- PipelineTester has version number (and logs it)

- Also reports number of files
- Adds some test files to rdkit_utils and a test data file

Author: Alan Christie

data/Kinase_inhibs.sdf.gz

@@ -1,7 +1,7 @@
 #!/usr/bin/env groovy
 
 /**
- * Copyright (c) 2017 Informatics Matters Ltd.
+ * Copyright (c) 2018 Informatics Matters Ltd.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -43,6 +43,9 @@ import groovy.text.SimpleTemplateEngine
  */
 class Tester {
 
+    // Version (try and update with every change/release)
+    String version = '1.0'
+
     // Supported test-script versions
     def supportedTestFileVersions = [1]
 
@@ -75,6 +78,7 @@ class Tester {
     int sectionNumber = 0
     int testsExecuted = 0
     int testsIgnored = 0
+    int filesUsed = 0
     def failedTests = []
     def observedFiles = []
 
@@ -99,7 +103,11 @@ class Tester {
      */
     boolean run() {
 
-        // before we start - cleanup (everything)
+        // Log versions
+        info("PipelineTester: v$version")
+        info("Supporting test file versions: $supportedTestFileVersions")
+
+        // Before we start - cleanup (everything)
         cleanUpOutput(true)
 
         // Find all the potential test files
@@ -115,6 +123,7 @@ class Tester {
             testScriptVersion = 0
             testTimeoutSeconds = 30
             collectionCreates = []
+            filesUsed += 1
 
             // We must not have duplicate test files -
             // this indicates there are pipelines in different projects
@@ -212,9 +221,10 @@ class Tester {
                 println "Failed: $name"
             }
         }
-        println "Num executed: $testsExecuted"
-        println "Num ignored : $testsIgnored"
-        println "Num failed  : $failedTests.size"
+        println "Test Files   : " + sprintf('%4d', filesUsed)
+        println "Tests        : " + sprintf('%4d', testsExecuted)
+        println "Tests ignored: " + sprintf('%4d', testsIgnored)
+        println "Tests failed : " + sprintf('%4d', failedTests.size())
         separate()
         println "Passed: ${testPassed.toString().toUpperCase()}"
 

src/groovy/PipelineTester.groovy

@@ -114,8 +114,8 @@
         // Metrics.
         //
         // If your pipeline creates standard metrics - a Java properties file
-        // with the name 'output_metrics.txt' you can use the metrics block
-        // here to check the generated values. You can specify a property
+        // with the name 'output_metrics.txt' - you can use the metrics block
+        // here to check its content. You can specify a property
         // (a key) and a regular expression string value.
 
         metrics: [ __StatusMessage__: 'kel: 0.171, t1/2: 4.06, V: 7.07, CL: 20.1' ]

src/groovy/pipeline.test.template

@@ -0,0 +1,19 @@
+// Automated pipeline test specification.
+
+[
+
+    version = 1,
+
+    // Testing filter.py reading from STDIN and writing to STDOUT
+    test_in_to_out = [
+
+        command: '''gunzip -c ../../data/Kinase_inhibs.sdf.gz |
+                    python -m rdkit_utils.filter
+                    --hacmin 25 --hacmax 30 -if sdf''',
+
+        see: [ 'No output format specified - using sdf',
+               'Filtered [1-9]\\d+ down to [1-9]\\d+ molecules'],
+
+    ],
+
+]

src/python/rdkit_utils/filter.test

@@ -0,0 +1,14 @@
+// Automated pipeline test specification.
+
+[
+
+    version = 1,
+
+    // Test basic startup
+    test_help = [
+
+        command: '''python -m rdkit_utils.sdf2json -h''',
+
+    ],
+
+]

src/python/rdkit_utils/sdf2json.test

@@ -0,0 +1,14 @@
+// Automated pipeline test specification.
+
+[
+
+    version = 1,
+
+    // Test basic startup
+    test_help = [
+
+        command: '''python -m rdkit_utils.splitter -h''',
+
+    ],
+
+]

src/python/rdkit_utils/splitter.test

@@ -5,11 +5,11 @@
 
 class UtilsTestCase(unittest.TestCase):
 
-
     def test_round_sig(self):
         """Rounding of significant figures
         """
         self.assertEquals(utils.round_sig(1.23456789, 2), 1.2)
         self.assertEquals(utils.round_sig(1.23456789, 3), 1.23)
         self.assertEquals(utils.round_sig(1.23456789, 6), 1.23457)
 
+        self.assertEquals(utils.round_sig(-1.23456789, 6), -1.23457)