Flex transformation updates

pom.xml

@@ -275,7 +275,7 @@
         <dependency>
             <groupId>com.github.conveyal</groupId>
             <artifactId>gtfs-lib</artifactId>
-            <version>5c383ab</version>
+            <version>32c084009930501ce992695be73a83ae7f7f767e</version>
             <!-- Exclusions added in order to silence SLF4J warnings about multiple bindings:
                 http://www.slf4j.org/codes.html#multiple_bindings
             -->

src/main/java/com/conveyal/datatools/manager/jobs/ProcessSingleFeedJob.java

@@ -13,6 +13,7 @@
 import com.conveyal.datatools.manager.models.transform.FeedTransformRules;
 import com.conveyal.datatools.manager.models.transform.FeedTransformZipTarget;
 import com.conveyal.datatools.manager.models.transform.ZipTransformation;
+import com.conveyal.gtfs.validator.ValidationResult;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import org.slf4j.Logger;
@@ -198,15 +199,22 @@ private String getErrorReasonMessage() {
     public String getNotificationMessage() {
         StringBuilder message = new StringBuilder();
         if (!status.error) {
-            message.append(String.format("New feed version created for %s (valid from %s - %s). ",
-                feedSource.name,
-                feedVersion.validationResult.firstCalendarDate,
-                feedVersion.validationResult.lastCalendarDate));
-            if (feedVersion.validationResult.errorCount > 0) {
-                message.append(String.format("During validation, we found %s issue(s)",
-                    feedVersion.validationResult.errorCount));
+            ValidationResult validationResult = feedVersion.validationResult;
+            if (validationResult != null) {
+                message.append(String.format("New feed version created for %s (valid from %s - %s). ",
+                    feedSource.name,
+                    feedVersion.validationResult.firstCalendarDate,
+                    feedVersion.validationResult.lastCalendarDate
+                ));
             } else {
-                message.append("The validation check found no issues with this new dataset!");
+                message.append(String.format("New feed version created for %s.", feedSource.name));
+            }
+            if (validationResult != null) {
+                if (validationResult.errorCount > 0) {
+                    message.append(String.format("During validation, we found %s issue(s)", validationResult.errorCount));
+                } else {
+                    message.append("The validation check found no issues with this new dataset!");
+                }
             }
         } else {
             // Processing did not complete. Depending on which sub-task this occurred in,

src/main/java/com/conveyal/datatools/manager/models/FeedVersion.java

@@ -554,7 +554,9 @@ public void delete() {
 
             feedStore.deleteFeed(id);
             // Delete feed version tables in GTFS database
-            GTFS.delete(this.namespace, DataManager.GTFS_DATA_SOURCE);
+            if (this.namespace != null) {
+                GTFS.delete(this.namespace, DataManager.GTFS_DATA_SOURCE);
+            }
             LOG.info("Dropped version's GTFS tables from Postgres.");
             // Remove this FeedVersion from all Deployments associated with this FeedVersion's FeedSource's Project
             // TODO TEST THOROUGHLY THAT THIS UPDATE EXPRESSION IS CORRECT

src/main/java/com/conveyal/datatools/manager/models/transform/FeedTransformation.java

@@ -2,6 +2,7 @@
 
 import com.conveyal.datatools.common.status.MonitorableJob;
 import com.conveyal.datatools.manager.utils.GtfsUtils;
+import com.conveyal.gtfs.loader.Table;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonSubTypes;
 import com.fasterxml.jackson.annotation.JsonTypeInfo;
@@ -100,8 +101,16 @@ public void doTransform(FeedTransformTarget target, MonitorableJob.Status status
      */
     protected void validateTableName(MonitorableJob.Status status) {
         // Validate fields before running transform.
-        if (GtfsUtils.getGtfsTable(table) == null) {
-            status.fail("Table must be valid GTFS spec table name (without .txt).");
+        if (GtfsUtils.getGtfsTable(table) == null && !Table.LOCATION_GEO_JSON_FILE_NAME.equals(table)) {
+            status.fail(String.format("Table must be valid GTFS spec table name (without .txt) or %s.", Table.LOCATION_GEO_JSON_FILE_NAME));
         }
     }
+
+    protected String getTableName() {
+        return Table.LOCATION_GEO_JSON_FILE_NAME.equals(table) ? table : table + ".txt";
+    }
+
+    protected String getTableSuffix() {
+        return Table.LOCATION_GEO_JSON_FILE_NAME.equals(table) ? ".geojson" : ".txt";
+    }
 }

src/main/java/com/conveyal/datatools/manager/models/transform/NormalizeFieldTransformation.java

@@ -179,6 +179,11 @@ public static List<String> getInvalidSubstitutionPatterns(List<Substitution> sub
 
     @Override
     public void transform(FeedTransformZipTarget zipTarget, MonitorableJob.Status status) {
+        if (Table.LOCATION_GEO_JSON_FILE_NAME.equals(table)) {
+            // It's not possible to select the locations.geojson file from the normalize field transformation list. This
+            // is here in case that changes.
+            throw new UnsupportedOperationException("It is not possible to normalize geo json fields.");
+        }
         String tableName = table + ".txt";
         try(
             // Hold output before writing to ZIP

src/main/java/com/conveyal/datatools/manager/models/transform/PreserveCustomFieldsTransformation.java

@@ -60,14 +60,14 @@ private static HashMap<String, Map<String, String>> createCsvHashMap(CsvMapReade
 
     @Override
     public void transform(FeedTransformZipTarget zipTarget, MonitorableJob.Status status) throws Exception{
-        String tableName = table + ".txt";
+        String tableName = getTableName();
         Path targetZipPath = Paths.get(zipTarget.gtfsFile.getAbsolutePath());
         Optional<Table> streamResult = Arrays.stream(Table.tablesInOrder)
                 .filter(t -> t.name.equals(table))
                 .findFirst();
 
-        if (!streamResult.isPresent()) {
-            throw new Exception(String.format("could not find specTable for table %s", table));
+        if (streamResult.isEmpty()) {
+            throw new IOException(String.format("could not find specTable for table %s", table));
         }
         Table specTable = streamResult.get();
 
@@ -77,8 +77,8 @@ public void transform(FeedTransformZipTarget zipTarget, MonitorableJob.Status st
 
             Path targetTxtFilePath = getTablePathInZip(tableName, targetZipFs);
 
-            final File tempFile = File.createTempFile(tableName + "-temp", ".txt");
-            File output = File.createTempFile(tableName + "-output-temp", ".txt");
+            final File tempFile = File.createTempFile(tableName + "-temp", getTableSuffix());
+            File output = File.createTempFile(tableName + "-output-temp", getTableSuffix());
             int rowsModified = 0;
             List<String> customFields;
 

src/main/java/com/conveyal/datatools/manager/models/transform/ReplaceFileFromVersionTransformation.java

@@ -42,7 +42,7 @@ public void validateParameters(MonitorableJob.Status status) {
     @Override
     public void transform(FeedTransformZipTarget zipTarget, MonitorableJob.Status status) {
         FeedVersion sourceVersion = getSourceVersion();
-        String tableName = table + ".txt";
+        String tableName = getTableName();
         // Run the replace transformation
         Path sourceZipPath = Paths.get(sourceVersion.retrieveGtfsFile().getAbsolutePath());
         try (FileSystem sourceZipFs = FileSystems.newFileSystem(sourceZipPath, (ClassLoader) null)) {

src/main/java/com/conveyal/datatools/manager/models/transform/StringTransformation.java

@@ -32,7 +32,7 @@ public void validateParameters(MonitorableJob.Status status) {
 
     @Override
     public void transform(FeedTransformZipTarget zipTarget, MonitorableJob.Status status) {
-        String tableName = table + ".txt";
+        String tableName = getTableName();
         Path targetZipPath = Paths.get(zipTarget.gtfsFile.getAbsolutePath());
         try (
             FileSystem targetZipFs = FileSystems.newFileSystem(targetZipPath, (ClassLoader) null);

src/test/java/com/conveyal/datatools/manager/jobs/NormalizeFieldTransformJobTest.java

@@ -1,6 +1,7 @@
 package com.conveyal.datatools.manager.jobs;
 
 import com.conveyal.datatools.DatatoolsTest;
+import com.conveyal.datatools.manager.auth.Auth0Connection;
 import com.conveyal.datatools.manager.models.FeedRetrievalMethod;
 import com.conveyal.datatools.manager.models.FeedSource;
 import com.conveyal.datatools.manager.models.FeedVersion;
@@ -18,12 +19,18 @@
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.Date;
+import java.util.stream.Stream;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipFile;
 
@@ -34,20 +41,21 @@
 
 
 public class NormalizeFieldTransformJobTest extends DatatoolsTest {
+    private static final Logger LOG = LoggerFactory.getLogger(NormalizeFieldTransformJobTest.class);
     private static final String TABLE_NAME = "routes";
     private static final String FIELD_NAME = "route_long_name";
     private static Project project;
     private static FeedSource feedSource;
     private FeedVersion targetVersion;
 
-
     /**
      * Initialize Data Tools and set up a simple feed source and project.
      */
     @BeforeAll
     public static void setUp() throws IOException {
         // start server if it isn't already running
         DatatoolsTest.setUp();
+        Auth0Connection.setAuthDisabled(true);
 
         // Create a project.
         project = createProject();
@@ -58,6 +66,7 @@ public static void setUp() throws IOException {
      */
     @AfterAll
     public static void tearDown() {
+        Auth0Connection.setAuthDisabled(Auth0Connection.getDefaultAuthDisabled());
         // Project delete cascades to feed sources.
         project.delete();
     }
@@ -75,50 +84,59 @@ public void tearDownTest() {
      * Test that a {@link NormalizeFieldTransformation} will successfully complete.
      * FIXME: On certain Windows machines, this test fails.
      */
-    @Test
-    public void canNormalizeField() throws IOException {
-        // Create transform.
-        // In this test, as an illustration, replace "Route" with the "Rte" abbreviation in routes.txt.
-        FeedTransformation<FeedTransformZipTarget> transformation = NormalizeFieldTransformationTest.createTransformation(
-            TABLE_NAME, FIELD_NAME, null, Lists.newArrayList(
-                new Substitution("Route", "Rte")
-            )
-        );
-        initializeFeedSource(transformation);
+    @ParameterizedTest
+    @MethodSource("createNormalizedFieldCases")
+    void canNormalizeField(TransformationCase transformationCase) throws IOException {
+        initializeFeedSource(transformationCase.table, createTransformation(transformationCase));
 
         // Create target version that the transform will operate on.
         targetVersion = createFeedVersion(
             feedSource,
-            zipFolderFiles("fake-agency-with-only-calendar")
+            zipFolderFiles("fake-agency-for-field-normalizing")
         );
 
         try (ZipFile zip = new ZipFile(targetVersion.retrieveGtfsFile())) {
-            // Check that new version has routes table modified.
-            ZipEntry entry = zip.getEntry(TABLE_NAME + ".txt");
-            assertNotNull(entry);
-
-            // Scan the first data row in routes.txt and check that the substitution
-            // that was defined in setUp was done.
-            try (
-                InputStream stream = zip.getInputStream(entry);
-                InputStreamReader streamReader = new InputStreamReader(stream);
-                BufferedReader reader = new BufferedReader(streamReader)
-            ) {
-                String[] columns = reader.readLine().split(",");
-                int fieldIndex = ArrayUtils.indexOf(columns, FIELD_NAME);
-
-                String row1 = reader.readLine();
-                String[] row1Fields = row1.split(",");
-                assertTrue(row1Fields[fieldIndex].startsWith("Rte "), row1);
-            }
+            // Check that new version has expected modifications.
+            checkTableForModification(zip, transformationCase);
+        }
+    }
+
+    private static Stream<Arguments> createNormalizedFieldCases() {
+        return Stream.of(
+            Arguments.of(new TransformationCase("routes", "route_long_name", "Route", "Rte")),
+            Arguments.of(new TransformationCase("booking_rules", "pickup_message", "Message", "Msg")),
+            Arguments.of(new TransformationCase("areas", "area_name", "Area", "Place"))
+        );
+    }
+
+    private void checkTableForModification(ZipFile zip, TransformationCase transformationCase) throws IOException {
+        String tableName = transformationCase.table + ".txt";
+        LOG.info("Getting table {} from zip {}", tableName, zip.getName());
+        // Check that the new version has been modified.
+        ZipEntry entry = zip.getEntry(tableName);
+        assertNotNull(entry);
+
+        // Scan the first data row and check that the substitution that was defined in the set-up was done.
+        try (
+            InputStream stream = zip.getInputStream(entry);
+            InputStreamReader streamReader = new InputStreamReader(stream);
+            BufferedReader reader = new BufferedReader(streamReader)
+        ) {
+            String[] columns = reader.readLine().split(",");
+            int fieldIndex = ArrayUtils.indexOf(columns, transformationCase.fieldName);
+
+            String rowOne = reader.readLine();
+            assertNotNull(rowOne, String.format("First row in table %s is null!", transformationCase.table));
+            String[] row1Fields = rowOne.split(",");
+            assertTrue(row1Fields[fieldIndex].contains(transformationCase.replacement), rowOne);
         }
     }
 
     /**
      * Test that a {@link NormalizeFieldTransformation} will fail if invalid substitution patterns are provided.
      */
     @Test
-    public void canHandleInvalidSubstitutionPatterns() throws IOException {
+    void canHandleInvalidSubstitutionPatterns() throws IOException {
         // Create transform.
         // In this test, we provide an invalid pattern '\Cir\b' (instead of '\bCir\b'),
         // when trying to replace e.g. 'Piedmont Cir' with 'Piedmont Circle'.
@@ -127,7 +145,7 @@ public void canHandleInvalidSubstitutionPatterns() throws IOException {
                 new Substitution("\\Cir\\b", "Circle")
             )
         );
-        initializeFeedSource(transformation);
+        initializeFeedSource(TABLE_NAME, transformation);
 
         // Create target version that the transform will operate on.
         targetVersion = createFeedVersion(
@@ -140,25 +158,50 @@ public void canHandleInvalidSubstitutionPatterns() throws IOException {
         assertTrue(targetVersion.hasCriticalErrors());
     }
 
+    private FeedTransformation<FeedTransformZipTarget> createTransformation(TransformationCase transformationCase) {
+        return NormalizeFieldTransformationTest
+            .createTransformation(
+                transformationCase.table,
+                transformationCase.fieldName,
+                null,
+                Lists.newArrayList(
+                    new Substitution(transformationCase.pattern, transformationCase.replacement)
+                )
+            );
+    }
+
     /**
      * Create and persist a feed source using the given transformation.
      */
-    private static void initializeFeedSource(FeedTransformation<FeedTransformZipTarget> transformation) {
-        FeedTransformRules transformRules = new FeedTransformRules(transformation);
+    private void initializeFeedSource(String table, FeedTransformation<FeedTransformZipTarget> transformation) {
 
         // Create feed source with above transform.
-        feedSource = new FeedSource("Normalize Field Test Feed", project.id, FeedRetrievalMethod.MANUALLY_UPLOADED);
+        feedSource = new FeedSource(table + " Normalize Field Test Feed", project.id, FeedRetrievalMethod.MANUALLY_UPLOADED);
         feedSource.deployable = false;
-        feedSource.transformRules.add(transformRules);
+        feedSource.transformRules.add(new FeedTransformRules(transformation));
         Persistence.feedSources.create(feedSource);
     }
 
     // FIXME: Refactor (almost same code as AutoDeployJobTest in PR #361,
     //        and some common code with PersistenceTest#createProject).
     private static Project createProject() {
         Project project = new Project();
-        project.name = String.format("Test Project %s", new Date().toString());
+        project.name = String.format("Test Project %s", new Date());
         Persistence.projects.create(project);
         return project;
     }
+
+    private static class TransformationCase {
+        public String table;
+        public String fieldName;
+        public String pattern;
+        public String replacement;
+
+        public TransformationCase(String table, String fieldName, String pattern, String replacement) {
+            this.table = table;
+            this.fieldName = fieldName;
+            this.pattern = pattern;
+            this.replacement = replacement;
+        }
+    }
 }

src/test/resources/com/conveyal/datatools/gtfs/fake-agency-for-field-normalizing/areas.txt

@@ -0,0 +1,2 @@
+area_id,area_name
+Area One,"This is area one"

src/test/resources/com/conveyal/datatools/gtfs/fake-agency-for-field-normalizing/booking_rules.txt

@@ -0,0 +1,2 @@
+booking_rule_id,booking_type,prior_notice_duration_min,prior_notice_duration_max,prior_notice_last_day,prior_notice_last_time,prior_notice_start_day,prior_notice_start_time,prior_notice_service_id,message,pickup_message,drop_off_message,phone_number,info_url,booking_url
+Booking 1,1,30,60,1,17:00:00,7,00:00:00,"04100312-8fe1-46a5-a9f2-556f39478f57","This is a message","This is a pickup message","This is a drop off message","123456789","http://www.info_url.com","http://www.booking_url.com"

src/test/resources/com/conveyal/datatools/gtfs/fake-agency-for-field-normalizing/routes.txt

@@ -0,0 +1,3 @@
+agency_id,route_id,route_short_name,route_long_name,route_desc,route_type,route_url,route_color,route_text_color,route_branding_url
+1,1,1,Route 1,,3,,7CE6E7,FFFFFF,
+1,2,2,Route 2,,3,,7CE6E7,FFFFFF,

src/test/resources/com/conveyal/datatools/gtfs/fake-agency-for-field-normalizing/stops.txt

@@ -0,0 +1,2 @@
+stop_id,stop_code,stop_name,stop_desc,stop_lat,stop_lon,zone_id,stop_url,location_type,parent_station,stop_timezone,wheelchair_boarding
+4u6g,4u6g,Butler Ln,,37.0612132,-122.0074332,,,0,,,

src/test/resources/com/conveyal/datatools/gtfs/fake-agency-for-field-normalizing/trips.txt

@@ -0,0 +1,3 @@
+route_id,trip_id,trip_headsign,trip_short_name,direction_id,block_id,shape_id,bikes_allowed,wheelchair_accessible,service_id
+1,only-calendar-trip1,,,0,,,0,0,common_id
+2,only-calendar-trip2,,,0,,,0,0,common_id