| 1 | /** |
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| 2 | * Importer service |
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| 3 | * |
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| 4 | * The importer service handles the import of tabular, comma delimited and Excel format |
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| 5 | * based files. |
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| 6 | * |
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| 7 | * @package importer |
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| 8 | * @author t.w.abma@umcutrecht.nl |
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| 9 | * @since 20100126 |
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| 10 | * |
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| 11 | * Revision information: |
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| 12 | * $Rev: 1093 $ |
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| 13 | * $Author: t.w.abma@umcutrecht.nl $ |
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| 14 | * $Date: 2010-11-06 15:01:11 +0000 (za, 06 nov 2010) $ |
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| 15 | */ |
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| 16 | |
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| 17 | package dbnp.importer |
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| 18 | import org.apache.poi.ss.usermodel.* |
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| 19 | |
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| 20 | import dbnp.studycapturing.TemplateFieldType |
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| 21 | import dbnp.studycapturing.Template |
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| 22 | import dbnp.studycapturing.SamplingEvent |
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| 23 | import dbnp.studycapturing.Study |
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| 24 | import dbnp.studycapturing.Subject |
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| 25 | import dbnp.studycapturing.Event |
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| 26 | import dbnp.studycapturing.Sample |
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| 27 | |
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| 28 | class ImporterService { |
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| 29 | def AuthenticationService |
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| 30 | |
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| 31 | boolean transactional = true |
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| 32 | |
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| 33 | /** |
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| 34 | * @param is input stream representing the (workbook) resource |
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| 35 | * @return high level representation of the workbook |
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| 36 | */ |
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| 37 | Workbook getWorkbook(InputStream is) { |
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| 38 | WorkbookFactory.create(is) |
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| 39 | } |
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| 40 | |
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| 41 | /** |
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| 42 | * @param wb high level representation of the workbook |
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| 43 | * @param sheetindex sheet to use within the workbook |
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| 44 | * @return header representation as a MappingColumn hashmap |
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| 45 | */ |
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| 46 | def getHeader(Workbook wb, int sheetindex, int headerrow, int datamatrix_start, theEntity=null){ |
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| 47 | |
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| 48 | def sheet = wb.getSheetAt(sheetindex) |
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| 49 | def sheetrow = sheet.getRow(datamatrix_start) |
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| 50 | //def header = [] |
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| 51 | def header = [:] |
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| 52 | def df = new DataFormatter() |
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| 53 | def property = new String() |
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| 54 | |
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| 55 | //for (Cell c: sheet.getRow(datamatrix_start)) { |
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| 56 | |
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| 57 | (0..sheetrow.getLastCellNum() -1 ).each { columnindex -> |
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| 58 | |
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| 59 | //def index = c.getColumnIndex() |
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| 60 | def datamatrix_celltype = sheet.getRow(datamatrix_start).getCell(columnindex,Row.CREATE_NULL_AS_BLANK).getCellType() |
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| 61 | def datamatrix_celldata = df.formatCellValue(sheet.getRow(datamatrix_start).getCell(columnindex)) |
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| 62 | def datamatrix_cell = sheet.getRow(datamatrix_start).getCell(columnindex) |
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| 63 | def headercell = sheet.getRow(headerrow-1+sheet.getFirstRowNum()).getCell(columnindex) |
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| 64 | def tft = TemplateFieldType.STRING //default templatefield type |
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| 65 | |
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| 66 | // Check for every celltype, currently redundant code, but possibly this will be |
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| 67 | // a piece of custom code for every cell type like specific formatting |
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| 68 | |
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| 69 | switch (datamatrix_celltype) { |
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| 70 | case Cell.CELL_TYPE_STRING: |
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| 71 | //parse cell value as double |
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| 72 | def doubleBoolean = true |
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| 73 | def fieldtype = TemplateFieldType.STRING |
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| 74 | |
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| 75 | // is this string perhaps a double? |
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| 76 | try { |
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| 77 | formatValue(datamatrix_celldata, TemplateFieldType.DOUBLE) |
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| 78 | } catch (NumberFormatException nfe) { doubleBoolean = false } |
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| 79 | finally { |
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| 80 | if (doubleBoolean) fieldtype = TemplateFieldType.DOUBLE |
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| 81 | } |
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| 82 | |
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| 83 | header[columnindex] = new dbnp.importer.MappingColumn(name:df.formatCellValue(headercell), |
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| 84 | templatefieldtype:fieldtype, |
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| 85 | index:columnindex, |
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| 86 | entity:theEntity, |
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| 87 | property:property); |
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| 88 | |
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| 89 | break |
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| 90 | case Cell.CELL_TYPE_NUMERIC: |
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| 91 | def fieldtype = TemplateFieldType.INTEGER |
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| 92 | def doubleBoolean = true |
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| 93 | def integerBoolean = true |
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| 94 | |
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| 95 | // is this cell really an integer? |
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| 96 | try { |
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| 97 | Integer.valueOf(datamatrix_celldata) |
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| 98 | } catch (NumberFormatException nfe) { integerBoolean = false } |
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| 99 | finally { |
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| 100 | if (integerBoolean) fieldtype = TemplateFieldType.INTEGER |
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| 101 | } |
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| 102 | |
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| 103 | // it's not an integer, perhaps a double? |
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| 104 | if (!integerBoolean) |
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| 105 | try { |
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| 106 | formatValue(datamatrix_celldata, TemplateFieldType.DOUBLE) |
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| 107 | } catch (NumberFormatException nfe) { doubleBoolean = false } |
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| 108 | finally { |
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| 109 | if (doubleBoolean) fieldtype = TemplateFieldType.DOUBLE |
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| 110 | } |
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| 111 | |
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| 112 | if (DateUtil.isCellDateFormatted(datamatrix_cell)) fieldtype = TemplateFieldType.DATE |
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| 113 | |
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| 114 | header[columnindex] = new dbnp.importer.MappingColumn(name:df.formatCellValue(headercell), |
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| 115 | templatefieldtype:fieldtype, |
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| 116 | index:columnindex, |
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| 117 | entity:theEntity, |
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| 118 | property:property); |
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| 119 | break |
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| 120 | case Cell.CELL_TYPE_BLANK: |
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| 121 | header[columnindex] = new dbnp.importer.MappingColumn(name:df.formatCellValue(headercell), |
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| 122 | templatefieldtype:TemplateFieldType.STRING, |
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| 123 | index:columnindex, |
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| 124 | entity:theEntity, |
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| 125 | property:property); |
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| 126 | break |
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| 127 | default: |
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| 128 | header[columnindex] = new dbnp.importer.MappingColumn(name:df.formatCellValue(headercell), |
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| 129 | templatefieldtype:TemplateFieldType.STRING, |
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| 130 | index:columnindex, |
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| 131 | entity:theEntity, |
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| 132 | property:property); |
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| 133 | break |
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| 134 | } // end of switch |
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| 135 | } // end of cell loop |
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| 136 | return header |
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| 137 | } |
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| 138 | |
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| 139 | /** |
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| 140 | * This method is meant to return a matrix of the rows and columns |
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| 141 | * used in the preview |
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| 142 | * |
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| 143 | * @param wb workbook object |
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| 144 | * @param sheetindex sheet index used |
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| 145 | * @param rows amount of rows returned |
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| 146 | * @return two dimensional array (matrix) of Cell objects |
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| 147 | */ |
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| 148 | |
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| 149 | Cell[][] getDatamatrix(Workbook wb, header, int sheetindex, int datamatrix_start, int count) { |
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| 150 | def sheet = wb.getSheetAt(sheetindex) |
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| 151 | def rows = [] |
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| 152 | def df = new DataFormatter() |
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| 153 | |
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| 154 | // walk through all rows |
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| 155 | (count <= sheet.getLastRowNum()) ? |
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| 156 | ((datamatrix_start+sheet.getFirstRowNum())..count).each { rowindex -> |
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| 157 | def row = [] |
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| 158 | |
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| 159 | // walk through every cell |
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| 160 | /*for (Cell c: sheet.getRow(rowindex)) { |
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| 161 | row.add(c) |
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| 162 | println c.getColumnIndex() + "=" +c |
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| 163 | }*/ |
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| 164 | |
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| 165 | (0..header.size()-1).each { columnindex -> |
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| 166 | def c = sheet.getRow(rowindex).getCell(columnindex, Row.CREATE_NULL_AS_BLANK) |
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| 167 | //row.add(df.formatCellValue(c)) |
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| 168 | row.add(c) |
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| 169 | //if (c.getCellType() == c.CELL_TYPE_STRING) println "STR"+c.getStringCellValue() |
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| 170 | //if (c.getCellType() == c.CELL_TYPE_NUMERIC) println "INT" +c.getNumericCellValue() |
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| 171 | } |
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| 172 | //row.add(df.formatCellValue(c)) |
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| 173 | rows.add(row) |
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| 174 | } : 0 |
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| 175 | |
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| 176 | return rows |
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| 177 | } |
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| 178 | |
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| 179 | /** |
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| 180 | * This method will move a file to a new location. |
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| 181 | * |
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| 182 | * @param file File object to move |
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| 183 | * @param folderpath folder to move the file to |
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| 184 | * @param filename (new) filename to give |
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| 185 | * @return if file has been moved succesful, the new path and filename will be returned, otherwise an empty string will be returned |
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| 186 | */ |
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| 187 | def moveFile(File file, String folderpath, String filename) { |
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| 188 | try { |
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| 189 | def rnd = ""; //System.currentTimeMillis() |
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| 190 | file.transferTo(new File(folderpath, rnd+filename)) |
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| 191 | return folderpath + filename |
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| 192 | } catch(Exception exception) { |
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| 193 | log.error "File move error, ${exception}" |
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| 194 | return "" |
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| 195 | } |
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| 196 | } |
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| 197 | |
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| 198 | /** |
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| 199 | * @return random numeric value |
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| 200 | */ |
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| 201 | def random = { |
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| 202 | return System.currentTimeMillis() + Runtime.runtime.freeMemory() |
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| 203 | } |
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| 204 | |
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| 205 | /** |
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| 206 | * Method to read data from a workbook and to import data into a two dimensional |
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| 207 | * array |
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| 208 | * |
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| 209 | * @param template_id template identifier to use fields from |
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| 210 | * @param wb POI horrible spreadsheet formatted workbook object |
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| 211 | * @param mcmap linked hashmap (preserved order) of MappingColumns |
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| 212 | * @param sheetindex sheet to use when using multiple sheets |
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| 213 | * @param rowindex first row to start with reading the actual data (NOT the header) |
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| 214 | * @return two dimensional array containing records (with entities) |
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| 215 | * |
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| 216 | * @see dbnp.importer.MappingColumn |
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| 217 | */ |
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| 218 | def importData(template_id, Workbook wb, int sheetindex, int rowindex, mcmap) { |
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| 219 | def sheet = wb.getSheetAt(sheetindex) |
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| 220 | def table = [] |
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| 221 | def failedcells = [:] // map [recordhash, [mappingcolumnlist]] values |
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| 222 | |
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| 223 | // walk through all rows and fill the table with records |
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| 224 | (rowindex..sheet.getLastRowNum()).each { i -> |
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| 225 | //table.add(createRecord(template_id, sheet.getRow(i), mcmap)) |
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| 226 | // Create an entity record based on a row read from Excel and store the cells which failed to be mapped |
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| 227 | def (record, failed) = createRecord(template_id, sheet.getRow(i), mcmap) |
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| 228 | |
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| 229 | // Add record with entity and its values to the table |
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| 230 | table.add(record) |
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| 231 | |
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| 232 | // If failed cells have been found, add them to the failed cells map |
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| 233 | // the record hashcode is later on used to put the failed data back |
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| 234 | // in the data matrix |
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| 235 | if (failed.size()!=0) failedcells.put(record.hashCode(), failed) |
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| 236 | } |
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| 237 | |
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| 238 | failedcells.each { record -> |
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| 239 | record.each { cell -> |
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| 240 | cell.each { |
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| 241 | println it.value.dump() |
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| 242 | } |
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| 243 | } |
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| 244 | } |
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| 245 | |
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| 246 | |
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| 247 | return [table,failedcells] |
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| 248 | } |
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| 249 | |
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| 250 | /** Method to put failed cells back into the datamatrix. Failed cells are cell values |
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| 251 | * which could not be stored in an entity (e.g. Humu Supiuns in an ontology field). |
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| 252 | * Empty corrections should not be stored |
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| 253 | * |
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| 254 | * @param datamatrix two dimensional array containing entities and possibly also failed cells |
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| 255 | * @param failedcells list with maps of failed cells in [mappingcolumn, cell] format |
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| 256 | * @param correctedcells map of corrected cells in [cellhashcode, value] format |
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| 257 | **/ |
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| 258 | def saveCorrectedCells(datamatrix, failedcells, correctedcells) { |
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| 259 | // Loop through all failed cells |
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| 260 | failedcells.each { mcrecord -> |
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| 261 | mcrecord.each { mappingcolumn -> |
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| 262 | // Get the corrected value |
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| 263 | def correctedvalue = correctedcells.find { it.key.toInteger() == mappingcolumn.hashCode()}.value |
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| 264 | |
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| 265 | // Find the record in the table which the mappingcolumn belongs to |
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| 266 | def tablerecord = datamatrix.find { it.hashCode() == mcrecord.key } |
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| 267 | |
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| 268 | // Loop through all entities in the record |
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| 269 | tablerecord.each { rec -> |
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| 270 | rec.each { entity -> |
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| 271 | try { |
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| 272 | // Update the entity field |
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| 273 | entity.setFieldValue(mappingcolumn.value.property[0], correctedvalue) |
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| 274 | println "Adjusted " + mappingcolumn.value.property[0] + " to " + correctedvalue |
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| 275 | } |
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| 276 | catch (Exception e) { |
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| 277 | println "Could not map corrected ontology" |
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| 278 | } |
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| 279 | } |
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| 280 | } // end of table record |
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| 281 | } // end of mapping record |
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| 282 | } // end of failed cells loop |
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| 283 | } |
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| 284 | |
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| 285 | /** |
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| 286 | * Method to store a matrix containing the entities in a record like structure. Every row in the table |
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| 287 | * contains one or more entity objects (which contain fields with values). So actually a row represents |
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| 288 | * a record with fields from one or more different entities. |
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| 289 | * |
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| 290 | * @param study entity Study |
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| 291 | * @param datamatrix two dimensional array containing entities with values read from Excel file |
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| 292 | */ |
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| 293 | def saveDatamatrix(Study study, datamatrix) { |
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| 294 | def validatedSuccesfully = 0 |
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| 295 | def entitystored = null |
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| 296 | study.refresh() |
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| 297 | |
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| 298 | // go through the data matrix, read every record and validate the entity and try to persist it |
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| 299 | datamatrix.each { record -> |
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| 300 | record.each { entity -> |
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| 301 | switch (entity.getClass()) { |
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| 302 | case Study : print "Persisting Study `" + entity + "`: " |
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| 303 | entity.owner = AuthenticationService.getLoggedInUser() |
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| 304 | if (persistEntity(entity)) validatedSuccesfully++ |
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| 305 | break |
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| 306 | case Subject : print "Persisting Subject `" + entity + "`: " |
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| 307 | entity.parent = study |
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| 308 | |
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| 309 | // is the current entity not already in the database? |
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| 310 | entitystored = isEntityStored(entity) |
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| 311 | |
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| 312 | // this entity is new, so add it to the study |
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| 313 | if (entitystored==null) study.addToSubjects(entity) |
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| 314 | else // existing entity, so update it |
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| 315 | updateEntity(entitystored, entity) |
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| 316 | |
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| 317 | if (persistEntity(study)) validatedSuccesfully++ |
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| 318 | break |
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| 319 | case Event : print "Persisting Event `" + entity + "`: " |
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| 320 | entity.parent = study |
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| 321 | study.addToEvents(entity) |
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| 322 | if (persistEntity(entity)) validatedSuccesfully++ |
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| 323 | break |
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| 324 | case Sample : print "Persisting Sample `" + entity +"`: " |
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| 325 | entity.parent = study |
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| 326 | study.addToSamples(entity) |
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| 327 | if (persistEntity(entity)) validatedSuccesfully++ |
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| 328 | break |
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| 329 | case SamplingEvent: print "Persisting SamplingEvent `" + entity + "`: " |
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| 330 | entity.parent = study |
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| 331 | study.addToSamplingEvents(entity) |
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| 332 | if (persistEntity(entity)) validatedSuccesfully++ |
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| 333 | break |
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| 334 | default : println "Skipping persisting of `" + entity.getclass() +"`" |
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| 335 | break |
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| 336 | } // end switch |
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| 337 | } // end record |
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| 338 | } // end datamatrix |
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| 339 | return validatedSuccesfully |
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| 340 | } |
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| 341 | |
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| 342 | /** |
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| 343 | * Check whether an entity already exist. A unique field in the entity is |
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| 344 | * used to check whether the instantiated entity (read from Excel) is new. |
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| 345 | * If the entity is found in the database it will be returned as is. |
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| 346 | * |
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| 347 | * @param entity entity object like a Study, Subject, Sample et cetera |
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| 348 | * @return entity if found, otherwise null |
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| 349 | */ |
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| 350 | def isEntityStored(entity) { |
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| 351 | switch (entity.getClass()) { |
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| 352 | case Study : return Study.findByCode(entity.code) |
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| 353 | break |
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| 354 | case Subject : return Subject.findByParentAndName(entity.parent, entity.name) |
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| 355 | break |
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| 356 | case Event : break |
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| 357 | case Sample : break |
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| 358 | case SamplingEvent : break |
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| 359 | default : // unknown entity |
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| 360 | return null |
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| 361 | } |
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| 362 | } |
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| 363 | |
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| 364 | /** |
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| 365 | * Find the entity and update the fields. The entity is an instance |
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| 366 | * read from Excel. This method looks in the database for the entity |
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| 367 | * having the same identifier. If it has found the same entity |
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| 368 | * already in the database, it will update the record. |
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| 369 | * |
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| 370 | * @param entitystored existing record in the database to update |
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| 371 | * @param entity entity read from Excel |
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| 372 | */ |
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| 373 | def updateEntity(entitystored, entity) { |
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| 374 | switch (entity.getClass()) { |
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| 375 | case Study : break |
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| 376 | case Subject : entitystored.properties = entity.properties |
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| 377 | entitystored.save() |
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| 378 | break |
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| 379 | case Event : break |
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| 380 | case Sample : break |
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| 381 | case SamplingEvent : break |
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| 382 | default : // unknown entity |
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| 383 | return null |
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| 384 | } |
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| 385 | } |
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| 386 | |
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| 387 | /** |
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| 388 | * Method to persist entities into the database |
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| 389 | * Checks whether entity already exists (based on identifier column 'name') |
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| 390 | * |
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| 391 | * @param entity entity object like Study, Subject, Protocol et cetera |
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| 392 | * |
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| 393 | */ |
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| 394 | boolean persistEntity(entity) { |
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| 395 | println "persisting ${entity}" |
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| 396 | // if not validated |
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| 397 | if (entity.validate()) { |
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| 398 | if (entity.save()) { //.merge? |
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| 399 | return true |
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| 400 | } |
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| 401 | else { // if save was unsuccesful |
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| 402 | entity.errors.allErrors.each { |
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| 403 | println it |
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| 404 | } |
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| 405 | return false |
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| 406 | } |
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| 407 | } |
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| 408 | else { // if not validated |
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| 409 | entity.errors.each { |
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| 410 | println it |
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| 411 | } |
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| 412 | return false |
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| 413 | } |
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| 414 | } |
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| 415 | |
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| 416 | /** |
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| 417 | * This method creates a record (array) containing entities with values |
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| 418 | * |
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| 419 | * @param template_id template identifier |
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| 420 | * @param excelrow POI based Excel row containing the cells |
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| 421 | * @param mcmap map containing MappingColumn objects |
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| 422 | * @return list of entities and list of failed cells |
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| 423 | */ |
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| 424 | def createRecord(template_id, Row excelrow, mcmap) { |
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| 425 | def df = new DataFormatter() |
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| 426 | def template = Template.get(template_id) |
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| 427 | def record = [] // list of entities and the read values |
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| 428 | def failed = [] // list of failed columns [mappingcolumn] with the value which couldn't be mapped into the entity |
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| 429 | |
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| 430 | // Initialize all possible entities with the chosen template |
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| 431 | def study = new Study(template: template) |
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| 432 | def subject = new Subject(template: template) |
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| 433 | def samplingEvent = new SamplingEvent(template: template) |
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| 434 | def event = new Event(template: template) |
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| 435 | def sample = new Sample(template: template) |
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| 436 | |
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| 437 | // Go through the Excel row cell by cell |
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| 438 | for (Cell cell: excelrow) { |
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| 439 | // get the MappingColumn information of the current cell |
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| 440 | def mc = mcmap[cell.getColumnIndex()] |
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| 441 | def value |
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| 442 | |
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| 443 | // Check if column must be imported |
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| 444 | if (mc!=null) if (!mc.dontimport) { |
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| 445 | try { |
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| 446 | value = formatValue(df.formatCellValue(cell), mc.templatefieldtype) |
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| 447 | } catch (NumberFormatException nfe) { |
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| 448 | value = "" |
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| 449 | } |
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| 450 | |
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| 451 | try { |
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| 452 | |
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| 453 | // which entity does the current cell (field) belong to? |
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| 454 | switch (mc.entity) { |
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| 455 | case Study: // does the entity already exist in the record? If not make it so. |
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| 456 | (record.any {it.getClass() == mc.entity}) ? 0 : record.add(study) |
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| 457 | study.setFieldValue(mc.property, value) |
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| 458 | break |
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| 459 | case Subject: (record.any {it.getClass() == mc.entity}) ? 0 : record.add(subject) |
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| 460 | subject.setFieldValue(mc.property, value) |
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| 461 | break |
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| 462 | case SamplingEvent: (record.any {it.getClass() == mc.entity}) ? 0 : record.add(samplingEvent) |
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| 463 | samplingEvent.setFieldValue(mc.property, value) |
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| 464 | break |
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| 465 | case Event: (record.any {it.getClass() == mc.entity}) ? 0 : record.add(event) |
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| 466 | event.setFieldValue(mc.property, value) |
|---|
| 467 | break |
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| 468 | case Sample: (record.any {it.getClass() == mc.entity}) ? 0 : record.add(sample) |
|---|
| 469 | sample.setFieldValue(mc.property, value) |
|---|
| 470 | break |
|---|
| 471 | case Object: // don't import |
|---|
| 472 | break |
|---|
| 473 | } // end switch |
|---|
| 474 | } catch (IllegalArgumentException iae) { |
|---|
| 475 | // store the mapping column and value which failed |
|---|
| 476 | def temp = new MappingColumn() |
|---|
| 477 | temp.properties = mc.properties |
|---|
| 478 | temp.value = value |
|---|
| 479 | failed.add(temp) |
|---|
| 480 | } |
|---|
| 481 | } // end |
|---|
| 482 | } // end for |
|---|
| 483 | |
|---|
| 484 | // a failed column means that using the entity.setFieldValue() threw an exception |
|---|
| 485 | return [record, failed] |
|---|
| 486 | } |
|---|
| 487 | |
|---|
| 488 | /** |
|---|
| 489 | * Method to parse a value conform a specific type |
|---|
| 490 | * @param value string containing the value |
|---|
| 491 | * @return object corresponding to the TemplateFieldType |
|---|
| 492 | */ |
|---|
| 493 | def formatValue(String value, TemplateFieldType type) throws NumberFormatException { |
|---|
| 494 | switch (type) { |
|---|
| 495 | case TemplateFieldType.STRING : return value.trim() |
|---|
| 496 | case TemplateFieldType.TEXT : return value.trim() |
|---|
| 497 | case TemplateFieldType.INTEGER : return (int) Double.valueOf(value) |
|---|
| 498 | case TemplateFieldType.FLOAT : return Float.valueOf(value.replace(",",".")); |
|---|
| 499 | case TemplateFieldType.DOUBLE : return Double.valueOf(value.replace(",",".")); |
|---|
| 500 | case TemplateFieldType.STRINGLIST : return value.trim() |
|---|
| 501 | case TemplateFieldType.ONTOLOGYTERM : return value.trim() |
|---|
| 502 | case TemplateFieldType.DATE : return value |
|---|
| 503 | default : return value |
|---|
| 504 | } |
|---|
| 505 | } |
|---|
| 506 | |
|---|
| 507 | } |
|---|
