diff --git a/README.md b/README.md index 206f9caf..6662d840 100644 --- a/README.md +++ b/README.md @@ -9,12 +9,12 @@ 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 -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 8a8e9fc2..3462f9db 100644 --- a/asclepius/README.md +++ b/asclepius/README.md @@ -1,12 +1,22 @@ 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. -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` @@ -44,12 +54,12 @@ 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 @@ -59,27 +69,34 @@ 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" } ] ``` ### `/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 @@ -101,8 +118,10 @@ 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/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 69c26d42..2adf0d15 100644 --- a/asclepius/asclepius/enrich.py +++ b/asclepius/asclepius/enrich.py @@ -1,8 +1,82 @@ -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 hashlib import sha1 +import csv +import sys +import dinto +import clize +import socket +import time +from clize.parameters import one_of + +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 % 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 1', 'Drug 2', 'DDI Type', 'Time', 'Unit') + + writer = csv.DictWriter(sys.stdout, fieldnames=fieldnames, + lineterminator='\n') + writer.writeheader() + + for ddi in enrich(dinto.all_ddis()): + 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/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 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/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/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 42b927dd..fb02f36b 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. +## [2.0] 2017-04-09 + +### Added +- Added tool to generate mock DDI data, for both badness and agonism +- Added exported data from running the mock DDI data generation 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 @@ -153,7 +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/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 24ee3664..c9f8c90a 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 @@ -20,19 +20,101 @@ $ 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 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 + +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 + +### 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. + +This is the same data that our production services use and will display to the +user. + +## 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. + +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 @@ -48,7 +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 @@ -171,14 +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/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 diff --git a/export-mock-ddi-data.sh b/export-mock-ddi-data.sh new file mode 100755 index 00000000..e0283cad --- /dev/null +++ b/export-mock-ddi-data.sh @@ -0,0 +1,39 @@ +#!/bin/bash +usage() { +cat < + +Resultant CSV file is of the format: + Drug 1, Drug 2, DDI Type, Time, Unit + +Usage: + $0 +EOF +} + +main() { + if [ $# -ne 2 ]; then + usage + exit 1 + fi + + local readonly flavour="$1" + local readonly outfile="$2" + + case "$flavour" in + harmful|agonism) + sudo docker-compose -p export run asclepius python3 asclepius/enrich.py "$flavour" > "$outfile" + sudo docker-compose -p export down + exit 0 + ;; + + *) + usage + exit 1 + ;; + esac +} + +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 +norfloxacin,warfarin,antagonism,3,hr +norfloxacin,zinc,agonism,32,min +norfloxacin,ziprasidone,agonism,5,yr +norfloxacin,zuclopenthixol,antagonism,21,hr +warfarin,paracetamol,agonism,25,week +warfarin,acetylsalicylic acid,agonism,44,min +warfarin,allopurinol,agonism,29,week +warfarin,aminoglutethimide,agonism,31,sec +warfarin,4-aminosalicylic acid,antagonism,32,min +warfarin,amiodarone,antagonism,31,sec +warfarin,amobarbital,antagonism,21,hr +warfarin,amprenavir,antagonism,1,sec +warfarin,aprepitant,antagonism,1,yr +warfarin,atazanavir,antagonism,5,day +warfarin,avanafil,agonism,3,yr +warfarin,azathioprine,agonism,5,yr +warfarin,azithromycin,antagonism,26,min +warfarin,betamethasone,agonism,4,day +warfarin,bezafibrate,antagonism,9,hr +warfarin,bosentan,agonism,4,day +warfarin,butabarbital,antagonism,41,week +warfarin,butalbital,agonism,1,day +warfarin,capecitabine,agonism,1,day +warfarin,carbamazepine,antagonism,6,day +warfarin,cefotetan,antagonism,49,sec +warfarin,cefoxitin,agonism,25,sec +warfarin,ceftriaxone,agonism,4,yr +warfarin,celecoxib,antagonism,4,day +warfarin,cholestyramine,agonism,56,min +warfarin,cimetidine,antagonism,38,min +warfarin,cisapride,antagonism,31,sec +warfarin,citalopram,agonism,25,sec +warfarin,clarithromycin,antagonism,5,day +warfarin,clofibrate,antagonism,4,yr +warfarin,clopidogrel,antagonism,20,min +warfarin,colestipol hydrochloride,antagonism,26,min +warfarin,cyclophosphamide,antagonism,6,day +warfarin,danazol,agonism,6,day +warfarin,delavirdine,agonism,23,week +warfarin,demeclocycline,antagonism,47,week +warfarin,desogestrel,antagonism,2,day +warfarin,dexamethasone,agonism,17,week +warfarin,dextrothyroxine,agonism,4,yr +warfarin,diclofenac,antagonism,37,sec +warfarin,dicloxacillin,agonism,38,min +warfarin,diflunisal,antagonism,3,hr +warfarin,disulfiram,agonism,26,min +warfarin,doxycycline,antagonism,39,week +warfarin,dronedarone,antagonism,1,yr +warfarin,drospirenone,antagonism,5,yr +warfarin,drotrecogin alfa,antagonism,21,hr +warfarin,erythromycin,agonism,2,min +warfarin,ethchlorvynol,agonism,25,sec +warfarin,ethinyl estradiol,agonism,21,hr +warfarin,ethynodiol diacetate,antagonism,1,yr +warfarin,etodolac,antagonism,14,min +warfarin,etonogestrel,antagonism,1,day +warfarin,etoricoxib,antagonism,21,hr +warfarin,ezetimibe,antagonism,3,hr +warfarin,fenofibrate,antagonism,6,day +warfarin,fenoprofen,antagonism,3,hr +warfarin,5-fluoro-2'-deoxyuridine,antagonism,23,week +warfarin,fluconazole,antagonism,26,min +warfarin,fludrocortisone,antagonism,4,yr +warfarin,5-fluorouracil,agonism,15,hr +warfarin,fluoxetine,antagonism,21,hr +warfarin,fluoxymesterone,agonism,6,day +warfarin,flurbiprofen,agonism,3,day +warfarin,"(3S,5R)-fluvastatin",agonism,8,min +warfarin,fluvoxamine,agonism,6,day +warfarin,fosamprenavir,antagonism,2,day +warfarin,fosphenytoin,agonism,50,min +warfarin,gadofosveset trisodium,agonism,3,day +warfarin,gefitinib,antagonism,3,day +warfarin,gemcitabine,agonism,15,hr +warfarin,gemfibrozil,antagonism,3,day +warfarin,ginkgo biloba,agonism,50,min +warfarin,ginseng,antagonism,21,hr +warfarin,glutethimide,agonism,25,week +warfarin,griseofulvin,agonism,20,min +warfarin,homoharringtonine,antagonism,14,min +warfarin,cortisol,agonism,20,min +warfarin,ibuprofen,antagonism,5,day +warfarin,imatinib,agonism,25,sec +warfarin,indinavir,antagonism,1,sec +warfarin,indometacin,antagonism,15,hr +warfarin,isoniazid,antagonism,32,min +warfarin,itraconazole,antagonism,3,yr +warfarin,ketoconazole,antagonism,3,hr +warfarin,ketoprofen,agonism,3,week +warfarin,ketorolac,antagonism,37,sec +warfarin,leflunomide,antagonism,3,hr +warfarin,levamisole,agonism,1,day +warfarin,levofloxacin,antagonism,21,hr +warfarin,levonorgestrel,agonism,21,hr +warfarin,L-thyroxine,antagonism,2,yr +warfarin,liothyronine,antagonism,2,yr +warfarin,liotrix,agonism,14,min +warfarin,lomitapide,antagonism,37,week +warfarin,lovastatin,agonism,14,min +warfarin,lumiracoxib,agonism,2,yr +warfarin,meclofenamic acid,agonism,3,yr +warfarin,medroxyprogesterone,agonism,38,min +warfarin,mefenamic acid,antagonism,15,hr +warfarin,mefloquine,antagonism,14,min +warfarin,meloxicam,antagonism,38,min +warfarin,mercaptopurine,antagonism,3,day +warfarin,mestranol,agonism,5,yr +warfarin,methimazole,agonism,13,sec +warfarin,methohexital,agonism,55,sec +warfarin,metronidazole,agonism,55,sec +warfarin,miconazole,antagonism,13,week +warfarin,minocycline,agonism,7,day +warfarin,mirabegron,agonism,49,week +warfarin,mitotane,antagonism,4,day +warfarin,moxifloxacin,antagonism,32,min +warfarin,nabumetone,antagonism,3,day +warfarin,nafcillin,agonism,25,sec +warfarin,nandrolone decanoate,agonism,2,yr +warfarin,nandrolone phenpropionate,agonism,26,min +warfarin,naproxen,agonism,9,hr +warfarin,nelfinavir,agonism,25,sec +warfarin,nevirapine,agonism,7,day +warfarin,nicardipine,agonism,49,week +warfarin,norethisterone,agonism,55,sec +warfarin,norgestimate,agonism,7,sec +warfarin,ofloxacin,agonism,50,min +warfarin,orlistat,agonism,4,day +warfarin,oxandrolone,antagonism,38,min +warfarin,oxaprozin,agonism,3,hr +warfarin,oxyphenbutazone,antagonism,27,week +warfarin,paroxetine,antagonism,7,day +warfarin,pentobarbital,antagonism,26,min +warfarin,pentoxifylline,antagonism,7,sec +warfarin,phenobarbital,antagonism,19,week +warfarin,phenylbutazone,agonism,1,day +warfarin,phenytoin,agonism,15,hr +warfarin,phytonadione,antagonism,5,yr +warfarin,piroxicam,antagonism,45,week +warfarin,prasugrel,antagonism,49,week +warfarin,prednisolone,agonism,3,yr +warfarin,prednisone,agonism,50,min +warfarin,primidone,antagonism,13,sec +warfarin,propafenone hydrochloride,antagonism,4,day +warfarin,propoxyphene,agonism,3,day +warfarin,6-propyl-2-thiouracil,agonism,4,yr +warfarin,quinidine,agonism,11,week +warfarin,quinine,agonism,9,week +warfarin,ranitidine,antagonism,3,day +warfarin,rifabutin,agonism,1,day +warfarin,rifampicin,agonism,3,day +warfarin,S-adenosyl-L-methionine,agonism,2,day +warfarin,salicylate-sodium,agonism,6,day +warfarin,secobarbital,antagonism,38,min +warfarin,sitaxentan,agonism,19,week +warfarin,st. john's wort,agonism,19,sec +warfarin,sucralfate,agonism,13,sec +warfarin,sulfadiazine,antagonism,3,yr +warfarin,sulfamethoxazole,agonism,21,week +warfarin,sulfinpyrazone,agonism,2,day +warfarin,sulfisoxazole,agonism,2,day +warfarin,sulindac,antagonism,23,week +warfarin,tamoxifen,antagonism,26,min +warfarin,telithromycin,antagonism,9,hr +warfarin,tenoxicam,agonism,49,sec +warfarin,testolactone,antagonism,5,yr +warfarin,testosterone,agonism,1,yr +warfarin,testosterone propionate,antagonism,3,day +warfarin,tetracycline,agonism,8,min +warfarin,thiopental,agonism,3,day +warfarin,tiaprofenic acid,antagonism,1,sec +warfarin,ticlopidine,agonism,51,week +warfarin,tigecycline,antagonism,9,hr +warfarin,tolbutamide,agonism,32,min +warfarin,tolmetin sodium dihydrate,agonism,32,min +warfarin,treprostinil,agonism,3,day +warfarin,triamcinolone acetonide,agonism,23,week +warfarin,triflusal,antagonism,9,hr +warfarin,trimetrexate,antagonism,1,day +warfarin,trisalicylate-choline,agonism,9,hr +warfarin,vemurafenib,antagonism,49,week +warfarin,vilazodone,antagonism,47,week +yohimbine,asenapine,agonism,43,sec +yohimbine,atomoxetine,antagonism,13,sec +zafirlukast,acenocoumarol,antagonism,39,week +zafirlukast,aminophylline,agonism,15,hr +zafirlukast,capecitabine,agonism,23,week +zafirlukast,cisapride,antagonism,55,sec +zafirlukast,delavirdine,antagonism,1,yr +zafirlukast,erythromycin,antagonism,37,sec +zafirlukast,5-fluoro-2'-deoxyuridine,antagonism,44,min +zafirlukast,fluconazole,agonism,21,hr 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+ziprasidone,flecainide,antagonism,25,week +ziprasidone,fluconazole,antagonism,32,min +ziprasidone,fluoxetine,antagonism,3,hr +ziprasidone,flupenthixol,antagonism,15,hr +ziprasidone,phosphonoformic acid,agonism,26,min +ziprasidone,galanthamine,antagonism,1,day +ziprasidone,gatifloxacin,antagonism,2,min +ziprasidone,halofantrine,agonism,5,day +ziprasidone,haloperidol,antagonism,3,day +ziprasidone,ibutilide,antagonism,3,hr +ziprasidone,iloperidone,agonism,21,hr +ziprasidone,imipramine,agonism,15,hr +ziprasidone,indapamide,antagonism,4,yr +ziprasidone,isradipine,antagonism,9,hr +ziprasidone,ketoconazole,antagonism,26,min +ziprasidone,lapatinib,antagonism,38,min +ziprasidone,L-dopa,agonism,43,week +ziprasidone,levofloxacin,antagonism,3,hr +ziprasidone,loxapine,agonism,38,min +ziprasidone,lumefantrine,agonism,15,hr +ziprasidone,maprotiline,agonism,1,yr +ziprasidone,mefloquine,antagonism,13,sec +ziprasidone,mesoridazine,antagonism,56,min +ziprasidone,methadone,antagonism,3,hr 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+rifapentine,abiraterone,agonism,3,yr +saquinavir,abiraterone,antagonism,13,sec diff --git a/mock-enriched-ddis/harmful.csv b/mock-enriched-ddis/harmful.csv new file mode 100644 index 00000000..4ca34256 --- /dev/null +++ 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 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A,danazol,bad,3,day +cyclosporin A,diclofenac,good,21,hr +cyclosporin A,digoxin,good,49,sec +cyclosporin A,dihydroquinidine barbiturate,good,37,sec +cyclosporin A,dronedarone,bad,5,day +cyclosporin A,erythromycin,bad,6,day +cyclosporin A,ethinyl estradiol,bad,3,yr +cyclosporin A,ethotoin,good,25,sec +cyclosporin A,etodolac,good,3,hr +cyclosporin A,etoposide,good,15,hr +cyclosporin A,ezetimibe,good,9,hr +cyclosporin A,fenoprofen,good,11,week +cyclosporin A,fidaxomicin,bad,50,min +cyclosporin A,fluconazole,bad,38,min +cyclosporin A,fluoxetine,bad,32,min +cyclosporin A,flurbiprofen,bad,1,yr +cyclosporin A,"(3S,5R)-fluvastatin",good,15,hr +cyclosporin A,fosamprenavir,good,51,week +cyclosporin A,fosphenytoin,bad,4,day +cyclosporin A,glimepiride,bad,2,day +cyclosporin A,glipizide,bad,56,min +cyclosporin A,glyburide,bad,5,day +cyclosporin A,griseofulvin,bad,1,day +cyclosporin A,heptabarbital,bad,50,min +cyclosporin A,hexobarbital,good,49,week +cyclosporin A,ibuprofen,bad,7,day +cyclosporin A,imatinib,bad,5,yr +cyclosporin A,imipenem,good,37,week +cyclosporin A,indinavir,bad,44,min +cyclosporin A,indometacin,bad,26,min +cyclosporin A,itraconazole,good,19,week +josamycin,cyclosporin A,bad,32,min +cyclosporin A,ketoconazole,good,13,sec +cyclosporin A,ketoprofen,bad,2,day +cyclosporin A,meclofenamic acid,bad,4,yr +cyclosporin A,mefenamic acid,good,49,sec +cyclosporin A,mephenytoin,bad,2,min +cyclosporin A,mestranol,good,55,sec +cyclosporin A,methotrexate,bad,2,day +cyclosporin A,methylphenidate,good,37,sec +cyclosporin A,mephobarbital,bad,2,yr +cyclosporin A,modafinil,bad,1,day +cyclosporin A,muromonab,good,19,sec +cyclosporin A,nabumetone,good,21,hr +cyclosporin A,nafcillin,bad,4,yr +cyclosporin A,naproxen,good,15,hr +cyclosporin A,nefazodone,bad,3,yr +cyclosporin A,nelfinavir,bad,7,day +cyclosporin A,nicardipine,bad,1,yr +cyclosporin A,nifedipine,bad,4,yr +cyclosporin A,octreotide,bad,4,yr +cyclosporin A,omeprazole,bad,4,day +cyclosporin A,orlistat,bad,1,yr +cyclosporin A,oxaprozin,good,19,sec +cyclosporin A,oxcarbazepine,bad,56,min +cyclosporin A,pentobarbital,good,15,hr +cyclosporin A,phenobarbital,bad,32,min +cyclosporin A,phenytoin,bad,5,yr +cyclosporin A,piroxicam,bad,6,day +pitavastatin,cyclosporin A,bad,1,day +cyclosporin A,posaconazole,bad,2,yr +cyclosporin A,pravastatin sodium,good,21,hr +cyclosporin A,primidone,bad,7,day +cyclosporin A,probucol,good,21,hr +cyclosporin A,propafenone hydrochloride,bad,8,min +cyclosporin A,pyrazinecarboxamide,good,17,week +cyclosporin A,quinidine barbiturate,good,21,week +cyclosporin A,quinupristin,good,31,sec +cyclosporin A,repaglinide,bad,7,day +cyclosporin A,rifabutin,good,39,week +cyclosporin A,rilonacept,good,3,hr +cyclosporin A,ritonavir,good,15,hr +cyclosporin A,roxithromycin,good,9,week +cyclosporin A,saquinavir,bad,7,day +cyclosporin A,secobarbital,good,9,hr +cyclosporin A,sevelamer,good,23,week +cyclosporin A,sibutramine,good,9,hr +cyclosporin A,simvastatin,good,47,week +cyclosporin A,sirolimus,bad,5,yr +cyclosporin A,st. john's wort,bad,1,day +cyclosporin A,sulfadiazine,good,19,week +cyclosporin A,sulfamethoxazole,good,9,hr +cyclosporin A,sulfasalazine,good,19,sec +cyclosporin 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 +dapsone,magnesium,bad,6,day +dapsone,rifabutin,good,25,sec +dapsone,telithromycin,good,15,hr +dapsone,trimethoprim,good,33,week +dapsone,voriconazole,good,35,week +lisinopril,azilsartan medoxomil,good,55,sec +lisinopril,drospirenone,good,3,week +lisinopril,lithium,bad,32,min +lisinopril,potassium,bad,8,min +lisinopril,spironolactone,bad,4,day +lisinopril,tizanidine,good,1,sec +lisinopril,tobramycin,good,9,hr +lisinopril,treprostinil,good,7,sec +lisinopril,triamterene,bad,20,min +demeclocycline,acenocoumarol,good,49,sec +demeclocycline,all-trans-acitretin,good,9,hr +demeclocycline,aluminium,bad,50,min +demeclocycline,attapulgite,good,43,sec +demeclocycline,bexarotene,good,43,sec +demeclocycline,calcium,good,27,week +demeclocycline,calcium acetate,bad,1,day +demeclocycline,calcium chloride,good,55,sec +demeclocycline,clavulanic acid,bad,26,min +demeclocycline,cloxacillin,bad,1,yr +demeclocycline,colesevelam,good,21,hr +demeclocycline,dicloxacillin,bad,38,min +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 +dicloxacillin,doxycycline,good,5,week +dicloxacillin,ethinyl estradiol,bad,38,min +dicloxacillin,mestranol,bad,3,yr +dicloxacillin,methacycline,good,3,hr +methotrexate,dicloxacillin,bad,5,day +dicloxacillin,minocycline,good,3,hr +dicloxacillin,rolitetracycline,bad,44,min +dicoumarol,paracetamol,bad,3,day +dicoumarol,acetohexamide,good,25,week +dicoumarol,amiodarone,bad,1,yr +amprenavir,dicoumarol,bad,14,min +dicoumarol,aprepitant,bad,32,min +dicoumarol,bosentan,bad,50,min +celecoxib,dicoumarol,bad,2,yr +dicoumarol,cholestyramine,bad,6,day +dicoumarol,colestipol hydrochloride,good,3,hr +dicoumarol,dextrothyroxine,good,15,week +dicoumarol,diclofenac,good,9,hr +dicoumarol,disulfiram,good,21,hr +dicoumarol,doxycycline,good,43,week +dicoumarol,erythromycin,bad,4,yr +dicoumarol,ethchlorvynol,good,3,hr +dicoumarol,ethinyl estradiol,good,19,sec +dicoumarol,etodolac,good,47,week +dicoumarol,etoricoxib,good,7,sec +dicoumarol,fenofibrate,good,13,week +dicoumarol,fenoprofen,good,55,sec +dicoumarol,fluconazole,bad,3,yr +dicoumarol,fludrocortisone,good,7,sec +dicoumarol,5-fluorouracil,good,37,sec +dicoumarol,fluoxetine,bad,50,min +dicoumarol,fluoxymesterone,good,25,week +dicoumarol,flurbiprofen,good,15,hr +dicoumarol,"(3S,5R)-fluvastatin",bad,1,yr +dicoumarol,fluvoxamine,good,7,sec +dicoumarol,fosamprenavir,good,45,week +dicoumarol,fosphenytoin,good,21,hr +dicoumarol,gefitinib,bad,50,min +dicoumarol,gemfibrozil,good,43,sec +dicoumarol,glutethimide,good,9,hr +dicoumarol,glyburide,good,25,sec +dicoumarol,griseofulvin,good,5,week +dicoumarol,ibuprofen,bad,5,day +dicoumarol,imatinib,bad,1,yr +dicoumarol,indinavir,good,1,sec +dicoumarol,indometacin,bad,50,min +dicoumarol,isoniazid,good,45,week +dicoumarol,itraconazole,good,9,hr +dicoumarol,ketoconazole,bad,44,min +dicoumarol,ketoprofen,bad,2,min +dicoumarol,ketorolac,good,31,week +dicoumarol,leflunomide,bad,14,min +dicoumarol,levamisole,good,37,sec +dicoumarol,levofloxacin,bad,44,min +dicoumarol,lumiracoxib,bad,3,day +dicoumarol,medroxyprogesterone,bad,8,min +dicoumarol,mefenamic acid,bad,1,yr +dicoumarol,mefloquine,good,45,week +dicoumarol,meloxicam,good,49,sec +dicoumarol,mercaptopurine,bad,6,day +dicoumarol,methimazole,good,21,hr +dicoumarol,metronidazole,good,21,hr +dicoumarol,miconazole,bad,32,min +dicoumarol,minocycline,bad,2,yr +dicoumarol,mitotane,good,55,sec +dicoumarol,moxifloxacin,bad,6,day +dicoumarol,nabumetone,good,37,week +dicoumarol,naproxen,bad,7,day +dicoumarol,nelfinavir,good,35,week +dicoumarol,nevirapine,good,21,hr +dicoumarol,ofloxacin,bad,4,yr +dicoumarol,orlistat,good,19,sec +dicoumarol,oxaprozin,good,49,sec +dicoumarol,oxyphenbutazone,good,41,week +dicoumarol,paroxetine,bad,50,min +dicoumarol,pentoxifylline,good,51,week +dicoumarol,phenobarbital,bad,2,day +dicoumarol,phenylbutazone,bad,2,min +dicoumarol,phenytoin,good,3,hr +dicoumarol,piroxicam,good,25,week +dicoumarol,prednisolone,bad,32,min +dicoumarol,prednisone,good,5,week +dicoumarol,primidone,bad,56,min +dicoumarol,propafenone hydrochloride,good,21,hr +dicoumarol,propoxyphene,good,49,sec +dicoumarol,6-propyl-2-thiouracil,good,31,sec +dicoumarol,ranitidine,good,7,week +dicoumarol,rifabutin,bad,2,yr +dicoumarol,telithromycin,good,19,sec +dicoumarol,tenoxicam,good,43,sec +dicoumarol,testosterone,good,3,hr +dicoumarol,triamcinolone acetonide,good,45,week +dicyclomine,donepezil,bad,6,day +galanthamine,dicyclomine,bad,2,yr +dicyclomine,haloperidol,good,21,week +dicyclomine,rivastigmine,good,3,hr +dicyclomine,tacrine,good,15,hr +trimethobenzamide,dicyclomine,good,11,week +dicyclomine,triprolidine,bad,5,day +dicyclomine,trospium,bad,7,day +diethylpropion,fluoxetine,good,15,hr +diethylpropion,fluphenazine,good,43,week +diethylpropion,fluvoxamine,bad,5,yr +diethylpropion,guanethidine,good,9,hr +diethylpropion,isocarboxazid,bad,1,yr +diethylpropion,mesoridazine,bad,38,min +diethylpropion,methdilazine,good,15,hr +diethylpropion,methotrimeprazine,good,37,sec +diethylpropion,paroxetine,good,25,week +diethylpropion,perphenazine,good,31,week +diethylpropion,phenelzine,bad,4,yr +diethylpropion,prochlorperazine,good,3,hr +diethylpropion,promazine,bad,4,yr +diethylpropion,promethazine,good,49,sec +diethylpropion,propiomazine,good,21,week +diethylpropion,rasagiline,good,3,hr +diethylpropion,thiethylperazine,good,43,sec +diethylpropion,thioridazine,bad,44,min +diethylpropion,tranylcypromine,good,15,hr +diethylpropion,trifluoperazine,bad,1,yr +diethylpropion,triflupromazine,bad,4,day +diethylpropion,trimeprazine,good,21,hr +diethylpropion,venlafaxine,good,31,week +difenoxin,alvimopan,bad,4,yr +digoxin,amiodarone,good,25,week +digoxin,bleomycin,good,31,sec +bosutinib,digoxin,bad,3,yr +digoxin,canagliflozin,bad,56,min +digoxin,chlorthalidone,bad,3,day +digoxin,cholestyramine,bad,2,day +digoxin,cinitapride,good,31,sec +digoxin,colestipol hydrochloride,bad,5,yr +digoxin,dextrothyroxine,bad,26,min +digoxin,diazepam,bad,4,day +digoxin,dihydroquinidine barbiturate,good,1,sec +digoxin,doxorubicin,good,3,hr +digoxin,dronedarone,good,9,hr +digoxin,erythromycin,bad,1,yr +digoxin,ethacrynic acid,good,21,hr +digoxin,furosemide,bad,14,min +digoxin,gatifloxacin,bad,5,day +digoxin,ginseng,bad,56,min +digoxin,hydrochlorothiazide,good,9,hr +digoxin,hydroflumethiazide,good,15,hr +digoxin,hydroxychloroquine,good,43,sec +digoxin,indapamide,bad,1,yr +digoxin,itraconazole,bad,5,day +josamycin,digoxin,good,21,week +digoxin,liothyronine,good,51,week +digoxin,liotrix,bad,6,day +digoxin,liraglutide,bad,7,day +digoxin,methimazole,good,9,hr +methotrexate,digoxin,bad,3,day +digoxin,methyclothiazide,good,39,week +digoxin,metolazone,bad,3,yr +digoxin,milnacipran,bad,3,yr +digoxin,mirabegron,good,21,week +digoxin,penbutolol,good,13,sec +digoxin,penciclovir,good,5,week +digoxin,penicillamine,good,3,hr +digoxin,polythiazide,bad,44,min +digoxin,prazosin,good,7,sec +digoxin,procarbazine,good,47,week +digoxin,propafenone hydrochloride,good,3,hr +digoxin,6-propyl-2-thiouracil,good,21,hr +digoxin,quinethazone,bad,3,yr +digoxin,quinidine barbiturate,good,21,hr +digoxin,rabeprazole,bad,1,day +digoxin,ranolazine,good,19,sec +digoxin,ritonavir,good,15,hr +digoxin,spironolactone,good,49,week +digoxin,st. john's wort,good,19,sec +digoxin,sulfasalazine,good,9,hr +digoxin,telaprevir,good,9,hr +digoxin,telithromycin,good,19,sec +digoxin,telmisartan,good,33,week +digoxin,thyroglobulin,bad,7,day +digoxin,ticlopidine,bad,2,day +digoxin,tolvaptan,bad,3,yr +digoxin,trichlormethiazide,bad,2,min +digoxin,trimetrexate,bad,6,day +digoxin,verapamil,good,49,sec +digoxin,vincristine,bad,2,day +digoxin,voriconazole,bad,2,min +dihydroergotamine,almotriptan,good,7,sec +amprenavir,dihydroergotamine,bad,5,yr +dihydroergotamine,n-pentyl nitrite,bad,14,min +dihydroergotamine,boceprevir,bad,32,min +dihydroergotamine,desvenlafaxine,good,7,week 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anhydrous,testosterone propionate,good,3,hr +docetaxel anhydrous,trastuzumab,bad,2,min +docetaxel anhydrous,valrubicin,bad,6,day +docetaxel anhydrous,voriconazole,good,43,sec +dofetilide,chlorthalidone,good,9,hr +dofetilide,erythromycin,bad,4,yr +dofetilide,fingolimod,good,17,week +dofetilide,hydrochlorothiazide,bad,4,yr +dofetilide,indapamide,bad,3,day +dofetilide,itraconazole,good,35,week +dofetilide,ketoconazole,bad,5,day +dofetilide,mesoridazine,good,15,hr +dofetilide,metolazone,bad,50,min +dofetilide,quinupristin,good,31,sec +dofetilide,ranolazine,bad,2,yr +dofetilide,tacrolimus (anhydrous),good,39,week +dofetilide,telithromycin,bad,20,min +dofetilide,thioridazine,bad,3,yr +dofetilide,thiothixene,good,35,week +dofetilide,toremifene,good,9,week +dofetilide,trichlormethiazide,bad,3,day +dofetilide,trimethoprim,bad,5,yr +dofetilide,trimipramine,bad,6,day +dofetilide,verapamil,bad,26,min +dofetilide,voriconazole,good,31,sec +vorinostat,dofetilide,good,15,hr 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+methacycline,magnesium,good,21,hr +moxifloxacin,magnesium,good,23,week +somatropin recombinant,insulin glulisine,bad,4,day +somatropin recombinant,insulin aspart,good,1,sec +somatropin recombinant,insulin detemir,bad,4,yr +butabarbital,oxtriphylline,bad,8,min +erythromycin,oxtriphylline,good,1,sec +oxtriphylline,fosphenytoin,bad,7,day +"interferon alfa-2a, recombinant",oxtriphylline,good,9,hr +"interferon alfa-2b, recombinant",oxtriphylline,good,9,hr +interferon alfa-n1,oxtriphylline,bad,2,yr +josamycin,oxtriphylline,bad,14,min +oxtriphylline,metocurine,good,43,week +peginterferon alfa-2a,oxtriphylline,good,31,sec +peginterferon alfa-2b,oxtriphylline,bad,14,min +propafenone hydrochloride,oxtriphylline,bad,6,day +sotalol,oxtriphylline,bad,2,day +oxtriphylline,st. john's wort,good,13,week +abacavir,fosamprenavir,good,1,sec +atorvastatin,fosamprenavir,bad,6,day +fosamprenavir,bromazepam,good,31,sec +ergotamine,fosamprenavir,bad,2,yr +lurasidone,fosamprenavir,bad,3,yr +ranolazine,fosamprenavir,bad,20,min +rifabutin,fosamprenavir,bad,4,yr +fosamprenavir,st. john's wort,good,5,week +tadalafil,fosamprenavir,good,49,sec +tamoxifen,fosamprenavir,good,9,hr +teniposide,fosamprenavir,bad,3,day +tipranavir,fosamprenavir,good,9,week +tramadol hydrochloride,fosamprenavir,good,25,week +vardenafil,fosamprenavir,bad,4,yr +bleomycin,fosphenytoin,good,21,hr +boceprevir,fosphenytoin,good,49,sec +conjugated estrogens,fosphenytoin,good,29,week +fosphenytoin,cortisone acetate,good,37,week +diethylstilbestrol,fosphenytoin,good,39,week +fosphenytoin,estradiol valerate/dienogest,bad,32,min +fosphenytoin,estriol,good,47,week +fosphenytoin,estropipate,bad,5,day +fluconazole,fosphenytoin,good,21,hr +folic acid,fosphenytoin,bad,4,day +gabapentin,fosphenytoin,good,3,hr +fosphenytoin,lopinavir,bad,38,min +lurasidone,fosphenytoin,good,9,hr +methotrexate,fosphenytoin,good,7,sec +fosphenytoin,metocurine,bad,6,day +fosphenytoin,paramethasone,good,33,week +posaconazole,fosphenytoin,bad,14,min +fosphenytoin,quinestrol,bad,3,day +roflumilast,fosphenytoin,bad,3,yr +fosphenytoin,thiotepa,good,3,hr +topiramate,fosphenytoin,bad,2,min +tramadol hydrochloride,fosphenytoin,bad,5,yr +triamcinolone acetonide,fosphenytoin,bad,2,min +trioxsalen,fosphenytoin,bad,2,day +vigabatrin,fosphenytoin,bad,1,yr +lormetazepam,kava,bad,14,min +temazepam,kava,bad,6,day +amprenavir,st. john's wort,bad,1,day +boceprevir,st. john's wort,good,3,week +cabozantinib,st. john's wort,bad,4,yr +st. john's wort,estradiol valerate/dienogest,bad,5,yr +indinavir,st. john's wort,good,37,sec +ivacaftor,st. john's wort,bad,5,yr +nelfinavir,st. john's wort,bad,4,day +paclitaxel,st. john's wort,bad,5,day +perampanel,st. john's wort,bad,3,yr +rasagiline,st. john's wort,good,43,week +regorafenib,st. john's wort,bad,5,day +roflumilast,st. john's wort,good,31,sec +tipranavir,st. john's wort,bad,44,min +tramadol hydrochloride,st. john's wort,bad,4,day +pipecuronium,lincomycin,bad,3,day +metocurine,lincomycin,bad,8,min +abciximab,ginkgo biloba,good,11,week +alteplase,ginkgo biloba,bad,26,min +argatroban,ginkgo biloba,bad,5,yr +bivalirudin,ginkgo biloba,good,9,hr +diclofenac,ginkgo biloba,bad,3,day +eptifibatide,ginkgo biloba,good,37,sec +indometacin,ginkgo biloba,bad,6,day +lepirudin,ginkgo biloba,good,9,week +oxaprozin,ginkgo biloba,good,49,sec +reteplase,ginkgo biloba,bad,5,yr +tenecteplase,ginkgo biloba,good,21,hr +tolmetin sodium dihydrate,ginkgo biloba,bad,3,day +urokinase,ginkgo biloba,good,43,week +trastuzumab,cortisone acetate,bad,6,day +glycodiazine,oxprenolol,good,9,hr +methotrexate,salsalate,bad,38,min +probenecid,salsalate,good,47,week +tolmetin sodium dihydrate,salsalate,good,37,sec +triamcinolone acetonide,salsalate,good,49,sec +methotrexate,magnesium salicylate,good,15,hr +probenecid,magnesium salicylate,good,19,sec +triamcinolone acetonide,magnesium salicylate,good,49,sec +methotrexate,salicylate-sodium,bad,5,day +probenecid,salicylate-sodium,bad,38,min +triamcinolone acetonide,salicylate-sodium,bad,56,min +methotrexate,methicillin acyl-serine,bad,7,day +indapamide,digitoxin,bad,4,day +metolazone,digitoxin,good,35,week +atorvastatin,colchicine,good,7,sec +erythromycin,colchicine,good,3,hr +pitavastatin,colchicine,bad,50,min +Delta(9)-tetrahydrocannabinol,trospium,good,9,hr +galanthamine,trospium,good,37,sec +imipramine,trospium,bad,7,day +trospium,molindone,bad,26,min +trospium,phenindamine,bad,8,min +rivastigmine,trospium,good,39,week +secretin,trospium,bad,2,yr +trospium,solifenacin,bad,20,min +trospium,thiothixene,good,37,sec +trimethobenzamide,trospium,good,25,sec +abacavir,indinavir,good,1,sec +abiraterone,indinavir,bad,7,day +atorvastatin,indinavir,good,15,hr +indinavir,bromazepam,good,31,sec +ergotamine,indinavir,good,21,hr +lurasidone,indinavir,bad,4,yr +indinavir,ponatinib,good,3,hr +indinavir,prazepam,good,1,sec +indinavir,quazepam,bad,32,min +indinavir,ranolazine,bad,2,day 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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 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 | 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/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" } } } 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} ], } ] 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);