WIP: OmexTextCase (ndjson, csv) unifies unit/nightly test reports

vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestCase.java

@@ -0,0 +1,97 @@
+package org.vcell.cli.testsupport;
+
+public class OmexTestCase {
+
+    public enum TestDataRepo {
+        vcell, sysbio
+    }
+    public enum TestCollection {
+        VCELL_BIOMD(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/misc-projects"),
+        VCELL_BSTS_VCML(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/vcml"),
+        VCELL_BSTS_SBML_CORE(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/sbml-core"),
+        VCELL_BSTS_SYNTHS(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/synths"),
+        SYSBIO_BIOMD(TestDataRepo.sysbio, "omex_files");
+
+        public final TestDataRepo repo;
+        public final String pathPrefix;
+
+        TestCollection(TestDataRepo repo, String pathPrefix) {
+            this.repo = repo;
+            this.pathPrefix = pathPrefix;
+        }
+    }
+    public enum Status {
+        PASS,
+        FAIL,
+        SKIP
+    }
+
+    public TestCollection test_collection;
+    public String file_path;
+    public Boolean should_fail;
+    public Status known_status;
+    public FailureType known_failure_type;
+    public String known_failure_desc;
+
+    // from csv
+    public OmexTestCase(String[] csvLine) {
+        test_collection = TestCollection.valueOf(csvLine[0]);
+        file_path = csvLine[1];
+        should_fail = Boolean.parseBoolean(csvLine[2]);
+        if (csvLine[3].trim().isEmpty()) {
+            known_status = null;
+        } else {
+            known_status = Status.valueOf(csvLine[3]);
+        }
+        if (csvLine[4].trim().isEmpty()) {
+            known_failure_type = null;
+        } else {
+            known_failure_type = FailureType.valueOf(csvLine[4]);
+        }
+        known_failure_desc = parseCsvStringField(csvLine[5]);
+    }
+
+    // to csv
+    public String[] toCsvLine() {
+        return new String[] {
+                test_collection.toString(),
+                file_path,
+                should_fail.toString(),
+                (known_status !=null) ? known_status.toString() : "",
+                (known_failure_type !=null) ? known_failure_type.toString() : "",
+                printCsvStringField(known_failure_desc)
+        };
+    }
+
+    @Override
+    public String toString() {
+        return "OmexTestCase{" +
+                "test_collection=" + test_collection +
+                ", file_path='" + file_path + '\'' +
+                ", should_fail=" + should_fail +
+                ", known_status=" + known_status +
+                ", known_failure_type=" + known_failure_type +
+                ", known_failure_desc="+((known_failure_desc!=null)?('\'' + known_failure_desc + '\''):null) +
+                '}';
+    }
+    private String parseCsvStringField(String str) {
+        str = str.strip();
+        // strip leading and trailing double quotes
+        if (str.startsWith("\"") && str.endsWith("\"")) {
+            str = str.substring(1, str.length()-1);
+        }
+        // strip escaped double quotes
+        str = str.replace("\"\"", "\"");
+        if (str.isEmpty()){
+            return null;
+        }
+        return str;
+    }
+
+    private String printCsvStringField(String str) {
+        if (str == null){
+            return "";
+        }
+        return "\"" + str.replace("\"", "\"\"") + "\"";
+    }
+}

vcell-cli/src/main/java/org/vcell/cli/testsupport/OmexTestingDatabase.java

@@ -0,0 +1,60 @@
+package org.vcell.cli.testsupport;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class OmexTestingDatabase {
+
+    // read a newline-delimited json file into a list of OmexTextCase objects
+    public static List<OmexTestCase> readOmexTestCasesFromNdjson(String path) throws IOException {
+        List<OmexTestCase> testCases = new ArrayList<>();
+        ObjectMapper objectMapper = new ObjectMapper();
+        try (BufferedReader reader = new BufferedReader(new FileReader(path));) {
+            String line = reader.readLine();
+            while (line != null) {
+                // use jackson objectmapper to read an OmexTestCase object from a json string
+                OmexTestCase testCase = objectMapper.readValue(line, OmexTestCase.class);
+                testCases.add(testCase);
+            }
+        }
+        return testCases;
+    }
+
+    // read a csv file into a list of OmexTextCase objects
+    public static List<OmexTestCase> readOmexTestCasesFromCsv(String path) throws IOException{
+        List<OmexTestCase> testCases = new ArrayList<>();
+        try (BufferedReader reader = new BufferedReader(new FileReader(path));) {
+            String line = reader.readLine(); // read header
+            line = reader.readLine(); // read first line
+            while (line != null) {
+                line = line + " "; // add a space to the end of the line to handle empty fields at the end
+                line = line.replace(",,",", ,"); // replace empty fields with ", ,"
+                String[] fields = line.split(",");
+                testCases.add(new OmexTestCase(fields));
+                line = reader.readLine();
+            }
+        }
+        return testCases;
+    }
+
+    public static void main(String[] args) {
+        try {
+            List<OmexTestCase> testCases = readOmexTestCasesFromCsv("/Users/jimschaff/Documents/workspace/vcell/vcell-cli/src/main/resources/known_problems.csv");
+            ObjectMapper objectMapper = new ObjectMapper();
+            for (OmexTestCase testCase : testCases) {
+                System.out.println(Arrays.stream(testCase.toCsvLine()).collect(Collectors.joining(",")));
+                System.out.println(testCase);
+                System.out.println(objectMapper.writeValueAsString(testCase));
+            }
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+}