merge: Integrate v2.1 progress into public repository

This pull request integrates the changes planned for the v2.1 release of
OpenDC into the public Github repository in order to sync the progress
of both repositories.

6 files changed, 472 insertions, 0 deletions

diff --git a/opendc-trace/opendc-trace-gwf/build.gradle.kts b/opendc-trace/opendc-trace-gwf/build.gradle.kts
new file mode 100644
index 00000000..f3dfd6ef
--- /dev/null
+++ b/opendc-trace/opendc-trace-gwf/build.gradle.kts
@@ -0,0 +1,37 @@
+/*
+ * Copyright (c) 2021 AtLarge Research
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+description = "Support for GWF traces in OpenDC"
+
+/* Build configuration */
+plugins {
+    `kotlin-library-conventions`
+    `testing-conventions`
+    `jacoco-conventions`
+}
+
+dependencies {
+    api(platform(projects.opendcPlatform))
+    api(projects.opendcTrace.opendcTraceApi)
+
+    implementation(libs.jackson.dataformat.csv)
+}
diff --git a/opendc-trace/opendc-trace-gwf/src/main/kotlin/org/opendc/trace/gwf/GwfTaskTableReader.kt b/opendc-trace/opendc-trace-gwf/src/main/kotlin/org/opendc/trace/gwf/GwfTaskTableReader.kt
new file mode 100644
index 00000000..aa4c543b
--- /dev/null
+++ b/opendc-trace/opendc-trace-gwf/src/main/kotlin/org/opendc/trace/gwf/GwfTaskTableReader.kt
@@ -0,0 +1,209 @@
+/*
+ * Copyright (c) 2021 AtLarge Research
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package org.opendc.trace.gwf
+
+import com.fasterxml.jackson.core.JsonToken
+import com.fasterxml.jackson.dataformat.csv.CsvParser
+import com.fasterxml.jackson.dataformat.csv.CsvSchema
+import org.opendc.trace.*
+import java.time.Duration
+import java.time.Instant
+import java.util.regex.Pattern
+
+/**
+ * A [TableReader] implementation for the GWF format.
+ */
+internal class GwfTaskTableReader(private val parser: CsvParser) : TableReader {
+    init {
+        parser.schema = schema
+    }
+
+    override fun nextRow(): Boolean {
+        // Reset the row state
+        reset()
+
+        if (!nextStart()) {
+            return false
+        }
+
+        while (true) {
+            val token = parser.nextValue()
+
+            if (token == null || token == JsonToken.END_OBJECT) {
+                break
+            }
+
+            when (parser.currentName) {
+                "WorkflowID" -> workflowId = parser.text
+                "JobID" -> jobId = parser.text
+                "SubmitTime" -> submitTime = Instant.ofEpochSecond(parser.longValue)
+                "RunTime" -> runtime = Duration.ofSeconds(parser.longValue)
+                "NProcs" -> nProcs = parser.intValue
+                "ReqNProcs" -> reqNProcs = parser.intValue
+                "Dependencies" -> parseParents(parser.valueAsString)
+            }
+        }
+
+        return true
+    }
+
+    override fun resolve(column: TableColumn<*>): Int = columns[column] ?: -1
+
+    override fun isNull(index: Int): Boolean {
+        check(index in 0..columns.size) { "Invalid column" }
+        return false
+    }
+
+    override fun get(index: Int): Any? {
+        return when (index) {
+            COL_JOB_ID -> jobId
+            COL_WORKFLOW_ID -> workflowId
+            COL_SUBMIT_TIME -> submitTime
+            COL_RUNTIME -> runtime
+            COL_REQ_NPROC -> getInt(index)
+            COL_NPROC -> getInt(index)
+            COL_DEPS -> dependencies
+            else -> throw IllegalArgumentException("Invalid column")
+        }
+    }
+
+    override fun getBoolean(index: Int): Boolean {
+        throw IllegalArgumentException("Invalid column")
+    }
+
+    override fun getInt(index: Int): Int {
+        return when (index) {
+            COL_REQ_NPROC -> reqNProcs
+            COL_NPROC -> nProcs
+            else -> throw IllegalArgumentException("Invalid column")
+        }
+    }
+
+    override fun getLong(index: Int): Long {
+        throw IllegalArgumentException("Invalid column")
+    }
+
+    override fun getDouble(index: Int): Double {
+        throw IllegalArgumentException("Invalid column")
+    }
+
+    override fun close() {
+        parser.close()
+    }
+
+    /**
+     * The pattern used to parse the parents.
+     */
+    private val pattern = Pattern.compile("\\s+")
+
+    /**
+     * Parse the parents into a set of longs.
+     */
+    private fun parseParents(value: String): Set<Long> {
+        val result = mutableSetOf<Long>()
+        val deps = value.split(pattern)
+
+        for (dep in deps) {
+            if (dep.isBlank()) {
+                continue
+            }
+
+            result.add(dep.toLong(10))
+        }
+
+        return result
+    }
+
+    /**
+     * Advance the parser until the next object start.
+     */
+    private fun nextStart(): Boolean {
+        var token = parser.nextValue()
+
+        while (token != null && token != JsonToken.START_OBJECT) {
+            token = parser.nextValue()
+        }
+
+        return token != null
+    }
+
+    /**
+     * Reader state fields.
+     */
+    private var workflowId: String? = null
+    private var jobId: String? = null
+    private var submitTime: Instant? = null
+    private var runtime: Duration? = null
+    private var nProcs = -1
+    private var reqNProcs = -1
+    private var dependencies = emptySet<Long>()
+
+    /**
+     * Reset the state.
+     */
+    private fun reset() {
+        workflowId = null
+        jobId = null
+        submitTime = null
+        runtime = null
+        nProcs = -1
+        reqNProcs = -1
+        dependencies = emptySet()
+    }
+
+    private val COL_WORKFLOW_ID = 0
+    private val COL_JOB_ID = 1
+    private val COL_SUBMIT_TIME = 2
+    private val COL_RUNTIME = 3
+    private val COL_NPROC = 4
+    private val COL_REQ_NPROC = 5
+    private val COL_DEPS = 6
+
+    private val columns = mapOf(
+        TASK_ID to COL_JOB_ID,
+        TASK_WORKFLOW_ID to COL_WORKFLOW_ID,
+        TASK_SUBMIT_TIME to COL_SUBMIT_TIME,
+        TASK_RUNTIME to COL_RUNTIME,
+        TASK_ALLOC_NCPUS to COL_NPROC,
+        TASK_REQ_NCPUS to COL_REQ_NPROC,
+        TASK_PARENTS to COL_DEPS
+    )
+
+    companion object {
+        /**
+         * The [CsvSchema] that is used to parse the trace.
+         */
+        private val schema = CsvSchema.builder()
+            .addColumn("WorkflowID", CsvSchema.ColumnType.NUMBER)
+            .addColumn("JobID", CsvSchema.ColumnType.NUMBER)
+            .addColumn("SubmitTime", CsvSchema.ColumnType.NUMBER)
+            .addColumn("RunTime", CsvSchema.ColumnType.NUMBER)
+            .addColumn("NProcs", CsvSchema.ColumnType.NUMBER)
+            .addColumn("ReqNProcs", CsvSchema.ColumnType.NUMBER)
+            .addColumn("Dependencies", CsvSchema.ColumnType.STRING)
+            .setAllowComments(true)
+            .setUseHeader(true)
+            .setColumnSeparator(',')
+            .build()
+    }
+}
diff --git a/opendc-trace/opendc-trace-gwf/src/main/kotlin/org/opendc/trace/gwf/GwfTraceFormat.kt b/opendc-trace/opendc-trace-gwf/src/main/kotlin/org/opendc/trace/gwf/GwfTraceFormat.kt
new file mode 100644
index 00000000..d4287420
--- /dev/null
+++ b/opendc-trace/opendc-trace-gwf/src/main/kotlin/org/opendc/trace/gwf/GwfTraceFormat.kt
@@ -0,0 +1,82 @@
+/*
+ * Copyright (c) 2021 AtLarge Research
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package org.opendc.trace.gwf
+
+import com.fasterxml.jackson.dataformat.csv.CsvFactory
+import com.fasterxml.jackson.dataformat.csv.CsvParser
+import org.opendc.trace.*
+import org.opendc.trace.spi.TableDetails
+import org.opendc.trace.spi.TraceFormat
+import java.nio.file.Path
+
+/**
+ * A [TraceFormat] implementation for the GWF trace format.
+ */
+public class GwfTraceFormat : TraceFormat {
+    /**
+     * The name of this trace format.
+     */
+    override val name: String = "gwf"
+
+    /**
+     * The [CsvFactory] used to create the parser.
+     */
+    private val factory = CsvFactory()
+        .enable(CsvParser.Feature.ALLOW_COMMENTS)
+        .enable(CsvParser.Feature.TRIM_SPACES)
+
+    override fun create(path: Path) {
+        throw UnsupportedOperationException("Writing not supported for this format")
+    }
+
+    override fun getTables(path: Path): List<String> = listOf(TABLE_TASKS)
+
+    override fun getDetails(path: Path, table: String): TableDetails {
+        return when (table) {
+            TABLE_TASKS -> TableDetails(
+                listOf(
+                    TASK_WORKFLOW_ID,
+                    TASK_ID,
+                    TASK_SUBMIT_TIME,
+                    TASK_RUNTIME,
+                    TASK_REQ_NCPUS,
+                    TASK_ALLOC_NCPUS,
+                    TASK_PARENTS,
+                ),
+                listOf(TASK_WORKFLOW_ID)
+            )
+            else -> throw IllegalArgumentException("Table $table not supported")
+        }
+    }
+
+    override fun newReader(path: Path, table: String): TableReader {
+        return when (table) {
+            TABLE_TASKS -> GwfTaskTableReader(factory.createParser(path.toFile()))
+            else -> throw IllegalArgumentException("Table $table not supported")
+        }
+    }
+
+    override fun newWriter(path: Path, table: String): TableWriter {
+        throw UnsupportedOperationException("Writing not supported for this format")
+    }
+}
diff --git a/opendc-trace/opendc-trace-gwf/src/main/resources/META-INF/services/org.opendc.trace.spi.TraceFormat b/opendc-trace/opendc-trace-gwf/src/main/resources/META-INF/services/org.opendc.trace.spi.TraceFormat
new file mode 100644
index 00000000..99a874c8
--- /dev/null
+++ b/opendc-trace/opendc-trace-gwf/src/main/resources/META-INF/services/org.opendc.trace.spi.TraceFormat
@@ -0,0 +1 @@
+org.opendc.trace.gwf.GwfTraceFormat
diff --git a/opendc-trace/opendc-trace-gwf/src/test/kotlin/org/opendc/trace/gwf/GwfTraceFormatTest.kt b/opendc-trace/opendc-trace-gwf/src/test/kotlin/org/opendc/trace/gwf/GwfTraceFormatTest.kt
new file mode 100644
index 00000000..7fe403b2
--- /dev/null
+++ b/opendc-trace/opendc-trace-gwf/src/test/kotlin/org/opendc/trace/gwf/GwfTraceFormatTest.kt
@@ -0,0 +1,72 @@
+/*
+ * Copyright (c) 2021 AtLarge Research
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package org.opendc.trace.gwf
+
+import org.junit.jupiter.api.*
+import org.junit.jupiter.api.Assertions.*
+import org.opendc.trace.*
+import java.nio.file.Paths
+import java.time.Duration
+import java.time.Instant
+
+/**
+ * Test suite for the [GwfTraceFormat] class.
+ */
+internal class GwfTraceFormatTest {
+    private val format = GwfTraceFormat()
+
+    @Test
+    fun testTables() {
+        val path = Paths.get(checkNotNull(GwfTraceFormatTest::class.java.getResource("/trace.gwf")).toURI())
+
+        assertEquals(listOf(TABLE_TASKS), format.getTables(path))
+    }
+
+    @Test
+    fun testTableExists() {
+        val path = Paths.get(checkNotNull(GwfTraceFormatTest::class.java.getResource("/trace.gwf")).toURI())
+        assertDoesNotThrow { format.getDetails(path, TABLE_TASKS) }
+    }
+
+    @Test
+    fun testTableDoesNotExist() {
+        val path = Paths.get(checkNotNull(GwfTraceFormatTest::class.java.getResource("/trace.gwf")).toURI())
+
+        assertThrows<IllegalArgumentException> { format.getDetails(path, "test") }
+    }
+
+    @Test
+    fun testTableReader() {
+        val path = Paths.get(checkNotNull(GwfTraceFormatTest::class.java.getResource("/trace.gwf")).toURI())
+        val reader = format.newReader(path, TABLE_TASKS)
+
+        assertAll(
+            { assertTrue(reader.nextRow()) },
+            { assertEquals("0", reader.get(TASK_WORKFLOW_ID)) },
+            { assertEquals("1", reader.get(TASK_ID)) },
+            { assertEquals(Instant.ofEpochSecond(16), reader.get(TASK_SUBMIT_TIME)) },
+            { assertEquals(Duration.ofSeconds(11), reader.get(TASK_RUNTIME)) },
+            { assertEquals(emptySet<String>(), reader.get(TASK_PARENTS)) },
+        )
+    }
+}
diff --git a/opendc-trace/opendc-trace-gwf/src/test/resources/trace.gwf b/opendc-trace/opendc-trace-gwf/src/test/resources/trace.gwf
new file mode 100644
index 00000000..2f99616d
--- /dev/null
+++ b/opendc-trace/opendc-trace-gwf/src/test/resources/trace.gwf
@@ -0,0 +1,71 @@
+WorkflowID, JobID     , SubmitTime, RunTime   , NProcs    , ReqNProcs , Dependencies
+0         , 1         , 16        , 11        , 1         , 1         ,           
+0         , 2         , 40        , 11        , 1         , 1         , 1         
+0         , 3         , 40        , 11        , 1         , 1         , 1         
+0         , 4         , 64        , 11        , 1         , 1         , 2         
+0         , 5         , 63        , 11        , 1         , 1         , 3         
+0         , 6         , 64        , 11        , 1         , 1         , 3         
+0         , 7         , 87        , 11        , 1         , 1         , 4 5 6     
+1         , 8         , 4         , 11        , 1         , 1         ,           
+1         , 9         , 15        , 11        , 1         , 1         , 8         
+1         , 10        , 15        , 11        , 1         , 1         , 8         
+1         , 11        , 27        , 11        , 1         , 1         , 9         
+1         , 12        , 27        , 11        , 1         , 1         , 10        
+1         , 13        , 27        , 11        , 1         , 1         , 10        
+1         , 14        , 38        , 11        , 1         , 1         , 12 11 13  
+2         , 15        , 3         , 11        , 1         , 1         ,           
+2         , 16        , 27        , 11        , 1         , 1         , 15        
+2         , 17        , 27        , 11        , 1         , 1         , 15        
+2         , 18        , 52        , 11        , 1         , 1         , 16        
+2         , 19        , 51        , 11        , 1         , 1         , 17        
+2         , 20        , 51        , 11        , 1         , 1         , 17        
+2         , 21        , 75        , 11        , 1         , 1         , 20 18 19  
+3         , 22        , 3         , 11        , 1         , 1         ,           
+3         , 23        , 27        , 11        , 1         , 1         , 22        
+3         , 24        , 27        , 11        , 1         , 1         , 22        
+3         , 25        , 51        , 11        , 1         , 1         , 23        
+3         , 26        , 50        , 11        , 1         , 1         , 24        
+3         , 27        , 51        , 11        , 1         , 1         , 24        
+3         , 28        , 75        , 11        , 1         , 1         , 25 27 26  
+4         , 29        , 3         , 11        , 1         , 1         ,           
+4         , 30        , 27        , 11        , 1         , 1         , 29        
+4         , 31        , 27        , 11        , 1         , 1         , 29        
+4         , 32        , 50        , 11        , 1         , 1         , 30        
+4         , 33        , 50        , 11        , 1         , 1         , 31        
+4         , 34        , 51        , 11        , 1         , 1         , 31        
+4         , 35        , 74        , 11        , 1         , 1         , 33 32 34  
+5         , 36        , 3         , 11        , 1         , 1         ,           
+5         , 37        , 27        , 11        , 1         , 1         , 36        
+5         , 38        , 26        , 11        , 1         , 1         , 36        
+5         , 39        , 51        , 11        , 1         , 1         , 37        
+5         , 40        , 50        , 11        , 1         , 1         , 38        
+5         , 41        , 50        , 11        , 1         , 1         , 38        
+5         , 42        , 74        , 11        , 1         , 1         , 39 40 41  
+6         , 43        , 4         , 11        , 1         , 1         ,           
+6         , 44        , 27        , 11        , 1         , 1         , 43        
+6         , 45        , 27        , 11        , 1         , 1         , 43        
+6         , 46        , 51        , 11        , 1         , 1         , 44        
+6         , 47        , 51        , 11        , 1         , 1         , 45        
+6         , 48        , 51        , 11        , 1         , 1         , 45        
+6         , 49        , 75        , 11        , 1         , 1         , 46 47 48  
+7         , 50        , 3         , 0         , 1         , 1         ,           
+7         , 51        , 17        , 0         , 1         , 1         , 50        
+7         , 52        , 17        , 0         , 1         , 1         , 50        
+7         , 53        , 30        , 0         , 1         , 1         , 51        
+7         , 54        , 30        , 0         , 1         , 1         , 52        
+7         , 55        , 31        , 0         , 1         , 1         , 52        
+7         , 56        , 44        , 0         , 1         , 1         , 55 54 53  
+8         , 57        , 3         , 11        , 1         , 1         ,           
+8         , 58        , 26        , 11        , 1         , 1         , 57        
+8         , 59        , 27        , 11        , 1         , 1         , 57        
+8         , 60        , 50        , 11        , 1         , 1         , 58        
+8         , 61        , 51        , 11        , 1         , 1         , 59        
+8         , 62        , 50        , 11        , 1         , 1         , 59        
+8         , 63        , 74        , 11        , 1         , 1         , 62 61 60  
+9         , 64        , 3         , 11        , 1         , 1         ,           
+9         , 65        , 27        , 11        , 1         , 1         , 64        
+9         , 66        , 27        , 11        , 1         , 1         , 64        
+9         , 67        , 51        , 11        , 1         , 1         , 65        
+9         , 68        , 50        , 11        , 1         , 1         , 66        
+9         , 69        , 51        , 11        , 1         , 1         , 66        
+9         , 70        , 74        , 11        , 1         , 1         , 68 69 67