bad,14,min +dezocine,triprolidine,bad,3,day +acepromazine,donepezil,bad,50,min +galanthamine,acepromazine,bad,3,yr +diazoxide,chlorthalidone,good,37,sec +diazoxide,fosphenytoin,bad,3,day +diazoxide,glyburide,good,15,hr +diazoxide,hydrochlorothiazide,bad,3,yr +diazoxide,indapamide,bad,4,day +diazoxide,phenytoin,good,19,week +diazoxide,trandolapril,good,15,hr +pentamidine,mesoridazine,bad,5,yr +pentamidine,quinupristin,bad,14,min +pentamidine,tacrolimus (anhydrous),bad,5,yr +pentamidine,telavancin,bad,6,day +pentamidine,telavancin hydrochloride,bad,6,day +pentamidine,thioridazine,good,3,hr +pentamidine,thiothixene,good,3,hr +pentamidine,ticlopidine,bad,44,min +pentamidine,toremifene,bad,32,min +pentamidine,trimipramine,good,15,hr +pentamidine,voriconazole,good,15,hr +pentamidine,vorinostat,good,3,week +pentamidine,zuclopenthixol,bad,5,yr +dicloxacillin,acenocoumarol,good,31,week +dicloxacillin,dicoumarol,bad,4,day 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john's wort,good,1,sec +tacrine,tranylcypromine,bad,14,min +tamoxifen,tranylcypromine,bad,26,min +terbutaline,tranylcypromine,good,13,week +tizanidine,tranylcypromine,good,55,sec +tolcapone,tranylcypromine,good,31,sec +tramadol hydrochloride,tranylcypromine,bad,3,day +trimethobenzamide,tranylcypromine,good,15,hr +trimipramine,tranylcypromine,good,21,hr +triprolidine,tranylcypromine,bad,3,day +trospium,tranylcypromine,good,29,week +altretamine,phenelzine,good,3,hr +dextromethorphan,phenelzine,bad,3,yr +phenelzine,doxepin,bad,20,min +duloxetine,phenelzine,bad,50,min +phenelzine,ephedra,good,9,hr +phenelzine,ephedrine,good,7,sec +galanthamine,phenelzine,bad,3,yr +imipramine,phenelzine,good,47,week +mazindol,phenelzine,bad,2,day +meperidine,phenelzine,good,5,week +phenelzine,mephentermine,bad,44,min +phenelzine,methamphetamine,good,9,hr +methoxamine,phenelzine,good,55,sec +phenelzine,milnacipran,good,1,sec +nortriptyline,phenelzine,bad,1,yr +phenelzine,phendimetrazine,good,27,week 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+fluconazole,torasemide,bad,2,day +indometacin,torasemide,good,5,week +rituximab,torasemide,bad,7,day +drotrecogin alfa,tinzaparin,bad,1,day +amprenavir,ranolazine,good,37,week +dirithromycin,ranolazine,good,21,hr +erythromycin,ranolazine,bad,5,yr +fluconazole,ranolazine,bad,4,day +saquinavir,ranolazine,bad,2,min +sotalol,ranolazine,bad,2,yr +tamoxifen,ranolazine,good,13,sec +ranolazine,thiothixene,good,43,week +tipranavir,ranolazine,good,55,sec +topotecan,ranolazine,good,51,week +tramadol hydrochloride,ranolazine,bad,56,min +vorinostat,ranolazine,bad,3,yr +celecoxib,pralatrexate,good,7,week +diclofenac,pralatrexate,good,9,hr +indometacin,pralatrexate,good,3,hr +pralatrexate,oxaprozin,bad,2,yr +pralatrexate,palifermin,bad,5,day +pralatrexate,probenecid,good,27,week +pralatrexate,tolmetin sodium dihydrate,bad,4,day +pipobroman,oxprenolol,bad,1,day +sotalol,pipobroman,bad,2,yr +butabarbital,conjugated estrogens,bad,1,day +diethylstilbestrol,butabarbital,good,15,hr +folic acid,butabarbital,bad,2,yr +imipramine,butabarbital,good,25,sec +teniposide,butabarbital,bad,6,day +triamcinolone acetonide,butabarbital,bad,56,min +levofloxacin,calcium acetate,good,23,week +calcium acetate,liothyronine,bad,6,day +calcium acetate,liotrix,good,1,sec +tipranavir,conjugated estrogens,bad,6,day +conjugated estrogens,ursodeoxycholic acid,bad,38,min +isradipine,thiothixene,good,55,sec +tipranavir,isradipine,bad,3,day +vorinostat,isradipine,bad,2,day +trastuzumab,amsacrine,bad,3,day +colestipol hydrochloride,liothyronine,bad,3,yr +natalizumab,chlorambucil,bad,3,day +roflumilast,chlorambucil,good,43,sec +trastuzumab,chlorambucil,good,3,hr +bleomycin,brentuximab vedotin,good,13,sec +natalizumab,bleomycin,bad,5,day +roflumilast,bleomycin,bad,3,day +trastuzumab,bleomycin,bad,5,day +abacavir,ribavirin monophosphate,bad,3,day +natalizumab,thiotepa,bad,1,yr +trastuzumab,thiotepa,good,31,week +abacavir,lopinavir,good,43,sec +bromazepam,lopinavir,bad,26,min +pitavastatin,lopinavir,good,19,week +lopinavir,ponatinib,bad,2,day +roflumilast,lopinavir,bad,26,min +tadalafil,lopinavir,bad,2,day +tamoxifen,lopinavir,bad,4,yr +teniposide,lopinavir,bad,5,day +tipranavir,lopinavir,bad,2,day +topotecan,lopinavir,bad,38,min +tramadol hydrochloride,lopinavir,bad,8,min +vardenafil,lopinavir,bad,1,yr +methacycline,pivampicillin,bad,5,day +methotrexate,pivampicillin,bad,4,day +rolitetracycline,pivampicillin,bad,4,yr +bivalirudin,deferasirox,bad,6,day +galanthamine,phenindamine,bad,5,yr +trimethobenzamide,phenindamine,bad,2,day +galanthamine,molindone,good,9,week +trimethobenzamide,molindone,bad,4,day +atorvastatin,fluconazole,bad,26,min +fluconazole,bromazepam,good,9,hr +celecoxib,fluconazole,bad,4,day +ergotamine,fluconazole,good,9,hr +everolimus,fluconazole,good,9,hr +imipramine,fluconazole,bad,14,min +ivacaftor,fluconazole,good,9,hr +fluconazole,quazepam,good,55,sec +rifabutin,fluconazole,bad,5,yr +tamoxifen,fluconazole,good,19,week +fluconazole,thiothixene,good,37,week +tipranavir,fluconazole,bad,38,min +tramadol hydrochloride,fluconazole,bad,5,day +valdecoxib,fluconazole,bad,20,min +vorinostat,fluconazole,good,35,week +atorvastatin,erythromycin,good,21,hr +erythromycin,bromazepam,good,3,hr +ergotamine,erythromycin,bad,7,day +everolimus,erythromycin,good,41,week +ivacaftor,erythromycin,good,9,hr +levofloxacin,erythromycin,bad,20,min +erythromycin,lincomycin,bad,2,yr +moxifloxacin,erythromycin,good,21,hr +pitavastatin,erythromycin,good,31,week +rifabutin,erythromycin,bad,26,min +roflumilast,erythromycin,bad,2,day +sotalol,erythromycin,bad,26,min +erythromycin,thiothixene,bad,4,yr +topotecan,erythromycin,bad,2,day +tramadol hydrochloride,erythromycin,good,51,week +valproic acid,erythromycin,bad,4,yr +vardenafil,erythromycin,bad,1,day +vismodegib,erythromycin,bad,5,day +vorinostat,erythromycin,bad,1,yr +rifabutin,roflumilast,bad,4,yr +rifapentine,roflumilast,bad,3,yr +diarsenic trioxide,thiothixene,good,15,hr +flecainide,thiothixene,good,43,sec +galanthamine,thiothixene,bad,50,min +imipramine,thiothixene,good,23,week +indapamide,thiothixene,good,9,hr +levofloxacin,thiothixene,bad,3,yr +mefloquine,thiothixene,bad,4,day +moxifloxacin,thiothixene,bad,4,yr +octreotide,thiothixene,good,35,week +pergolide mesylate,thiothixene,good,7,sec +probucol,thiothixene,bad,5,day +propafenone hydrochloride,thiothixene,bad,26,min +sotalol,thiothixene,bad,5,day +trimethobenzamide,thiothixene,bad,6,day +vorinostat,thiothixene,bad,4,yr +galanthamine,isopropamide,good,3,hr +terbutaline,pargyline,good,33,week +attapulgite,lincomycin,good,47,week +kaolin,lincomycin,bad,2,day +galanthamine,pipotiazine,bad,3,yr +colesevelam,cholecalciferol,good,3,week +colestipol hydrochloride,cholecalciferol,bad,2,min +trastuzumab,daclizumab,bad,3,yr +drotrecogin alfa,nadroparin,good,15,week +ticagrelor,lomitapide,bad,5,yr +digoxin immune fab,cinitapride,bad,4,day +natalizumab,ado-trastuzumab emtansine,bad,3,yr +natalizumab,brentuximab vedotin,bad,32,min +natalizumab,certolizumab pegol,bad,5,day +paclitaxel,natalizumab,bad,8,min +temozolomide,natalizumab,good,15,hr +teniposide,natalizumab,bad,3,day +teriflunomide,natalizumab,good,11,week +thalidomide,natalizumab,good,1,week +topotecan,natalizumab,bad,38,min +tositumomab,natalizumab,good,3,week +trastuzumab,natalizumab,bad,1,day +octreotide,dihydrocodeine,bad,32,min +insulin lispro,octreotide,bad,50,min +vorinostat,octreotide,good,31,week +deferiprone,iron,bad,3,yr +deferiprone,zinc,bad,1,yr +atorvastatin,lomitapide,good,3,hr +boceprevir,lomitapide,good,3,hr +colestipol hydrochloride,lomitapide,good,3,hr +telaprevir,lomitapide,good,7,sec +celecoxib,azilsartan medoxomil,bad,4,day +azilsartan medoxomil,citric acid,good,19,sec +diclofenac,azilsartan medoxomil,good,17,week +indometacin,azilsartan medoxomil,bad,20,min +maraviroc,azilsartan medoxomil,good,19,week +azilsartan medoxomil,oxaprozin,bad,3,day +azilsartan medoxomil,rituximab,good,37,sec +azilsartan medoxomil,tadalafil,good,41,week +azilsartan medoxomil,tolmetin sodium dihydrate,bad,2,day +posaconazole,ivacaftor,bad,2,min +rifabutin,ivacaftor,bad,1,yr +ivacaftor,vismodegib,good,27,week +rifabutin,rilpivirine,bad,20,min +rifapentine,rilpivirine,good,9,hr +rifabutin,estradiol valerate/dienogest,good,49,sec +rifapentine,estradiol valerate/dienogest,good,15,hr +perampanel,dihydrocodeine,good,7,week +rifabutin,vemurafenib,bad,3,yr +rifapentine,vemurafenib,bad,4,day +saquinavir,vemurafenib,good,9,hr +ado-trastuzumab emtansine,belimumab,bad,4,day +hydroxyurea,belimumab,bad,3,yr +atorvastatin,boceprevir,good,21,hr +boceprevir,ponatinib,bad,4,yr +boceprevir,tadalafil,good,9,hr +posaconazole,regorafenib,good,9,hr +mirabegron,flecainide,good,33,week +mirabegron,propafenone hydrochloride,good,33,week +atorvastatin,telaprevir,good,31,sec +ergotamine,telaprevir,bad,7,day +telaprevir,ponatinib,good,21,hr +telaprevir,tadalafil,good,29,week +posaconazole,bromazepam,bad,5,day +rifabutin,bromazepam,bad,3,yr +rifapentine,bromazepam,good,7,sec +saquinavir,bromazepam,bad,20,min +tipranavir,bromazepam,good,9,hr +desmopressin,dihydrocodeine,bad,1,yr +alpha-methyl-L-tyrosine,dihydrocodeine,bad,7,day +oprelvekin,dihydrocodeine,good,9,hr +pegvisomant,dihydrocodeine,bad,8,min +rasagiline,phendimetrazine,good,51,week +tramadol hydrochloride,phendimetrazine,bad,4,day +rasagiline,methamphetamine,bad,3,yr +tramadol hydrochloride,methamphetamine,bad,4,yr +valganciclovir,cilastatin,good,37,sec +levofloxacin,zinc,bad,3,yr +moxifloxacin,zinc,bad,38,min +levofloxacin,iron,good,1,sec +moxifloxacin,iron,bad,26,min +pancrelipase,iron,good,55,sec +galanthamine,solifenacin,good,45,week +trimethobenzamide,solifenacin,good,1,sec +tipranavir,prazepam,bad,32,min +tipranavir,quazepam,good,43,week +colesevelam,ursodeoxycholic acid,bad,2,yr +colestipol hydrochloride,ursodeoxycholic acid,good,9,hr +diethylstilbestrol,ursodeoxycholic acid,bad,38,min +colestipol hydrochloride,thyroglobulin,bad,5,yr +colestipol hydrochloride,liotrix,bad,32,min +ergotamine,oxprenolol,bad,26,min +formoterol,oxprenolol,bad,2,yr +indometacin,oxprenolol,bad,5,day +insulin glargine,oxprenolol,bad,6,day +salmeterol,oxprenolol,bad,2,day +terbutaline,oxprenolol,good,31,sec +trastuzumab,efalizumab,good,31,sec +topotecan,filgrastim,bad,7,day +adalimumab,trastuzumab,good,31,sec +insulin glargine,somatropin recombinant,good,31,sec +pegaspargase,trastuzumab,good,45,week +abciximab,trastuzumab,good,3,hr +tenecteplase,drotrecogin alfa,bad,14,min +tolmetin sodium dihydrate,drotrecogin alfa,bad,26,min +urokinase,drotrecogin alfa,bad,4,yr +infliximab,trastuzumab,good,21,hr +trastuzumab,alemtuzumab,good,19,sec +anakinra,trastuzumab,bad,7,day +asparaginase,trastuzumab,bad,32,min +trastuzumab,basiliximab,good,33,week +denileukin diftitox,trastuzumab,bad,2,yr +etanercept,trastuzumab,bad,26,min +fludarabine phosphate,trastuzumab,good,3,hr +hydroxyurea,trastuzumab,bad,50,min +trastuzumab,ibritumomab,bad,20,min +methotrexate,trastuzumab,good,21,hr +trastuzumab,muromonab,good,9,hr +nelarabine,trastuzumab,good,31,week +paclitaxel,trastuzumab,bad,3,day +procarbazine,trastuzumab,bad,7,day +trastuzumab,rituximab,good,9,hr +temozolomide,trastuzumab,good,27,week +teniposide,trastuzumab,good,21,hr +thalidomide,trastuzumab,good,49,sec +topotecan,trastuzumab,bad,5,day +trastuzumab,tositumomab,good,7,sec +triamcinolone acetonide,trastuzumab,bad,2,day +rituximab,certolizumab pegol,bad,14,min +anakinra,certolizumab pegol,bad,38,min +thalidomide,anakinra,good,9,hr +trimethobenzamide,secretin,good,55,sec +posaconazole,ponatinib,good,7,week +saquinavir,ponatinib,bad,44,min +probenecid,glycerol phenylbutyrate,bad,26,min +valproic acid,glycerol phenylbutyrate,bad,2,yr +sotalol,insulin glargine,bad,4,day +telbivudine,peginterferon alfa-2a,bad,6,day +rifabutin,abiraterone,good,27,week +rifapentine,abiraterone,bad,3,yr +saquinavir,abiraterone,good,13,sec From 19f0d9574fa37c49d1427efd83e06018e17b43fe Mon Sep 17 00:00:00 2001 From: shawa Date: Wed, 5 Apr 2017 12:37:36 +0100 Subject: [PATCH 10/16] Update Features doc to include mock ddi data tests --- doc/FEATURES_RELEASE_2.md | 72 ++++++++++++++++++++++++++++++++++++--- 1 file changed, 68 insertions(+), 4 deletions(-) diff --git a/doc/FEATURES_RELEASE_2.md b/doc/FEATURES_RELEASE_2.md index 24ee3664..795efcaf 100644 --- a/doc/FEATURES_RELEASE_2.md +++ b/doc/FEATURES_RELEASE_2.md @@ -1,11 +1,11 @@ # Features - Release 2 -Each deliverable feature for Release 2 is outlined in this file. Each feature -is given a short description. For completed features, instructions on how to -verify the feature are provided. +Each deliverable feature for Release 2 is outlined in this file. Each feature is +given a short description. For completed features, instructions on how to verify +the feature are provided. Continuous integration testing has been set up for the project and can be -tracked [here](https://circleci.com/gh/tom-and-the-toothfairies/pathways). +tracked on [the CI dashboard](https://circleci.com/gh/tom-and-the-toothfairies/pathways). ## End to End Automated Testing @@ -27,6 +27,70 @@ format. These `feature` files can be found [here](../athloi/features). To manually verify features, run the project as outlined in the [README]. The homepage is available at [localhost:4000](http://localhost:4000). +## Mock DDI Characterisation Data - Complete + +### Description + +The system must provide and display mock data on DDI Harmfulness and DDI +interaction windows. + +### Testing + +Visit the [homepage]. Select `panacea/test/fixtures/ddis.pml` which contains a +DDI. Press `Submit`. The system should display the DDI information +for the DDI found, including whether its disposition is `Good` or `Bad`, +the timing window and units of this timing window, as well as the drugs involved. + + +## Real DDI Mock Good-Bad Time Generator - Complete + +### Description + +The system must provide a means of generating mock data about the disposition of +a DDI - whether it is `Good` or `Bad`. + +_A Good DDI is one which has an overall beneficial pharmacological effect._ + +_A Bad DDI is one which has an overall detrimental pharmacological effect._ + +### Testing + +Enter the root of the repository. Run the command + +```bash +$ ./export-mock-ddi-data.sh harmful harmful.csv +``` + +The file `harmful.csv` will be constructed, which can be viewed in a text editor. +The output of this command is also readily available to view in the +[mock-enriched-ddis directory](../mock-enriched-ddis/harmful.csv) of our repository. + + +## Real DDI Mock Agonist-Antagonist Time Generator - Complete + +### Description + +The system must provide a means of generating mock data about the agonism disposition of +a DDI - whether it is an `Agonism` or an `Antagonism`. + +_An agonism involving `Drug 1` and `Drug 2` is a DDI such that `Drug 1` **increases** the +effect of `Drug 2`_ + +_An antagonism involving `Drug 1` and `Drug 2` is a DDI such that `Drug 1` **decreases** the +effect of `Drug 2`_ + +### Testing + +Enter the root of the repository. Run the command + +```bash +$ ./export-mock-ddi-data.sh agonism agonism.csv +``` + +The file `agonism.csv` will be constructed, which can be viewed in a text editor. +The output of this command is also readily available to view in the +[mock-enriched-ddis directory](../mock-enriched-ddis/agonism.csv) of our repository. + ## Report Unnamed PML Construct - Complete ### Description From 322a4c3fe161c5a6760fb14a76c0c8a099af2b1d Mon Sep 17 00:00:00 2001 From: Eoin Houlihan Date: Wed, 5 Apr 2017 12:39:29 +0100 Subject: [PATCH 11/16] Units are properly displayed in the front end --- panacea/web/static/js/view.js | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/panacea/web/static/js/view.js b/panacea/web/static/js/view.js index b0ed0624..7857f3b9 100644 --- a/panacea/web/static/js/view.js +++ b/panacea/web/static/js/view.js @@ -200,6 +200,20 @@ const formatDdiConstructs = constructs => { }).join(', '); }; +const formatSpacingInfo = (spacing, unit) => { + const table = { + sec: 'second', + min: 'minute', + hr: 'hour', + day: 'day', + week: 'week', + yr: 'year' + }; + + const niceUnit = `${table[unit]}${spacing === 1 ? '' : 's'}`; + return `${spacing} ${niceUnit}`; +}; + const generateDdiElement = ddi => { const ddiContainer = document.createElement('div'); let containerClass = null; @@ -221,8 +235,7 @@ const generateDdiElement = ddi => { const harmfulElement = generateDdiInfoSnippet('Disposition', ddi.harmful ? 'Harmful' : 'Not Harmful'); const categoryElement = generateDdiInfoSnippet('Category', formatDdiCategoryAtom(ddi.category)); const constructsElement = generateDdiInfoSnippet('Enclosing Constructs', formatDdiConstructs(ddi.enclosing_constructs)); - const spacingUnit = ddi.spacing === 1 ? 'day' : 'days'; - const spacingElement = generateDdiInfoSnippet('Interaction Window', `${ddi.spacing} ${spacingUnit}`); + const spacingElement = generateDdiInfoSnippet('Interaction Window', formatSpacingInfo(ddi.spacing, ddi.unit)); ddiContainer.appendChild(interactionNameElement); ddiContainer.appendChild(drugInfoElement); From 7f68a8ac51d4fd5793e1e7eb10f99176471d9c3f Mon Sep 17 00:00:00 2001 From: Andrew Shaw Date: Wed, 5 Apr 2017 12:44:32 +0100 Subject: [PATCH 12/16] Update CHANGELOG.md --- doc/CHANGELOG.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/doc/CHANGELOG.md b/doc/CHANGELOG.md index 42b927dd..cc88702e 100644 --- a/doc/CHANGELOG.md +++ b/doc/CHANGELOG.md @@ -2,6 +2,16 @@ All notable changes to this project will be documented in this file. +## [Unreleased] + +### Added +- Added tool to generate mock DDI data, for both badness and agonism +- Added exported data from running this tool + +### Fixed +- Mock DDI data is deterministic across different runs of the app +- Display correct spacing time units in frontend + ## [1.3] 2017-04-02 ### Added From 32a0c09b52da04368a6ccb0e4d9bd4a1cf77f1a9 Mon Sep 17 00:00:00 2001 From: Laura Murphy-Clarkin Date: Wed, 5 Apr 2017 19:22:43 +0100 Subject: [PATCH 13/16] Remove unnecessary warning and error triggers from fixtures --- athloi/features/fixtures/alternative_non_ddi.pml | 2 +- athloi/features/fixtures/analysis/clashes.pml | 1 + athloi/features/fixtures/analysis/unnamed.pml | 3 +++ athloi/features/fixtures/parallel.pml | 2 +- athloi/features/fixtures/repeated_alternative.pml | 4 ++-- panacea/test/fixtures/alternative_non_ddi.pml | 2 +- panacea/test/fixtures/analysis/clashes.pml | 1 + panacea/test/fixtures/analysis/unnamed.pml | 3 +++ panacea/test/fixtures/parallel.pml | 2 +- panacea/test/fixtures/repeated_alternative.pml | 4 ++-- 10 files changed, 16 insertions(+), 8 deletions(-) diff --git a/athloi/features/fixtures/alternative_non_ddi.pml b/athloi/features/fixtures/alternative_non_ddi.pml index ead93601..dbea2037 100644 --- a/athloi/features/fixtures/alternative_non_ddi.pml +++ b/athloi/features/fixtures/alternative_non_ddi.pml @@ -1,5 +1,5 @@ process alternative_non_ddis { - selection { + selection sel1 { action s1 { requires { drug { "trandolapril" } } } diff --git a/athloi/features/fixtures/analysis/clashes.pml b/athloi/features/fixtures/analysis/clashes.pml index b5bcc429..55a5b9a2 100644 --- a/athloi/features/fixtures/analysis/clashes.pml +++ b/athloi/features/fixtures/analysis/clashes.pml @@ -1,5 +1,6 @@ process foo { action clash1 { + requires { drug { "paracetamol" } } } action clash2 { } diff --git a/athloi/features/fixtures/analysis/unnamed.pml b/athloi/features/fixtures/analysis/unnamed.pml index fdabcf7c..e8e65416 100644 --- a/athloi/features/fixtures/analysis/unnamed.pml +++ b/athloi/features/fixtures/analysis/unnamed.pml @@ -1,4 +1,7 @@ process foo { task { + action boo { + requires { drug { "paracetamol" } } + } } } diff --git a/athloi/features/fixtures/parallel.pml b/athloi/features/fixtures/parallel.pml index 276caa7c..b94c5d39 100644 --- a/athloi/features/fixtures/parallel.pml +++ b/athloi/features/fixtures/parallel.pml @@ -1,5 +1,5 @@ process parallel_ddis { - branch { + branch br1 { action b1 { requires { drug { "trandolapril" } } } diff --git a/athloi/features/fixtures/repeated_alternative.pml b/athloi/features/fixtures/repeated_alternative.pml index ceb88dc5..2dd9cb89 100644 --- a/athloi/features/fixtures/repeated_alternative.pml +++ b/athloi/features/fixtures/repeated_alternative.pml @@ -1,6 +1,6 @@ process repeated_alternative_ddis { - iteration { - selection { + iteration it1 { + selection sel1 { action s1 { requires { drug { "trandolapril" } } } diff --git a/panacea/test/fixtures/alternative_non_ddi.pml b/panacea/test/fixtures/alternative_non_ddi.pml index ead93601..dbea2037 100644 --- a/panacea/test/fixtures/alternative_non_ddi.pml +++ b/panacea/test/fixtures/alternative_non_ddi.pml @@ -1,5 +1,5 @@ process alternative_non_ddis { - selection { + selection sel1 { action s1 { requires { drug { "trandolapril" } } } diff --git a/panacea/test/fixtures/analysis/clashes.pml b/panacea/test/fixtures/analysis/clashes.pml index b5bcc429..55a5b9a2 100644 --- a/panacea/test/fixtures/analysis/clashes.pml +++ b/panacea/test/fixtures/analysis/clashes.pml @@ -1,5 +1,6 @@ process foo { action clash1 { + requires { drug { "paracetamol" } } } action clash2 { } diff --git a/panacea/test/fixtures/analysis/unnamed.pml b/panacea/test/fixtures/analysis/unnamed.pml index fdabcf7c..e8e65416 100644 --- a/panacea/test/fixtures/analysis/unnamed.pml +++ b/panacea/test/fixtures/analysis/unnamed.pml @@ -1,4 +1,7 @@ process foo { task { + action boo { + requires { drug { "paracetamol" } } + } } } diff --git a/panacea/test/fixtures/parallel.pml b/panacea/test/fixtures/parallel.pml index 276caa7c..b94c5d39 100644 --- a/panacea/test/fixtures/parallel.pml +++ b/panacea/test/fixtures/parallel.pml @@ -1,5 +1,5 @@ process parallel_ddis { - branch { + branch br1 { action b1 { requires { drug { "trandolapril" } } } diff --git a/panacea/test/fixtures/repeated_alternative.pml b/panacea/test/fixtures/repeated_alternative.pml index ceb88dc5..2dd9cb89 100644 --- a/panacea/test/fixtures/repeated_alternative.pml +++ b/panacea/test/fixtures/repeated_alternative.pml @@ -1,6 +1,6 @@ process repeated_alternative_ddis { - iteration { - selection { + iteration it1 { + selection sel1 { action s1 { requires { drug { "trandolapril" } } } From 5738eb12d1c58f095a1859915916c3755f86855c Mon Sep 17 00:00:00 2001 From: Laura Murphy-Clarkin Date: Wed, 5 Apr 2017 20:44:37 +0100 Subject: [PATCH 14/16] Fix line numbers in tests --- athloi/features/file_upload.feature | 6 +++--- panacea/test/controllers/pml_controller_test.exs | 6 +++--- panacea/test/panacea/pml/analysis/clashes_test.exs | 6 +++--- panacea/test/panacea/pml/analysis_test.exs | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/athloi/features/file_upload.feature b/athloi/features/file_upload.feature index f4182f07..56648352 100644 --- a/athloi/features/file_upload.feature +++ b/athloi/features/file_upload.feature @@ -66,9 +66,9 @@ Feature: File upload And I should see "2" in the warning number badge And I should see the following warnings in the clashes panel: | action clash1 on line 2 | - | action clash1 on line 8 | - | action clash2 on line 4 | - | action clash2 on line 6 | + | action clash1 on line 9 | + | action clash2 on line 5 | + | action clash2 on line 7 | Scenario: uploading a binary file When I select "example.png" diff --git a/panacea/test/controllers/pml_controller_test.exs b/panacea/test/controllers/pml_controller_test.exs index db975951..39278e29 100644 --- a/panacea/test/controllers/pml_controller_test.exs +++ b/panacea/test/controllers/pml_controller_test.exs @@ -68,15 +68,15 @@ defmodule Panacea.PmlControllerTest do %{ "name" => "clash1", "occurrences" => [ - %{"line" => 8, "type" => "action"}, + %{"line" => 9, "type" => "action"}, %{"line" => 2, "type" => "action"} ] }, %{ "name" => "clash2", "occurrences" => [ - %{"line" => 6, "type" => "action"}, - %{"line" => 4, "type" => "action"} + %{"line" => 7, "type" => "action"}, + %{"line" => 5, "type" => "action"} ] } ] diff --git a/panacea/test/panacea/pml/analysis/clashes_test.exs b/panacea/test/panacea/pml/analysis/clashes_test.exs index b2a88df1..c62b32b0 100644 --- a/panacea/test/panacea/pml/analysis/clashes_test.exs +++ b/panacea/test/panacea/pml/analysis/clashes_test.exs @@ -15,15 +15,15 @@ defmodule Panacea.Pml.Analysis.ClashesTest do %{ name: "clash1", occurrences: [ - %{line: 8, type: :action}, + %{line: 9, type: :action}, %{line: 2, type: :action} ] }, %{ name: "clash2", occurrences: [ - %{line: 6, type: :action}, - %{line: 4, type: :action} + %{line: 7, type: :action}, + %{line: 5, type: :action} ] } ] diff --git a/panacea/test/panacea/pml/analysis_test.exs b/panacea/test/panacea/pml/analysis_test.exs index 8e3bf12e..a6ba899b 100644 --- a/panacea/test/panacea/pml/analysis_test.exs +++ b/panacea/test/panacea/pml/analysis_test.exs @@ -30,15 +30,15 @@ defmodule Panacea.Pml.AnalysisTest do %{ name: "clash1", occurrences: [ - %{line: 8, type: :action}, + %{line: 9, type: :action}, %{line: 2, type: :action} ], }, %{ name: "clash2", occurrences: [ - %{line: 6, type: :action}, - %{line: 4, type: :action} + %{line: 7, type: :action}, + %{line: 5, type: :action} ], } ] From 7b8312cbdad9f0c2f13a94fbaa5fa1b94eb17a99 Mon Sep 17 00:00:00 2001 From: Eoin Houlihan Date: Sun, 9 Apr 2017 19:27:02 +0100 Subject: [PATCH 15/16] Doc fixup (#197) --- README.md | 29 +++++++++--------- asclepius/README.md | 40 ++++++++++++++----------- chiron/README.md | 2 +- doc/BUILDING_MANUALLY.md | 4 +-- doc/CHANGELOG.md | 2 +- doc/FEATURES_RELEASE_1.md | 19 ++++++------ doc/FEATURES_RELEASE_2.md | 62 ++++++++++++++++++++++++++------------- doc/UPDATING_DINTO.md | 12 ++++---- panacea/README.md | 24 ++++++++------- 9 files changed, 111 insertions(+), 83 deletions(-) diff --git a/README.md b/README.md index 206f9caf..39338bab 100644 --- a/README.md +++ b/README.md @@ -13,8 +13,8 @@ At the time of writing the current release is `1.3` ## Installing Dependencies -This project uses Docker and Docker Compose. For Ubuntu 16.04, an installation -script `install-docker.sh` is provided for convenience. +This project uses Docker and Docker Compose. An installation script, +`install-docker.sh`, is provided for Ubuntu 16.04. ```bash $ ./install-docker.sh @@ -22,9 +22,9 @@ $ ./install-docker.sh For platforms other than Ubuntu, follow the installation instructions on the [Docker Website][install docker ce]. Note - on other platforms, sudo is not -required for docker commands. +required for Docker commands. -You can test your docker installation by running docker's built in hello-world: +You can test your Docker installation by running Docker's built in hello-world: ```bash $ sudo docker run hello-world @@ -32,7 +32,7 @@ $ sudo docker run hello-world ## Running -The project can be run with `docker compose` +The project can be run with Docker Compose: ```bash $ sudo docker-compose up -d @@ -40,7 +40,7 @@ $ sudo docker-compose up -d The system is then accessible at [localhost:4000](http://localhost:4000). -To stop the project, run the following command +To stop the system, run the following command ```bash $ sudo docker-compose down @@ -60,14 +60,13 @@ document](./doc/FEATURES_RELEASE_1.md). ## Change Log -The change log for the project can be found [here](./doc/CHANGELOG.md) - +Changes to the project are recorded in the [change log](./doc/CHANGELOG.md). ## Architecture Overview The system is split into three distinct services; Panacea, Asclepius and Chiron. The auxiliary service, Athloi, is used for automated testing. -They each run inside a docker container. The containers can be easily managed +They each run inside a Docker container. The containers can be easily managed using `docker-compose` as mentioned earlier. ### Panacea @@ -75,14 +74,14 @@ using `docker-compose` as mentioned earlier. Panacea is responsible for the UI and PML analysis. It is a web application that serves the UI and exposes an API for uploading PML files for analysis. -More information about Panacea can be found [here](./panacea/README.md). +More information about Panacea can be found [in the Panacea README](./panacea/README.md). ### Chiron Chiron houses the DINTO data. The data is compiled into a triple store. Chiron exposes a HTTP API for querying the triple store. -More information about Chiron can be found [here](./chiron/README.md). +More information about Chiron can be found [in the Chiron README](./chiron/README.md). ### Asclepius @@ -90,20 +89,20 @@ Asclepius acts as an intermediary between Panacea and Chiron. It accepts requests to identify DDIs from Panacea, creates the necessary SPARQL query and passes it on to Chiron. -More information about Asclepius can be found [here](./asclepius/README.md). +More information about Asclepius can be found [in the Asclepius README](./asclepius/README.md). ### Athloi Athloi is the service that runs our end to end tests. -More information about Athloi can be found [here](./athloi/README.md). +More information about Athloi can be found [in the Athloi README](./athloi/README.md). ## Building Manually -Docker compose will pull down the required versions of each service from [Docker +Docker Compose will pull down the required versions of each service from [Docker Hub] when you run the project. If for some reason you wish to build these services manually, instructions for doing so can be -found [here](./doc/BUILDING_MANUALLY.md). +found [in the manual build documentation](./doc/BUILDING_MANUALLY.md). diff --git a/asclepius/README.md b/asclepius/README.md index 0d7cdebd..3462f9db 100644 --- a/asclepius/README.md +++ b/asclepius/README.md @@ -1,14 +1,17 @@ Asclepius ⚕ =========== -Flask endpoint for querying DINTO. Supports querying for all drugs listed, as well as finding all, or specific drug-drug interactions. +Flask endpoint for querying DINTO. Supports querying for all drugs listed, as +well as finding all, or specific drug-drug interactions. -This application acts as an adaptor to Chiron - an instance of Apache Fuseki, Chiron must be running before any queries can be served. +This application acts as an adaptor to Chiron - an instance of Apache Fuseki, +Chiron must be running before any queries can be served. CSV File Exporting ------------------ -When run as a program, the `enrich` module will export DDIs, along with mock timing and agonism/harmfulness information. +When run as a program, the `enrich` module will export DDIs, along with mock +timing and agonism/harmfulness information. Run as `python3 enrich.py > outfile.csv` to export to a CSV file. @@ -51,12 +54,12 @@ HTTP Endpoints ### `/all_ddis` -| | | -|-------------|--------------------------------------------------------------------------------------------------------| -| Description | Find all drug-drug interactions (DDIs) in the DINTO ontology | -| Methods | `GET` | -| Parameters | None | -| Returns | A list containing pairs of the canonical URI for a drug-drug interaction, as well as its English Label | +| | | +|-------------|---------------------------------------------------------------------------------------------------------------------------------------------| +| Description | Find all drug-drug interactions (DDIs) in the DINTO ontology | +| Methods | `GET` | +| Parameters | None | +| Returns | A list containing pairs of the canonical URI for a drug-drug interaction, as well as its English label and the labels of the drugs involved | #### Example @@ -87,12 +90,13 @@ HTTP Endpoints ### `/ddis` -| | | -|--------------|--------------------------------------------------------------------------------------------------| -| Description | Find all drug-drug interactions (DDI) in the DINTO ontology which involve only the *given* drugs | -| Methods | `POST` | -| Request Body | An object containing a list of *DINTO URIs* | -| Returns | A list of DDI objects; its label, its URI, the identifiers of the two drugs involved, the spacing between dosages required to avoid the DDI (in days) as well as whether or not it is a harmful interaction | +| | | +|--------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Description | Find all drug-drug interactions (DDI) in the DINTO ontology which involve only the *given* drugs | +| Methods | `POST` | +| Request Body | An object containing a list of *DINTO URIs* | +| Returns | A list of DDI objects; its label, its URI, the identifiers of the two drugs involved, the spacing between dosages required to avoid the DDI as well as whether or not it is a harmful interaction and an agonism/antagonism | +| | | #### Example ##### Request Body @@ -114,8 +118,10 @@ HTTP Endpoints "drug_b": "http://purl.obolibrary.org/obo/DINTO_DB00519", "label": "torasemide/trandolapril DDI", "uri": "http://purl.obolibrary.org/obo/DINTO_11031", - "harmful": false, - "spacing": 3 + "harmful": true, + "spacing": 2, + "unit": "yr", + "agonism": true } ] ``` diff --git a/chiron/README.md b/chiron/README.md index 5d78287b..b49e3e43 100644 --- a/chiron/README.md +++ b/chiron/README.md @@ -2,7 +2,7 @@ This service is an instance of [Apache Jena Fuseki](https://jena.apache.org/index.html). It stores DINTO's -owl in a triple store and provides a HTTP API for querying the store using +OWL in a triple store and provides a HTTP API for querying the store using SPARQL. Asclepius and Panacea depend on this service. diff --git a/doc/BUILDING_MANUALLY.md b/doc/BUILDING_MANUALLY.md index 7786884f..eea5e218 100644 --- a/doc/BUILDING_MANUALLY.md +++ b/doc/BUILDING_MANUALLY.md @@ -1,7 +1,7 @@ # Building Manually -There are DNS problems when running containers in *Ubuntu* within the *TCD -network*. This can be resolved while on the TCD network by editing the Docker +There are DNS problems when running containers in **Ubuntu** within the **TCD +network**. This can be resolved while on the TCD network by editing the Docker DNS config. ```bash diff --git a/doc/CHANGELOG.md b/doc/CHANGELOG.md index cc88702e..61dc8d65 100644 --- a/doc/CHANGELOG.md +++ b/doc/CHANGELOG.md @@ -6,7 +6,7 @@ All notable changes to this project will be documented in this file. ### Added - Added tool to generate mock DDI data, for both badness and agonism -- Added exported data from running this tool +- Added exported data from running the mock DDI data generation tool ### Fixed - Mock DDI data is deterministic across different runs of the app diff --git a/doc/FEATURES_RELEASE_1.md b/doc/FEATURES_RELEASE_1.md index 6406e082..2f5e4a2e 100644 --- a/doc/FEATURES_RELEASE_1.md +++ b/doc/FEATURES_RELEASE_1.md @@ -1,11 +1,11 @@ # Features - Release 1 -Each deliverable feature for Release 1 is outlined in this file. Each feature -is given a short description. For completed features, instructions on how to -verify the feature are provided. +Each deliverable feature for Release 1 is outlined in this file. Each feature is +given a short description. For completed features, instructions on how to verify +the feature are provided. Continuous integration testing has been set up for the project and can be -tracked [here](https://circleci.com/gh/tom-and-the-toothfairies/pathways). +tracked on [the CI dashboard](https://circleci.com/gh/tom-and-the-toothfairies/pathways). ## End to End Automated Testing @@ -20,7 +20,8 @@ $ sudo docker-compose -f docker-compose.e2e.yml -p integration run athloi; sudo Our to end to end tests are written using the Cucumber behaviour-driven-development test framework which allows tests to be written according to user stories in plain English in the friendly "Given When Then" -format. These `feature` files can be found [here](../athloi/features). +format. These `feature` files can be +found [in the Athloi directory](../athloi/features). ## Manually Verifying Features @@ -34,7 +35,7 @@ The system allows users to upload PML files for analysis. Users must be able to select these files from their local file system. ### Testing -Visit the [homepage]. Click the `Choose File` button and select a file +Visit the [homepage]. Click the `Choose PML File` button and select a file (`panacea/test/fixtures/ddis.pml` for example). The name of the chosen file should be displayed beside the file selection button. If you have selected the file suggested above, you should see `ddis.pml`. @@ -87,7 +88,7 @@ successful analysis displayed in the analysis tab. ### Description The successful or unsuccessful loading of PML files into the system is output -to the console logs of the panacea service. +to the console logs of the Panacea service. ### Testing First, open up the tail of the Panacea logs (the system must be running to do @@ -111,11 +112,11 @@ Administrative users must have the ability to update the OWL file used as the source of DDI information. As described in the [README], our system builds a queryable database out of the -OWL file. This database is built into a docker image that is then deployed to +OWL file. This database is built into a Docker image that is then deployed to the production environment. To change the OWL file, users must be able to specify which file should be used in the `docker build` process. -Instructions on how to specify an OWL file and releasing the new docker image +Instructions on how to specify an OWL file and releasing the new Docker image can be found [here](./UPDATING_DINTO.md) ## Load Selected Ontology - Complete diff --git a/doc/FEATURES_RELEASE_2.md b/doc/FEATURES_RELEASE_2.md index 795efcaf..c9f8c90a 100644 --- a/doc/FEATURES_RELEASE_2.md +++ b/doc/FEATURES_RELEASE_2.md @@ -20,7 +20,8 @@ $ sudo docker-compose -f docker-compose.e2e.yml -p integration run athloi; sudo Our to end to end tests are written using the Cucumber behaviour-driven-development test framework which allows tests to be written according to user stories in plain English in the friendly "Given When Then" -format. These `feature` files can be found [here](../athloi/features). +format. These `feature` files can be +found [in the Athloi directory](../athloi/features). ## Manually Verifying Features @@ -36,11 +37,21 @@ interaction windows. ### Testing -Visit the [homepage]. Select `panacea/test/fixtures/ddis.pml` which contains a -DDI. Press `Submit`. The system should display the DDI information -for the DDI found, including whether its disposition is `Good` or `Bad`, -the timing window and units of this timing window, as well as the drugs involved. +Facilities to export this mock characterisation data as a CSV file indicating +whether an interaction is `Good`/`Bad` or an `Antagonism`/`Agonism` has been +provided by the +[Real DDI Mock Good-Bad Time Generator](#real-ddi-mock-good-bad-time-generator---complete) and +[Real DDI Mock Agonist-Antagonist Time Generator](#real-ddi-mock-agonist-antagonist-time-generator---complete) features. + +This mock DDI characterisation data is displayed in the user interface. Visit +the [homepage]. Select `panacea/test/fixtures/ddis.pml` which contains a DDI. +Press `Submit`. The system should display the DDI information for the DDI found, +including whether its disposition is `Not Harmful`(Good) or `Harmful`(Bad), the +timing window and units of this timing window, as well as the drugs involved. +Specifically, it should display that the mock classification for the +torasemide/trandolapril interaction is "Harmful" and that the mock interaction +window is "2 years". ## Real DDI Mock Good-Bad Time Generator - Complete @@ -61,10 +72,13 @@ Enter the root of the repository. Run the command $ ./export-mock-ddi-data.sh harmful harmful.csv ``` -The file `harmful.csv` will be constructed, which can be viewed in a text editor. -The output of this command is also readily available to view in the -[mock-enriched-ddis directory](../mock-enriched-ddis/harmful.csv) of our repository. +The file `harmful.csv` will be constructed, which can be viewed in a text +editor. The output of this command is also readily available to view in +the [mock-enriched-ddis directory](../mock-enriched-ddis/harmful.csv) of our +repository. +This is the same data that our production services use and will display to the +user. ## Real DDI Mock Agonist-Antagonist Time Generator - Complete @@ -87,16 +101,20 @@ Enter the root of the repository. Run the command $ ./export-mock-ddi-data.sh agonism agonism.csv ``` -The file `agonism.csv` will be constructed, which can be viewed in a text editor. -The output of this command is also readily available to view in the -[mock-enriched-ddis directory](../mock-enriched-ddis/agonism.csv) of our repository. +The file `agonism.csv` will be constructed, which can be viewed in a text +editor. The output of this command is also readily available to view in +the [mock-enriched-ddis directory](../mock-enriched-ddis/agonism.csv) of our +repository. + +This is the same data that our production services use and will display to the +user. ## Report Unnamed PML Construct - Complete ### Description The system must identify PML constructs that are not named. The system must -display useful error messages about such constructs to the user. +display useful warning messages about such constructs to the user. ### Testing @@ -112,7 +130,7 @@ Specifically, it should highlight an unnamed `task` on line `2`. ### Description The system must identify PML constructs that have the same name. The system -must display useful error messages about such constructs to the user. +must display useful warning messages about such constructs to the user. ### Testing @@ -235,14 +253,16 @@ A simple example of a pathway containing a delay is given below: ``` process Delays { task TakesTime { - requires { - time { - years { 20 } - days { 15 } - minutes { 6 } - hours { 10 } - seconds { 14 } - weeks { 12 } + action timetaker { + requires { + time { + years { 20 } + days { 15 } + minutes { 6 } + hours { 10 } + seconds { 14 } + weeks { 12 } + } } } } diff --git a/doc/UPDATING_DINTO.md b/doc/UPDATING_DINTO.md index 0010c88b..45d2d033 100644 --- a/doc/UPDATING_DINTO.md +++ b/doc/UPDATING_DINTO.md @@ -5,7 +5,7 @@ This file contains instructions on how to change the OWL file used in the system # Background As described in the [README], our system builds a queryable database out of the -OWL file. This database is built into a docker image (Chiron) that is then deployed to +OWL file. This database is built into a Docker image (Chiron) that is then deployed to the production environment. Within Chiron's [Dockerfile], the environment variable `OWL_FILE` specifies which file is used. @@ -23,14 +23,14 @@ the specified *URL*. # Rebuilding and Releasing new image Once the [Dockerfile] has been updated, the changes can be committed and merged -into the master branch after passing CI and code review. +into the `master` branch after passing CI and code review. -The docker images are automatically built on [Docker Hub] when a new git tag is -pushed to github. After the changes have made it into master, trigger a new +The Docker images are automatically built on [Docker Hub] when a new git tag is +pushed to Github. After the changes have made it into `master`, trigger a new build by tagging the release. The built images are tagged with the git tag. -In production, the [docker compose file] is used to pull and start the services. -Edit the [docker compose file] and update Chiron's version number to the new tag. +In production, the [Docker Compose file] is used to pull and start the services. +Edit the [Docker Compose file] and update Chiron's version number to the new tag. The new images can then be deployed to production. diff --git a/panacea/README.md b/panacea/README.md index 0ce12cf9..0cac034a 100644 --- a/panacea/README.md +++ b/panacea/README.md @@ -147,8 +147,10 @@ Tokens can be generated using: `Panacea.AccessToken.generate()` }, "label": "torasemide/trandolapril DDI", "uri": "http://purl.obolibrary.org/obo/DINTO_11031", - "harmful": false, - "spacing": 3, + "harmful": true, + "spacing": 2, + "unit": "yr", + "agonism": true, "category": "sequential", "enclosing_constructs": [ { @@ -161,6 +163,15 @@ Tokens can be generated using: `Panacea.AccessToken.generate()` } ``` +### `/api/ast` + +| | | +|-------------|------------------------------------------------------------------------- | +| Description | Convert an PML AST into a PML Document | +| Methods | `POST` | +| Parameters | An object containing the *pml ast* to be converted | +| Returns | The PML document as an attachment named `pml-tx.pml`, or an error object | + ### Error Objects All error responses take have the following format: @@ -175,12 +186,3 @@ All error responses take have the following format: } } ``` - -### `/api/ast` - -| | | -|-------------|------------------------------------------------------------------------- | -| Description | Convert an PML AST into a PML Document | -| Methods | `POST` | -| Parameters | An object containing the *pml ast* to be converted | -| Returns | The PML document as an attachment named `pml-tx.pml`, or an error object | From a6cf89df55eb21520053cc104d275a3038425331 Mon Sep 17 00:00:00 2001 From: Eoin Houlihan Date: Sun, 9 Apr 2017 19:41:26 +0100 Subject: [PATCH 16/16] Version bump for release 2 (#198) --- README.md | 2 +- doc/CHANGELOG.md | 4 ++-- docker-compose.e2e.yml | 8 ++++---- docker-compose.yml | 6 +++--- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 39338bab..6662d840 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ maximum convenience - click-able links for example* This file contains instructions on how to install and run the project, as well as an overview of the project's design. The target platform is Ubuntu 16.04. -At the time of writing the current release is `1.3` +At the time of writing the current release is `2.0` ## Installing Dependencies diff --git a/doc/CHANGELOG.md b/doc/CHANGELOG.md index 61dc8d65..fb02f36b 100644 --- a/doc/CHANGELOG.md +++ b/doc/CHANGELOG.md @@ -2,7 +2,7 @@ All notable changes to this project will be documented in this file. -## [Unreleased] +## [2.0] 2017-04-09 ### Added - Added tool to generate mock DDI data, for both badness and agonism @@ -163,7 +163,7 @@ All notable changes to this project will be documented in this file. docker service: pathways. - Installation instructions in README -[Unreleased]: https://github.com/tom-and-the-toothfairies/pathways/compare/1.3...release-2 +[2.0]: https://github.com/tom-and-the-toothfairies/pathways/compare/1.3...2.0 [1.3]: https://github.com/tom-and-the-toothfairies/pathways/compare/1.2...1.3 [1.2]: https://github.com/tom-and-the-toothfairies/pathways/compare/1.1...1.2 [1.1]: https://github.com/tom-and-the-toothfairies/pathways/compare/1.0...1.1 diff --git a/docker-compose.e2e.yml b/docker-compose.e2e.yml index 1a0d3272..13b08e33 100644 --- a/docker-compose.e2e.yml +++ b/docker-compose.e2e.yml @@ -2,17 +2,17 @@ version: '2' services: asclepius: - image: tomtoothfairies/asclepius:1.3 + image: tomtoothfairies/asclepius:2.0 depends_on: - chiron panacea: depends_on: - asclepius - image: tomtoothfairies/panacea:1.3 + image: tomtoothfairies/panacea:2.0 chiron: - image: tomtoothfairies/chiron:1.3 + image: tomtoothfairies/chiron:2.0 selenium: image: selenium/standalone-firefox:latest @@ -21,4 +21,4 @@ services: depends_on: - selenium - panacea - image: tomtoothfairies/athloi:1.3 + image: tomtoothfairies/athloi:2.0 diff --git a/docker-compose.yml b/docker-compose.yml index 72331b4b..179fbb22 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -4,14 +4,14 @@ services: asclepius: depends_on: - chiron - image: tomtoothfairies/asclepius:1.3 + image: tomtoothfairies/asclepius:2.0 panacea: depends_on: - asclepius - image: tomtoothfairies/panacea:1.3 + image: tomtoothfairies/panacea:2.0 ports: - '4000:4000' chiron: - image: tomtoothfairies/chiron:1.3 + image: tomtoothfairies/chiron:2.0