Merge pull request #193 from tom-and-the-toothfairies/release-2

Release 2

README.md

@@ -9,38 +9,38 @@ 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
 ```
 
 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
 ```
 
 ## Running
 
-The project can be run with `docker compose`
+The project can be run with Docker Compose:
 
 ```bash
 $ 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
@@ -60,50 +60,49 @@ 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
 
 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
 
 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).
 
 
 

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 <harmful|agonism> > 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
   }
 ]
 ```

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 .
     }}
     '''
 

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)

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

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"

athloi/features/fixtures/alternative_non_ddi.pml

@@ -1,5 +1,5 @@
 process alternative_non_ddis {
-  selection {
+  selection sel1 {
     action s1 {
       requires { drug { "trandolapril" } }
     }

athloi/features/fixtures/analysis/clashes.pml

@@ -1,5 +1,6 @@
 process foo {
   action clash1 {
+    requires { drug { "paracetamol" } }
   }
   action clash2 {
   }

athloi/features/fixtures/analysis/unnamed.pml

@@ -1,4 +1,7 @@
 process foo {
   task {
+    action boo {
+      requires { drug { "paracetamol" } }
+    }
   }
 }

athloi/features/fixtures/parallel.pml

@@ -1,5 +1,5 @@
 process parallel_ddis {
-  branch {
+  branch br1 {
     action b1 {
       requires { drug { "trandolapril" } }
     }

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" } }
       }

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.

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