Implement process reports

Refactors tests & move parser functionality out of KafkaTopology.kt.

.gitlab-ci.yml

@@ -11,7 +11,7 @@ test:
   tags:
     - mbr
   script:
-    - gradle --no-daemon --no-scan --no-build-cache test --fail-fast --tests "org.memobase.Tests"
+    - gradle --no-daemon --no-scan --no-build-cache test --fail-fast
 
 
 .build-image:

src/main/kotlin/App.kt

@@ -24,7 +24,8 @@ import org.apache.logging.log4j.LogManager
 class App {
     companion object {
         private val log = LogManager.getLogger("TableDataTransformApp")
-        @JvmStatic fun main(args: Array<String>) {
+        @JvmStatic
+        fun main(args: Array<String>) {
             try {
                 Service().run()
             } catch (ex: Exception) {

src/main/kotlin/Service.kt

@@ -26,15 +26,15 @@ class Service(file: String = "app.yml") {
     private val log = LogManager.getLogger("TableDataService")
 
     val settings = SettingsLoader(
-        listOf(
-            "sheet",
-            "header.count",
-            "header.line",
-            "identifier"
-        ),
-        file,
-        useStreamsConfig = true,
-        readSftpSettings = true
+            listOf(
+                    "sheet",
+                    "header.count",
+                    "header.line",
+                    "identifier"
+            ),
+            file,
+            useStreamsConfig = true,
+            readSftpSettings = true
     )
 
     val topology = KafkaTopology(settings).build()

src/main/kotlin/TableParser.kt

+/*
+ * Table Data Import Service
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package org.memobase
+
+import com.beust.klaxon.json
+import com.github.doyaaaaaken.kotlincsv.dsl.csvReader
+import java.io.File
+import org.apache.poi.ss.usermodel.CellType
+import org.apache.poi.ss.usermodel.WorkbookFactory
+import org.memobase.UtilityFunctions.retrieveCellValue
+import org.memobase.UtilityFunctions.retrieveCells
+import org.memobase.UtilityFunctions.zip
+import org.memobase.models.ErrorResult
+import org.memobase.models.Formats
+import org.memobase.models.Message
+import org.memobase.models.ParserResult
+import org.memobase.models.ProcessReport
+import org.memobase.models.Report
+import org.memobase.models.ReportMessages
+import org.memobase.models.ReportStatus
+import org.memobase.models.ResultMessage
+import org.memobase.settings.SettingsLoader
+import org.memobase.sftp.SftpClient
+
+class TableParser(settings: SettingsLoader) {
+    private val sftpClient: SftpClient = SftpClient(settings.sftpSettings)
+    private val sheetIndex = settings.appSettings.getProperty("sheet").toInt()
+    private val headerCount = settings.appSettings.getProperty("header.count").toInt()
+    private val propertyNamesIndex = settings.appSettings.getProperty("header.line").toInt()
+    private val identifierIndex = settings.appSettings.getProperty("identifier").toInt()
+
+    private val invalidPropertyNameCharacters = listOf('.', ':', '/', '+')
+
+    fun parseTable(key: String, inputMessage: Message): ParserResult {
+        return try {
+            val result: List<ResultMessage> = when (inputMessage.format) {
+                Formats.xls, Formats.xlsx -> excelMapper(key, inputMessage)
+                Formats.csv, Formats.tsv -> csvMapper(key, inputMessage)
+                else -> throw InvalidInputException(key, "Cannot parse the table with format ${inputMessage.format}.")
+            }
+
+            val failureCount = result.count { value -> value.report.status == ReportStatus.failure }
+            ParserResult(
+                    result,
+                    ProcessReport(
+                            "table-data-transform",
+                            ReportStatus.success,
+                            result.size,
+                            result.size - failureCount,
+                            failureCount
+                    )
+            )
+        } catch (ex: InvalidInputException) {
+            ParserResult(
+                    ex.key, ErrorResult.get(), Report(ex.key, ReportStatus.failure, ex.message ?: "Unknown issue."),
+                    ProcessReport(ReportStatus.failure, 1)
+            )
+        } catch (ex: IllegalArgumentException) { // Sheet index does not exist
+            ParserResult(
+                    key, ErrorResult.get(), Report(key, ReportStatus.failure, ex.localizedMessage),
+                    ProcessReport(ReportStatus.failure, 1)
+            )
+        }
+    }
+
+    private fun csvMapper(key: String, value: Message): List<ResultMessage> {
+        val resultMessages = mutableListOf<ResultMessage>()
+        val mutableSet = mutableSetOf<String>()
+        sftpClient.open(File(value.path)).use { inputStream ->
+            val reader =
+                    csvReader {
+                        this.quoteChar = '"'
+                        this.delimiter = if (value.format == Formats.csv) ',' else '\t'
+                        this.charset = Charsets.UTF_8.displayName()
+                        // this.skipEmptyLine = true
+                    }.readAll(inputStream)
+            var headerProperties = emptyList<String>()
+            var count = 0
+            for (line in reader) {
+                count += 1
+                if (count <= headerCount) {
+                    if (count == propertyNamesIndex) {
+                        headerProperties = line
+                        headerProperties.forEachIndexed { index, property ->
+                            val trimmedProperty = property.trim()
+                            if (trimmedProperty.isEmpty()) {
+                                throw InvalidInputException(
+                                        key,
+                                        "Missing a property name on row $count in column ${index + 1}!"
+                                )
+                            }
+                            if (trimmedProperty.any { value -> invalidPropertyNameCharacters.contains(value) }) {
+                                throw InvalidInputException(
+                                        key,
+                                        "Invalid property name $trimmedProperty on row $count in column ${index + 1}! You may not use the any of the following characters: + , . "
+                                )
+                            }
+                        }
+                    }
+                    continue
+                }
+                // the -1 ensures, that users can start columns beginning at 1!
+                val identifier: String = try {
+                    line[identifierIndex - 1].let { value ->
+                        when (value) {
+                            "" -> {
+                                throw InvalidInputException(
+                                        "$count.$identifierIndex",
+                                        "The row $count has an empty identifier in column $identifierIndex."
+                                )
+                            }
+                            in mutableSet -> {
+                                throw InvalidInputException(
+                                        "$count.$identifierIndex",
+                                        "The row $count contains a duplicated identifier in column $identifierIndex with another row."
+                                )
+                            }
+                            else -> {
+                                mutableSet.add(value)
+                                value
+                            }
+                        }
+                    }
+                } catch (ex: InvalidInputException) {
+                    resultMessages.add(
+                            ResultMessage(
+                                    ex.key,
+                                    ErrorResult.get(),
+                                    Report(
+                                            ex.key,
+                                            ReportStatus.failure,
+                                            ReportMessages.reportFailure(ex.localizedMessage)
+                                    )
+                            )
+                    )
+                    continue
+                }
+                val keyValueMap = json {
+                    obj(
+                            zip(headerProperties, line)
+                    )
+                }
+                val report = Report(
+                        identifier,
+                        ReportStatus.success,
+                        ReportMessages.reportSuccess(identifier, count)
+                )
+                resultMessages.add(ResultMessage(identifier, keyValueMap, report))
+            }
+        }
+        return resultMessages
+    }
+
+    private fun excelMapper(key: String, value: Message): List<ResultMessage> {
+        return sftpClient.open(File(value.path)).use { inputStream ->
+            WorkbookFactory.create(inputStream).use { workbook ->
+                val identifierSet = mutableSetOf<String>()
+                val propertiesList = mutableListOf<String>()
+                // sheet index is 0-based. This ensures that users can access sheet 1 with index 1!
+                val sheet = workbook.getSheetAt(sheetIndex - 1)
+                var count = 0
+                sheet.filter { row ->
+                    row.any { cell ->
+                        // filter all rows with no string, boolean or numeric cell
+                        when (cell.cellType) {
+                            CellType._NONE -> false
+                            CellType.NUMERIC -> true
+                            CellType.STRING -> true
+                            CellType.FORMULA -> false
+                            CellType.BLANK -> false
+                            CellType.BOOLEAN -> true
+                            CellType.ERROR -> false
+                            else -> false
+                        }
+                    }
+                }.map { row ->
+                    count += 1
+                    if (count <= headerCount) {
+                        if (count == propertyNamesIndex) {
+                            propertiesList.addAll(row.map { cell ->
+                                if (retrieveCellValue(cell).isNotEmpty()) {
+                                    if (retrieveCellValue(cell).any { char ->
+                                                invalidPropertyNameCharacters.contains(
+                                                        char
+                                                )
+                                            }) {
+                                        throw InvalidInputException(
+                                                key,
+                                                "The property in cell ${cell.address} contains one or more invalid characters: $invalidPropertyNameCharacters."
+                                        )
+                                    } else {
+                                        retrieveCellValue(cell)
+                                    }
+                                } else {
+                                    throw InvalidInputException(
+                                            key,
+                                            "The header index is missing a value in cell ${cell.address}"
+                                    )
+                                }
+                            }.map { it.trim() })
+                        }
+                        null
+                    } else {
+                        val rowIdentifier: String = try {
+                            row.getCell(identifierIndex - 1).let { cell ->
+                                if (cell != null) {
+                                    when (val cellValue = retrieveCellValue(cell)) {
+                                        "" -> {
+                                            throw InvalidInputException(
+                                                    "CellAddress: $count:$identifierIndex",
+                                                    "The row ${row.rowNum} has an empty identifier in column $identifierIndex."
+                                            )
+                                        }
+                                        in identifierSet -> {
+                                            throw InvalidInputException(
+                                                    "CellAddress: $count:$identifierIndex",
+                                                    "The row ${row.rowNum} contains a duplicated identifier in column $identifierIndex with another row."
+                                            )
+                                        }
+                                        else -> {
+                                            identifierSet.add(cellValue)
+                                            cellValue
+                                        }
+                                    }
+                                } else {
+                                    throw InvalidInputException(
+                                            "${row.rowNum}.$identifierIndex",
+                                            "No cell found in row ${row.rowNum} for column $identifierIndex."
+                                    )
+                                }
+                            }
+                        } catch (ex: InvalidInputException) {
+                            return@map ResultMessage(
+                                    ex.key, ErrorResult.get(), Report(
+                                    ex.key,
+                                    ReportStatus.failure,
+                                    ReportMessages.reportFailure(ex.localizedMessage)
+                            )
+                            )
+                        }
+
+                        val jsonObject = json {
+                            obj(
+                                    zip(
+                                            propertiesList,
+                                            retrieveCells(row, propertiesList.size - 1)
+                                    )
+                            )
+                        }
+                        ResultMessage(
+                                rowIdentifier, jsonObject, Report(
+                                rowIdentifier,
+                                ReportStatus.success,
+                                ReportMessages.reportSuccess(rowIdentifier, count)
+                        )
+                        )
+                    }
+                    // Empty rows create a null result. These are removed.
+                }.filterNotNull()
+            }
+        }
+    }
+}

src/main/kotlin/UtilityFunctions.kt

+/*
+ * Table Data Import Service
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package org.memobase
+
+import org.apache.poi.ss.usermodel.Cell
+import org.apache.poi.ss.usermodel.CellType
+import org.apache.poi.ss.usermodel.Row
+
+object UtilityFunctions {
+
+    /**
+     * Retrieves cells from a row of excel. Restricts the size to the actually
+     * used part of sheet as otherwise the row is many time larger with many empty cells.
+     *
+     * @param row: The row from which to retrieve cells.
+     * @param size: The number of cells active in the sheet.
+     *
+     * @return A list of the cell values as strings.
+     */
+    fun retrieveCells(row: Row, size: Int): List<String> {
+        return (0..size).map { i ->
+            val cell = row.getCell(i)
+            retrieveCellValue(cell)
+        }
+    }
+
+    /**
+     * Checks a cell and returns the content as string. If no valid value is found an empty
+     * string is returned.
+     *
+     * In case of a numeric value, the number is either interpreted as a time (if the number is below one) or
+     * as an integer.
+     *
+     * @param cell: A potential cell.
+     * @return Content of the cell as a string.
+     */
+    fun retrieveCellValue(cell: Cell?): String {
+        return if (cell != null) {
+            when (cell.cellType) {
+                CellType.BLANK -> ""
+                CellType.BOOLEAN -> cell.booleanCellValue.toString()
+                CellType._NONE -> ""
+                CellType.NUMERIC ->
+                    if (cell.numericCellValue >= 1) {
+                        cell.numericCellValue.toLong().toString()
+                    } else {
+                        cell.localDateTimeCellValue.toLocalTime().toString()
+                    }
+                CellType.STRING -> cell.stringCellValue
+                CellType.FORMULA -> ""
+                CellType.ERROR -> ""
+                else -> ""
+            }
+        } else ""
+    }
+
+    /**
+     * Creates pairs from header + line values in the same column.
+     *
+     * @param header: A list of all properties
+     * @param line: The content of the current line.
+     */
+    fun zip(header: List<String>, line: List<String>): List<Pair<String, String>> {
+        val result = mutableListOf<Pair<String, String>>()
+        header.forEachIndexed { index, s ->
+            if (line[index].isNotEmpty()) {
+                result.add(Pair(s, line[index].trim()))
+            }
+        }
+        return result
+    }
+}

src/main/kotlin/models/ErrorResult.kt

+/*
+ * Table Data Import Service
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package org.memobase.models
+
+import com.beust.klaxon.json
+
+object ErrorResult {
+    fun get() = json {
+        obj(Pair("message", Formats.error))
+    }
+}

src/main/kotlin/models/Formats.kt

+/*
+ * Table Data Import Service
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package org.memobase.models
+
+object Formats {
+    const val csv = "CSV"
+    const val tsv = "TSV"
+    const val xlsx = "XLSX"
+    const val xls = "XLS"
+    const val ods = "ODS"
+    const val invalid = "INVALID"
+    const val error = "ERROR"
+}

src/main/kotlin/models/Message.kt

+/*
+ * Table Data Import Service
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package org.memobase.models
+
+import com.beust.klaxon.Klaxon
+
+data class Message(
+    val format: String,
+    val path: String
+) {
+    fun toJson(): String {
+        return Klaxon().toJsonString(this)
+    }
+}

src/main/kotlin/models/ParserResult.kt

+/*
+ * Table Data Import Service
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package org.memobase.models
+
+import com.beust.klaxon.JsonObject
+
+data class ParserResult(
+    val messages: List<ResultMessage>,
+    val processReport: ProcessReport
+) {
+    constructor(key: String, jsonObject: JsonObject, report: Report, processReport: ProcessReport) : this(
+            listOf(ResultMessage(key, jsonObject, report)),
+            processReport
+    )
+}

src/main/kotlin/models/ProcessReport.kt

+/*
+ * Table Data Import Service
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package org.memobase.models
+
+import com.beust.klaxon.Klaxon
+
+data class ProcessReport(
+    val id: String = "table-data-transform",
+    val status: String,
+    val total: Int,
+    val successes: Int,
+    val failures: Int
+) {
+    constructor(status: String, total: Int) : this(
+            "table-data-transform",
+            status,
+            total,
+            if (ReportStatus.success == status) total else 0,
+            if (ReportStatus.failure == status) total else 0
+    )
+
+    fun toJson(): String {
+        return Klaxon().toJsonString(this)
+    }
+}

src/main/kotlin/Report.kt → src/main/kotlin/models/Report.kt

 /*
- * sftp-reader
+ * Table Data Import Service
  * Copyright (C) 2020 Memoriav
  *
  * This program is free software: you can redistribute it and/or modify
@@ -16,25 +16,16 @@
  * along with this program.  If not, see <https://www.gnu.org/licenses/>.
  */
 
-package org.memobase
+package org.memobase.models
+
+import com.beust.klaxon.Klaxon
 
 data class Report(
-    val id: String,
-    val status: String,
-    val message: String
+        val id: String,
+        val status: String,