Merge pull request #173 from tom-and-the-toothfairies/iteration-7

Iteration 7

README.md

@@ -9,7 +9,7 @@ maximum convenience - click-able links for example*
 This file contains instructions on how to install and run the project, as well
 as an overview of the project's design. The target platform is Ubuntu 16.04.
 
-At the time of writing the current release is `1.2`
+At the time of writing the current release is `1.3`
 
 ## Installing Dependencies
 

athloi/features/file_upload.feature

@@ -17,7 +17,9 @@ Feature: File upload
   Scenario: uploading a PML file with unidentifiable drugs
     When I select "unidentifiable_drugs.pml"
     And I submit the upload form
+    And I click the warnings tab
     Then I should see the unidentified drugs panel
+    And I should see "2" in the warning number badge
     And I should see the following drugs in the unidentified drugs panel:
       | marmalade           |
       | dimethylheptylpyran |
@@ -26,25 +28,42 @@ Feature: File upload
     When I select "no_drugs.pml"
     And I submit the upload form
     Then I should see the error panel
+    And I should see "1" in the error number badge
     And the error panel title should be "Pathway error"
 
   Scenario: uploading a PML file with syntax errors
     When I select "bad.pml"
     And I submit the upload form
     Then I should see the error panel
+    And I should see "1" in the error number badge
+    And the error panel title should be "Syntax error"
+
+  Scenario: uploading a PML file containing delays
+    When I select "delays.pml"
+    And I submit the upload form
+    Then I should see the found DDIs panel
+
+  Scenario: uploading a PML file with invalid delay timings
+    When I select "bad_delays.pml"
+    And I submit the upload form
+    Then I should see the error panel
     And the error panel title should be "Syntax error"
 
   Scenario: uploading a PML file with unnamed constructs
     When I select "analysis/unnamed.pml"
     And I submit the upload form
+    And I click the warnings tab
     Then I should see the unnamed panel
+    And I should see "1" in the warning number badge
     And I should see the following warnings in the unnamed panel:
       | task on line 2 |
 
   Scenario: uploading a PML file with clashing construct names
     When I select "analysis/clashes.pml"
     And I submit the upload form
+    And I click the warnings tab
     Then I should see the clashes panel
+    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 |
@@ -55,14 +74,15 @@ Feature: File upload
     When I select "example.png"
     And I submit the upload form
     Then I should see the error panel
+    And I should see "1" in the error number badge
     And the error panel title should be "Encoding error"
 
   Scenario: uploading a PML file with identifiable drugs that have an interaction
     When I select "ddis.pml"
     And I submit the upload form
     Then I should see the found DDIs panel
     And I should see the following DDIs in the found DDIs panel:
-      | torasemide and trandolapril |
+      | torasemide on line 8 and trandolapril on line 17 |
 
   Scenario: uploading a PML file with identifiable drugs that don't have an interaction
     When I select "no_ddis.pml"

athloi/features/fixtures/alternative_non_ddi.pml

@@ -0,0 +1,10 @@
+process alternative_non_ddis {
+  selection {
+    action s1 {
+      requires { drug { "trandolapril" } }
+    }
+    action s2 {
+      requires { drug { "torasemide" } }
+    }
+  }
+}

athloi/features/fixtures/bad_delays.pml

@@ -0,0 +1,15 @@
+process foo {
+  task bar {
+    action baz {
+      requires {
+        time {
+          days { 28 }
+          years { 1 }
+          minutes { 10 }
+          years { 3 }
+          hours { 7 }
+        }
+      }
+    }
+  }
+}

athloi/features/fixtures/delays.pml

@@ -0,0 +1,37 @@
+process foo {
+  task bar {
+    action baz {
+      tool { "pills" }
+      script { "eat the pills" }
+      agent { "patient" }
+      requires {
+        drug { "torasemide" }
+      }
+      provides { "a cured patient" }
+      requires {
+        time {
+          minutes { 45 }
+        }
+      }
+    }
+    action baz2 {
+      tool { "pills" }
+      script { "eat the pills" }
+      agent { (intangible)(inscrutable) pml.wtf && ("foo" || 1 != 2) }
+      requires {
+        drug { "trandolapril" }
+      }
+      provides { "a cured patient" }
+      requires {
+        time {
+          years { 20 }
+          weeks { 12 }
+          days { 15 }
+          hours { 10 }
+          minutes { 6 }
+          seconds { 14 }
+        }
+      }
+    }
+  }
+}

athloi/features/fixtures/parallel.pml

@@ -0,0 +1,10 @@
+process parallel_ddis {
+  branch {
+    action b1 {
+      requires { drug { "trandolapril" } }
+    }
+    action b2 {
+      requires { drug { "torasemide" } }
+    }
+  }
+}

athloi/features/fixtures/repeated_alternative.pml

@@ -0,0 +1,12 @@
+process repeated_alternative_ddis {
+  iteration {
+    selection {
+      action s1 {
+        requires { drug { "trandolapril" } }
+      }
+      action s2 {
+        requires { drug { "torasemide" } }
+      }
+    }
+  }
+}

athloi/features/step_definitions/file_upload_steps.rb

@@ -86,3 +86,15 @@
     expect(body).to have_content(clash)
   end
 end
+
+Then(/^I should see "([^"]*)" in the warning number badge$/) do |number|
+  badge = find('#warnings-badge')
+
+  expect(badge).to have_content(number)
+end
+
+Then(/^I should see "([^"]*)" in the error number badge$/) do |number|
+  badge = find('#errors-badge')
+
+  expect(badge).to have_content(number)
+end

athloi/features/step_definitions/shared_steps.rb

@@ -14,3 +14,7 @@
 When(/^I submit the upload form$/) do
   click_on 'Submit'
 end
+
+When(/^I click the warnings tab$/) do
+  click_on('Warnings', wait: 5)
+end

doc/CHANGELOG.md

@@ -1,6 +1,20 @@
 # Change Log
 
 All notable changes to this project will be documented in this file.
+
+## [1.3] 2017-04-02
+
+### Added
+- Added UI sections for displaying the different types of DDI sequencing
+  categories identified by the system: parallel, sequential, repeated
+  alternative, and alternative non-DDI
+- Added the ability to specify a delay in PML files
+
+### Changed
+- Redesigned the UI to use tabs for the different logical sections of the
+  application: Analysis, Warnings, and Errors
+- The syntax error UI now includes contextual line highlighting
+
 ## [1.2] 2017-03-26
 
 ### Added
@@ -139,7 +153,8 @@ 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/1.2...iteration-7
+[Unreleased]: https://github.com/tom-and-the-toothfairies/pathways/compare/1.3...release-2
+[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
 [1.0]: https://github.com/tom-and-the-toothfairies/pathways/compare/0.3...1.0

doc/FEATURES_RELEASE_1.md

@@ -1,4 +1,4 @@
-# Features
+# 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
@@ -11,7 +11,7 @@ tracked [here](https://circleci.com/gh/tom-and-the-toothfairies/pathways).
 
 We have developed a suite of end to end tests that verify the whole system's
 functionality by automating interactions with a web browser. These can be run
-with the following command
+from the project's root directory with the following command
 
 ```bash
 $ sudo docker-compose -f docker-compose.e2e.yml -p integration run athloi; sudo docker-compose -f docker-compose.e2e.yml -p integration down
@@ -63,9 +63,10 @@ Visit the [homepage] and select a file. Press the `Submit` button. The file
 should be sent to the system, and analysis results should now be displayed.
 Invalid files should result in an error dialogue, which displays a meaningful
 error message. For example, `panacea/test/fixtures/bad.pml` should result in a
-`Syntax error` being displayed when submitted. Valid files should result in a
-success dialogue. See [PML File Loading](#pml-file-loading---complete) for an
-example.
+`Syntax error` being displayed in the errors tab when submitted. Valid files
+such as `panacea/test/fixtures/ddis.pml` should result in analysis being
+displayed in the analysis tab.
+See [PML File Loading](#pml-file-loading---complete) for an example.
 
 ## On-Screen PML Reporting - Complete
 
@@ -77,9 +78,10 @@ must be easily identified, and the error messages must be useful.
 Visit the [homepage] and select a file. Some useful files can be found in the
 [fixtures directory]. Press the `Submit` button. Analysis results should be
 displayed. `panacea/test/fixtures/example.png` is not UTF-8 encoded and should
-result in an `Encoding error`. `panacea/test/fixtures/bad.pml` contains invalid
-PML and should result in a `Syntax error`. `panacea/test/fixtures/ddis.pml`
-contains valid PML and should result in a successful analysis.
+result in an `Encoding error` in the errors tab. `panacea/test/fixtures/bad.pml`
+contains invalid PML and should result in a `Syntax error`.
+`panacea/test/fixtures/ddis.pml` contains valid PML and should result in a
+successful analysis displayed in the analysis tab.
 
 ## PML Log File Generation - Complete
 
@@ -88,15 +90,15 @@ The successful or unsuccessful loading of PML files into the system is output
 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 this):
+First, open up the tail of the Panacea logs (the system must be running to do
+this):
 ```bash
 $ sudo docker-compose logs -f panacea
 ```
 Visit the [homepage] and select a file. Some useful files can be found in the
 [fixtures directory]. Press the `Submit` button. You should see log entries
-created indicating either a successful parse of the PML file and the drugs
-contained in it or that an error occurred parsing the PML file and what the
-error was.
+created indicating either a successful parse of the PML file or that an error
+occurred parsing the PML file and what the error was.
 
 ## PML Error and Warning highlights - Complete
 
@@ -116,7 +118,6 @@ 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
 can be found [here](./UPDATING_DINTO.md)
 
-
 ## Load Selected Ontology - Complete
 
 See [Select specific OWL Ontology](#select-specific-owl-ontology---complete)
@@ -131,7 +132,7 @@ Users can specify a drug using the following construct:
 `drug { "drug_name" }`
 
 Drugs to be administered to patients must be placed in `requires` blocks within
-the PML document. For example
+the PML document. For example:
 
 ```
 process foo {
@@ -154,7 +155,8 @@ and analysing it should result in `paracetamol` and `cocaine` being identified
 and presented in the UI.
 
 `no_drugs.pml` is a well-structured PML document that does not contain drug
-identifiers. Analysing it should result in no drugs being identified.
+identifiers. Analysing it should result in no drugs being identified with an
+error being displayed in the errors tab.
 
 ## Identify Drugs in DINTO - Complete
 
@@ -166,10 +168,11 @@ plain English into a format that can be used when querying DINTO.
 This feature can be manually tested by uploading files.
 
 Visit the [homepage] and select a PML file that contains drugs; for example
-`panacea/text/fixtures/no_ddis.pml`. Press the `Submit` button. You should see
+`panacea/test/fixtures/no_ddis.pml`. Press the `Submit` button. You should see
 that "cocaine" and "paracetamol" have been identified as drugs in DINTO. Testing
 `panacea/test/fixtures/unidentifiable_drugs.pml` returns drugs that cannot be
-identified in DINTO and are highlighted with a warning as a result.
+identified in DINTO and are highlighted with a warning in the warnings tab as a
+result.
 
 ## Identify DDIs - Complete
 
@@ -214,15 +217,15 @@ A record of queries made to DINTO (via Chiron/Asclepius) can be found in the
 console logs of the Chiron service.
 
 ### Testing
-This feature is tested manually by looking at the logs of the running sytem.
+This feature is tested manually by looking at the logs of the running system.
 
 First, open up the tail of the Chiron logs (the system must be running to do this):
 ```bash
 $ sudo docker-compose logs -f chiron
 ```
 
 Visit the [homepage] and select a PML file that contains drugs; for example
-`panacea/text/fixtures/ddis.pml`. Press the `Submit` button. You should see log
+`panacea/test/fixtures/ddis.pml`. Press the `Submit` button. You should see log
 entries indicating that queries were made (there will be requests such as `POST
 http://chiron:3030/dinto/query`) and the contents of those queries.