Merge pull request #133 from tom-and-the-toothfairies/iteration1-2

Iteration 1 - Again

README.md

@@ -9,7 +9,7 @@ maximum conveniece - the ability to click 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 `1.0`
+At the time of writing the current release is `1.1`
 
 ## Installing Dependencies
 

asclepius/README.md

@@ -79,7 +79,7 @@ Endpoints
 | 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, and the identifiers of the two drugs involved         |
+| 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 |
 
 #### Example
 ##### Request Body
@@ -100,7 +100,9 @@ Endpoints
     "drug_a": "http://purl.obolibrary.org/obo/DINTO_DB00214",
     "drug_b": "http://purl.obolibrary.org/obo/DINTO_DB00519",
     "label": "torasemide/trandolapril DDI",
-    "uri": "http://purl.obolibrary.org/obo/DINTO_11031"
+    "uri": "http://purl.obolibrary.org/obo/DINTO_11031",
+    "harmful": false,
+    "spacing": 3
   }
 ]
 ```

asclepius/asclepius/enrich.py

@@ -0,0 +1,8 @@
+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
+
+    return [_enrich(ddi) for ddi in ddis]

asclepius/asclepius/main.py

@@ -5,7 +5,7 @@
 
 from app import app
 import dinto
-
+from enrich import enrich
 
 class InvalidUsage(Exception):
     status_code = 400
@@ -61,7 +61,7 @@ def ddis():
     except ValueError as e:
         raise InvalidUsage(str(e))
 
-    return jsonify(dinto_res)
+    return jsonify(enrich(dinto_res))
 
 
 @app.route('/uris', methods=["POST"])

athloi/features/fixtures/analysis_test.pml

@@ -0,0 +1,22 @@
+process foo {
+  task {
+    action baz {
+      tool { "pills" }
+      script { "eat the pills" }
+      agent { "patient" }
+      requires {
+        drug { "paracetamol" }
+      }
+      provides { "a cured patient" }
+    }
+    action baz2 {
+      tool { "pills" }
+      script { "eat the pills" }
+      agent { "patient" }
+      requires {
+        drug { "cocaine" }
+      }
+      provides { "a cured patient" }
+    }
+  }
+}

athloi/features/fixtures/ddis.pml

@@ -12,7 +12,7 @@ process foo {
     action baz2 {
       tool { "pills" }
       script { "eat the pills" }
-      agent { "patient" }
+      agent { (intangible)(inscrutable) pml.wtf && ("foo" || 1 != 2) }
       requires {
         drug { "trandolapril" }
       }

athloi/features/pml_download.feature

@@ -0,0 +1,11 @@
+Feature: PML Download
+  In order to refine PML analysis
+  As a clinician
+  I should be able to download the PML file resulting from PML TX transformations
+
+  Scenario: uploading a valid PML file
+    Given I am on the home page
+    When I select "ddis.pml"
+    And I submit the upload form
+    Then I should see the PML download button
+    And the PML download button should have the correct href

athloi/features/step_definitions/file_upload_steps.rb

@@ -1,7 +1,3 @@
-When(/^I submit the upload form$/) do
-  click_on 'Submit'
-end
-
 Then(/^I should see the found drugs panel$/) do
   panel = find('#drugs-panel', wait: 15)
 

athloi/features/step_definitions/pml_download_steps.rb

@@ -0,0 +1,12 @@
+Then(/^I should see the PML download button$/) do
+  button = find('#pml-download-anchor')
+
+  expect(button).to be_visible
+end
+
+Then(/^the PML download button should have the correct href$/) do
+  button = find('#pml-download-anchor')
+
+  expect(button[:href]).to have_content('authorization_token=')
+  expect(button[:href]).to have_content('ast=')
+end

athloi/features/step_definitions/shared_steps.rb

@@ -10,3 +10,7 @@
 
   execute_script("document.getElementById('file-input').classList.add('hidden')")
 end
+
+When(/^I submit the upload form$/) do
+  click_on 'Submit'
+end

circle.yml

@@ -12,17 +12,22 @@ dependencies:
 
 compile:
   override:
-    - echo "panacea asclepius athloi" | parallel --trim r -d " " "docker build --rm=false -t tomtoothfairies/{} {}"
+    - docker build --rm=false -t tomtoothfairies/panacea panacea
+    - docker build --rm=false -t tomtoothfairies/asclepius asclepius
+    - docker build --rm=false -t tomtoothfairies/athloi athloi
 
 test:
   pre:
-    - mkdir -p $CIRCLE_TEST_REPORTS/exunit
-    - mkdir -p $CIRCLE_TEST_REPORTS/pytest
-    - mkdir -p $CIRCLE_TEST_REPORTS/cucumber
-    - mkdir -p $CIRCLE_ARTIFACTS/screenshots
+    - mkdir -p $CIRCLE_TEST_REPORTS/{exunit,pytest,cucumber}
+    - mkdir -p $CIRCLE_ARTIFACTS/{screenshots,logs}
 
   override:
-    - docker-compose -f docker-compose.e2e.yml -f docker-compose.e2e.ci.yml up -d
     - docker run -t -e "MIX_ENV=test" -e "CI=true" -v $CIRCLE_TEST_REPORTS/exunit:/test-reports tomtoothfairies/panacea mix test
     - docker run -t -v $CIRCLE_TEST_REPORTS/pytest:/test-reports tomtoothfairies/asclepius pytest --junitxml=/test-reports/test-junit-report.xml
-    - ./end-2-end.sh
+    - docker-compose -f docker-compose.e2e.yml -f docker-compose.e2e.ci.yml run athloi
+
+  post:
+    - docker logs pathways_panacea_1 > $CIRCLE_ARTIFACTS/logs/panacea.log
+    - docker logs pathways_asclepius_1 > $CIRCLE_ARTIFACTS/logs/asclepius.log
+    - docker logs pathways_chiron_1 > $CIRCLE_ARTIFACTS/logs/chiron.log
+    - docker logs pathways_selenium_1 > $CIRCLE_ARTIFACTS/logs/selenium.log

doc/CHANGELOG.md

@@ -2,6 +2,12 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.1] 2017-03-19
+
+### Added
+- Added support for PML TX file downloads. Valid pml files uploaded to the
+  system for transformation can now be downloaded via the UI.
+
 ## [1.0] 2017-03-12
 
 ### Changed
@@ -114,7 +120,8 @@ 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/1.0...iteration1-2
+[Unreleased]: https://github.com/tom-and-the-toothfairies/pathways/compare/1.1...iteration-6
+[1.1]: https://github.com/tom-and-the-toothfairies/pathways/compare/1.0...1.1
 [1.0]: https://github.com/tom-and-the-toothfairies/pathways/compare/0.3...1.0
 [0.3]: https://github.com/tom-and-the-toothfairies/pathways/compare/0.2...0.3
 [0.2]: https://github.com/tom-and-the-toothfairies/pathways/compare/0.1...0.2

doc/FEATURES.md

@@ -230,6 +230,18 @@ http://chiron:3030/dinto/query`) and the contents of those queries.
 
 See [On Screen DINTO Reporting](#on-screen-dinto-reporting---complete)
 
+## PML-TX Save PML to File - Complete
+
+### Description
+The system should be able to allow saving of transformed PML files.
+
+### Testing
+Visit the [homepage] and select a valid PML file; for example
+`panacea/text/fixtures/ddis.pml`. Press the `Submit` button. You should now see
+a `Download PML TX File` button. Clicking the button, depending on your
+browser, will either download the file automatically or prompt you to provide a
+filename and location and download the file.
+
 [README]: ../README.md
 [homepage]: http://localhost:4000
 [fixtures directory]: ../panacea/test/fixtures

docker-compose.yml

@@ -4,14 +4,14 @@ services:
   asclepius:
     depends_on:
       - chiron
-    image: tomtoothfairies/asclepius:1.0
+    image: tomtoothfairies/asclepius:1.1
 
   panacea:
     depends_on:
       - asclepius
-    image: tomtoothfairies/panacea:1.0
+    image: tomtoothfairies/panacea:1.1
     ports:
       - '4000:4000'
 
   chiron:
-    image: tomtoothfairies/chiron:1.0
+    image: tomtoothfairies/chiron:1.1

panacea/README.md

@@ -8,7 +8,10 @@ Chiron to provide DDI analysis, these must be running for Panacea to work.
 Api Endpoints
 -------------
 
-All API endpoints require the *Authorization* header to contain a valid token.
+All API endpoints require a valid *authorization token* to be provided. The
+*token* can be sent in the *Authorization* header or as the
+*authorization_token* query parameter.
+
 Tokens can be generated using: `Panacea.AccessToken.generate()`
 
 ### `/api/pml`
@@ -36,11 +39,22 @@ Tokens can be generated using: `Panacea.AccessToken.generate()`
       "label": "cocaine",
       "line": 2
     }
-  ]
+  ],
+  "unnamed": [
+    {
+      "type": "task",
+      "line": 3
+    },
+    {
+      "type": "sequence",
+      "line": 6
+    }
+  ],
+  "ast": "AST representation of the provided PML file - base64 encoded"
 }
 ```
 
-### `api/uris`
+### `/api/uris`
 
 |              |                                                             |
 |--------------|-------------------------------------------------------------|
@@ -108,7 +122,9 @@ Tokens can be generated using: `Panacea.AccessToken.generate()`
       "drug_a": "http://purl.obolibrary.org/obo/DINTO_DB00214",
       "drug_b": "http://purl.obolibrary.org/obo/DINTO_DB00519",
       "label": "torasemide/trandolapril DDI",
-      "uri": "http://purl.obolibrary.org/obo/DINTO_11031"
+      "uri": "http://purl.obolibrary.org/obo/DINTO_11031",
+      "harmful": false,
+      "spacing": 3
     }
   ]
 }
@@ -128,3 +144,12 @@ 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 |

panacea/lib/panacea/pml/analysis.ex

@@ -0,0 +1,18 @@
+defmodule Panacea.Pml.Analysis do
+  alias __MODULE__
+  alias Panacea.Pml.Analysis.{Drugs, Unnamed}
+
+  defstruct [:drugs, :unnamed, :ast]
+
+  def run(ast) do
+    drugs = Drugs.run(ast)
+    unnamed = Unnamed.run(ast)
+
+    encoded_ast =
+      ast
+      |> :erlang.term_to_binary()
+      |> Base.encode64()
+
+    {:ok, %Analysis{drugs: drugs, unnamed: unnamed, ast: encoded_ast}}
+  end
+end

panacea/lib/panacea/pml/analysis/drugs.ex

@@ -0,0 +1,22 @@
+defmodule Panacea.Pml.Analysis.Drugs do
+
+  def run(ast) do
+    analyse([], ast)
+  end
+
+  defp analyse(result, {:requires, _, {:drug, [line: line], label}}) do
+    [%{label: strip_quotes(label), line: line} | result]
+  end
+  defp analyse(result, {_, _, children}) when is_list(children) do
+    Enum.reduce(children, result, fn(child, acc) ->
+      analyse(acc, child)
+    end)
+  end
+  defp analyse(result, _), do: result
+
+  defp strip_quotes(char_list) do
+    char_list
+    |> :string.strip(:both, ?")
+    |> to_string()
+  end
+end

panacea/lib/panacea/pml/analysis/unnamed.ex

@@ -0,0 +1,22 @@
+defmodule Panacea.Pml.Analysis.Unnamed do
+
+  @composite [:task, :sequence, :branch, :selection, :iteration, :action, :process]
+
+  def run(ast) do
+    analyse([], ast)
+  end
+
+  defp analyse(result, {type, attrs, children}) when type in @composite do
+    result =
+      if !Keyword.has_key?(attrs, :name) do
+        [%{type: type, line: Keyword.get(attrs, :line)} | result]
+      else
+        result
+      end
+
+    Enum.reduce(children, result, fn (child, acc) ->
+      analyse(acc, child)
+    end)
+  end
+  defp analyse(result, _), do: result
+end

panacea/lib/panacea/pml/ast.ex

@@ -0,0 +1,38 @@
+defmodule Panacea.Pml.Ast do
+  @multi_line_constructs ~w(process action task sequence selection branch iteration)a
+  @single_line_constructs ~w(requires provides agent tool script input output)a
+
+  @doc """
+  Takes an AST and returns the PML it represents in an IO-List
+  """
+  def to_pml(ast) do
+    do_unquote(ast, 0)
+  end
+
+  defp do_unquote({type, attrs, children}, depth) when type in @multi_line_constructs do
+    optional_name = get_with_default(attrs, :name)
+    optional_type = get_with_default(attrs, :type)
+
+    [indent(depth), to_string(type), optional_name, optional_type, " {\n",
+     Enum.map(children, fn(child) -> [do_unquote(child, depth + 1), "\n"] end),
+     indent(depth), "}"
+    ]
+  end
+
+  defp do_unquote({type, _, value}, depth) when type in @single_line_constructs do
+    [indent(depth), to_string(type), " { ", do_unquote(value), " }"]
+  end
+
+  defp do_unquote({:expression, _, value}), do: value
+  defp do_unquote({:drug, _, value}), do: ["drug { ", value, " }"]
+  defp do_unquote(x) when is_list(x), do: x
+
+  defp indent(depth), do: String.duplicate(" ", 2 * depth)
+
+  defp get_with_default(attrs, key) do
+    case Keyword.get(attrs, key) do
+      nil -> ""
+      x   -> [" ", x]
+    end
+  end
+end