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IRSA-581: Expose to public Firefly API table selection info. #423

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Jul 26, 2017
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IRSA-581: Expose to public Firefly API table selection info. #423

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38 changes: 34 additions & 4 deletions src/firefly/html/demo/ffapi-highlevel-test.html
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Expand Up @@ -57,10 +57,16 @@
<a href='javascript:firefly.getViewer().showTable(tblReq3)'>Open a table</a>
<a href='javascript:firefly.getViewer().showTable(tblReq1)'>Open allwise</a>
<a href='javascript:tblReq1.sortInfo="ASC,ra"; firefly.getViewer().fetchTable(tblReq1)'>Sort allwise by ra</a>
<a href='javascript:launchLC()'>Launch WISE LcViewer</a></div>
<div>
<div id="tables-2" style="display: inline-block; width: 550px; height: 300px; margin: 10px; background-color: white"></div>
<div id="tables-1" style="display: inline-block; width: 550px; height: 300px; margin: 10px; background-color: white; position: absolute"></div>
<a href='javascript:launchLC()'>Launch WISE LcViewer</a>
<div style="display: inline-flex; background-color: white">
<div id="tables-2" style="width: 550px; height: 300px; margin: 10px"></div>
<div id="tables-1" style="width: 550px; height: 300px; margin: 10px"></div>
<div>
<div style="font-size: small">show getSelectedData API call to 2nd table of 2nd tablpanel ('http://web.ip....')</div>
<input type="button" value="show selected" onclick="javascript:loadSelectRows()">
<div id="selectedRows" style="height: 275px; overflow: auto"></div>
</div>
</div>
</div>
<div>XYPlot from API calls:
<a href='javascript:firefly.getViewer().showXYPlot(xyPlotOpsReq3)'>Show XY Plot</a>
Expand Down Expand Up @@ -175,6 +181,30 @@

<script type="text/javascript">
{
function loadSelectRows() {
firefly.util.table.getSelectedData(tblReq3.tbl_id, ['crval1', 'crval2'])
.then( function (tableModel) {
var rowCnt = tableModel.totalRows;
var cell = firefly.util.table.getCellValue;
var cnames = firefly.util.table.getColumns(tableModel).map(function (c) {return c.name});

var txt = "<table border='1'><tr>"
cnames.forEach( function(col) {
txt += "<td>" + col + "</td>";
});
txt += "</tr>";
for (var idx =0; idx < rowCnt; idx++) {
txt += "<tr>";
cnames.forEach( function(col) {
txt += "<td>" + cell(tableModel, idx, col) + "</td>";
});
txt += "</tr>";
}
txt += "</table>"
document.getElementById("selectedRows").innerHTML = txt;
});
}

function launchLC(req) {
var req = firefly.util.table.makeFileRequest(null, 'http://web.ipac.caltech.edu/staff/ejoliet/demo/WISE-mep-2764p772_ac51-010204.tbl',null,
{ tbl_id: 'raw_table',
Expand Down
16 changes: 11 additions & 5 deletions src/firefly/java/edu/caltech/ipac/firefly/server/query/SearchServerCommands.java
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Expand Up @@ -21,9 +21,11 @@
import edu.caltech.ipac.firefly.server.rpc.SearchServicesImpl;
import edu.caltech.ipac.firefly.server.util.QueryUtil;
import edu.caltech.ipac.firefly.server.util.ipactable.DataGroupPart;
import edu.caltech.ipac.firefly.server.util.ipactable.IpacTableParser;
import edu.caltech.ipac.firefly.server.util.ipactable.JsonTableUtil;
import edu.caltech.ipac.firefly.server.SrvParam;
import edu.caltech.ipac.util.CollectionUtil;
import edu.caltech.ipac.util.DataGroup;
import edu.caltech.ipac.util.DataObject;
import edu.caltech.ipac.util.StringUtils;
import org.json.simple.JSONObject;
Expand Down Expand Up @@ -70,12 +72,16 @@ public String doCommand(SrvParam params) throws Exception {
String filePath = params.getRequired("filePath");
try {
String selRows = params.getRequired("selectedRows");
String columnName = params.getRequired("columnName");
List<String> columnNames = StringUtils.asList(params.getRequired("columnNames"), ",");
List<Integer> rows = StringUtils.convertToListInteger(selRows, ",");
List<String> values = new SearchManager().getDataFileValues(ServerContext.convertToFile(filePath), rows, columnName);
Map<String, List<String>> rval = new HashMap<>(1);
rval.put("values", values);
return QueryUtil.toJsonObject(rval).toJSONString();
File file = ServerContext.convertToFile(filePath);

if (!file.canRead() ||
!file.getAbsolutePath().startsWith(ServerContext.getWorkingDir().getAbsolutePath())) {
throw new DataAccessException("Unable to access this file:" + file.getAbsolutePath());
}
DataGroup data = IpacTableParser.getSelectedData(file, rows, columnNames.toArray(new String[0]));
return JsonTableUtil.toJsonTableModel(new DataGroupPart(null, data, 0, data.size()), null).toJSONString();
} catch (IOException e) {
throw new DataAccessException("Unable to resolve a search processor for this request. SelectedValues aborted.");
}
Expand Down
92 changes: 81 additions & 11 deletions src/firefly/java/edu/caltech/ipac/firefly/server/util/ipactable/IpacTableParser.java
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Expand Up @@ -5,6 +5,8 @@

import edu.caltech.ipac.util.DataGroup;
import edu.caltech.ipac.util.DataObject;
import edu.caltech.ipac.util.DataType;
import edu.caltech.ipac.util.FileUtil;
import edu.caltech.ipac.util.IpacTableUtil;

import java.io.File;
Expand All @@ -17,6 +19,7 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;

/**
* Date: May 14, 2009
Expand All @@ -26,6 +29,68 @@
*/
public class IpacTableParser {

public static DataGroup getSelectedData(File inf, Collection<Integer> indices, String... colNames) throws IOException {

Arrays.sort(colNames);

TableDef meta = IpacTableUtil.getMetaInfo(inf);

List<DataType> selCols;
if (colNames.length == 0) {
selCols = meta.getCols().stream().map(DataType::copyOf).collect(Collectors.toList());
} else {
selCols = Arrays.stream(colNames).map( (s -> {
if (s.equals(DataGroup.ROWID_NAME)) {
return new DataType(s, Long.class);
} else {
DataType dt = meta.getColByName(s);
return dt != null ? dt.copyOf() : new DataType(s, String.class);
}
})).collect(Collectors.toList());
}

DataGroup results = new DataGroup(inf.getName(), selCols);
results.setAttributes(meta.getAttributes());

RandomAccessFile reader = new RandomAccessFile(inf,"r");
try {
ArrayList<Integer> sortedIndices = new ArrayList<Integer>(indices);
Collections.sort(sortedIndices);

DataGroup dg = new DataGroup("dummy", meta.getCols());
boolean hasRowid = dg.containsKey(DataGroup.ROWID_NAME);
long cidx = 0, pidx = -1;
for(int idx : sortedIndices) {
cidx = idx;
advanceReaderToNextIdx(pidx, cidx, meta, reader);
String line = reader.readLine();
if (line != null) {
DataObject row = IpacTableUtil.parseRow(dg, line);
DataObject resRow = new DataObject(results);
for (String s : colNames) {
Object val = null;
if (s.equals(DataGroup.ROWID_NAME) && !hasRowid) {
val = cidx;
} else if (dg.containsKey(s)) {
val = row.getDataElement(s);
}
if (val != null) {
resRow.setDataElement(results.getDataDefintion(s), val);
}
}
results.add(resRow);
}
pidx = idx;
}

} finally {
FileUtil.silentClose(reader);
}

return results;
}


public static MappedData getData(File inf, Collection<Integer> indices, String... colNames) throws IOException {

MappedData results = new MappedData();
Expand All @@ -44,17 +109,7 @@ public static MappedData getData(File inf, Collection<Integer> indices, String..
long cidx = 0, pidx = -1;
for(int idx : sortedIndices) {
cidx = idx;
if (pidx == -1) {
long skip = (cidx * (long)meta.getLineWidth()) + (long)meta.getRowStartOffset();
reader.seek(skip);
} else if (cidx - pidx == 1) {
// next line.. no skipping
} else if (cidx - pidx > 10) {
long skip = (cidx * (long)meta.getLineWidth()) + (long)meta.getRowStartOffset();
reader.seek(skip);
} else {
reader.skipBytes((int) ((cidx-pidx-1) * meta.getLineWidth()));
}
advanceReaderToNextIdx(pidx, cidx, meta, reader);
String line = reader.readLine();
if (line != null) {
DataObject row = IpacTableUtil.parseRow(dg, line);
Expand Down Expand Up @@ -159,4 +214,19 @@ private String makeKey(int idx, String colName) {
}

}

private static void advanceReaderToNextIdx(long pidx, long cidx, TableDef meta, RandomAccessFile reader) throws IOException {
if (pidx == -1) {
long skip = (cidx * (long)meta.getLineWidth()) + (long)meta.getRowStartOffset();
reader.seek(skip);
} else if (cidx - pidx == 1) {
// next line.. no skipping
} else if (cidx - pidx > 10) {
long skip = (cidx * (long)meta.getLineWidth()) + (long)meta.getRowStartOffset();
reader.seek(skip);
} else {
reader.skipBytes((int) ((cidx-pidx-1) * meta.getLineWidth()));
}

}
}
21 changes: 19 additions & 2 deletions src/firefly/java/edu/caltech/ipac/firefly/server/util/ipactable/JsonTableUtil.java
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Expand Up @@ -36,7 +36,8 @@ public class JsonTableUtil {
*/
public static JSONObject toJsonTableModel(DataGroupPart page, TableServerRequest request) throws IOException {

TableDef meta = page.getTableDef().clone();
TableDef meta = mergeAttributes(page.getTableDef(), page.getData());

if (request != null && request.getMeta() != null) {
for (String key : request.getMeta().keySet()) {
meta.setAttribute(key, request.getMeta(key));
Expand All @@ -52,7 +53,7 @@ public static JSONObject toJsonTableModel(DataGroupPart page, TableServerRequest
tableModel.put("totalRows", page.getRowCount());

if (page.getData() != null ) {
tableModel.put("tableData", toJsonTableData(page.getData(), page.getTableDef()));
tableModel.put("tableData", toJsonTableData(page.getData(), meta));
}


Expand Down Expand Up @@ -96,6 +97,22 @@ public static JSONObject toJsonTableRequest(TableServerRequest req) {
return treq;
}

private static TableDef mergeAttributes(TableDef tblDef, DataGroup data) {
if (tblDef == null) {
tblDef = new TableDef();
}

List<DataGroup.Attribute> dataAttributes = data.getKeywords();
if (dataAttributes != null) {
for (DataGroup.Attribute a : dataAttributes) {
if (!tblDef.contains(a.getKey())) {
tblDef.setAttribute(a.getKey(), a.getValue());
}
}
}
return tblDef;
}

/**
* convert to JSON TableData
*
Expand Down
8 changes: 8 additions & 0 deletions src/firefly/java/edu/caltech/ipac/firefly/server/util/ipactable/TableDef.java
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Expand Up @@ -53,6 +53,14 @@ public List<DataType> getCols() {
return cols;
}

public DataType getColByName(String name) {
name = name == null ? "" : name;
for(DataType dt : cols) {
if (dt.getKeyName().equals(name)) return dt;
}
return null;
}

public void setCols(List<DataType> cols) { this.cols = cols; }

/**
Expand Down
12 changes: 12 additions & 0 deletions src/firefly/java/edu/caltech/ipac/util/DataType.java
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Expand Up @@ -315,6 +315,18 @@ public Object clone() throws CloneNotSupportedException {
return dt;
}

/**
* this is similar to clone without having to deal with exception and casting.
* @return
*/
public DataType copyOf() {
try {
return (DataType) clone();
} catch (CloneNotSupportedException e) {
return null; // should not happen;
}
}

/**
* FormatInfo defines the formatting behavior of this DataType.
* This includes column width, column header alignment, column data alignment,
Expand Down
4 changes: 3 additions & 1 deletion src/firefly/java/edu/caltech/ipac/util/StringUtils.java
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Expand Up @@ -3,6 +3,7 @@
*/
package edu.caltech.ipac.util;

import javax.validation.constraints.NotNull;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Arrays;
Expand Down Expand Up @@ -129,8 +130,9 @@ public static int[] convertToArrayInt(String str, String regExp) throws NumberFo
return intAry;
}

@NotNull
public static List<Integer> convertToListInteger(String str, String regExp) throws NumberFormatException {
if (isEmpty(str)) return null;
if (isEmpty(str)) return new ArrayList<>();
String[] reqkeys = str.split(regExp);
ArrayList<Integer> list = new ArrayList<Integer>(reqkeys.length);
for (int i = 0; i < reqkeys.length; i++) {
Expand Down
9 changes: 7 additions & 2 deletions src/firefly/js/api/ApiUtilTable.jsx
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Expand Up @@ -2,5 +2,10 @@
* License information at https://github.com/Caltech-IPAC/firefly/blob/master/License.txt
*/

export {getTblInfo, getActiveTableId, getTblById, uniqueTblId, getTableSourceUrl, getTableUiByTblId,
makeTblRequest, makeFileRequest, makeIrsaCatalogRequest} from '../tables/TableUtil.js';
export {getTblInfo, getActiveTableId, getTblById, getTableUiByTblId, getTblInfoById,
getTableGroup, findGroupByTblId, getTblIdsByGroup,
uniqueTblId, getTableSourceUrl, onTableLoaded,
makeTblRequest, makeFileRequest, makeIrsaCatalogRequest,
cloneRequest, doFetchTable, getTblRowAsObj,
getColumnIdx, getColumn, getColumns, getCellValue,
getColumnValues, getRowValues, getSelectedData} from '../tables/TableUtil.js';
33 changes: 9 additions & 24 deletions src/firefly/js/rpc/SearchServicesJson.js
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Expand Up @@ -84,19 +84,19 @@ export function findTableIndex(tableRequest, filterInfo) {
}

/**
* returns the values of the data from the given parameters
* returns the table data for the given parameters
* @param {Object} p parameters object
* @param {string} p.columnName name of the column
* @param {string[]} p.columnNames an array of column names
* @param {string} p.filePath location of the file on the server
* @param {string} p.selectedRows a comma-separated string of indices of the rows to get the data from
* @return {Promise}
* @return {Promise<TableModel>}
*/
export const selectedValues = function({columnName, filePath, selectedRows}) {
return doJsonRequest(ServerParams.SELECTED_VALUES, {columnName, filePath, selectedRows})
.then((data) => {
// JsonUtil may not interpret array values correctly due to error-checking.
// returning array as a prop 'values' inside an object instead.
return get(data, 'values');
export const selectedValues = function({columnNames, filePath, selectedRows}) {
columnNames = Array.isArray(columnNames) ? columnNames.join() : String(columnNames);
selectedRows = Array.isArray(selectedRows) ? selectedRows.join() : String(selectedRows);
return doJsonRequest(ServerParams.SELECTED_VALUES, {columnNames, filePath, selectedRows})
.then((tableModel) => {
return tableModel;
});
};

Expand Down Expand Up @@ -193,21 +193,6 @@ export const cancel= function(id) {
).then( () => true);
};

/**
*
* @param {string} id background id
* @return {Promise}
* @deprecated
*/
export const addIDToPushCriteria= function(id) {
// not used in converted code.

// var paramList = [];
// paramList.push({name: ServerParams.ID, value: id});
// return doJsonRequest(ServerParams.ADD_ID_TO_CRITERIA, paramList
// ).then( () => true);
};

/**
*
* @param {string} fileKey
Expand Down
1 change: 0 additions & 1 deletion src/firefly/js/tables/TableConnector.js
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Expand Up @@ -6,7 +6,6 @@ import {isEmpty, omitBy, isUndefined, cloneDeep, get, set} from 'lodash';
import * as TblCntlr from './TablesCntlr.js';
import * as TblUtil from './TableUtil.js';
import {SelectInfo} from './SelectInfo.js';
import {selectedValues} from '../rpc/SearchServicesJson.js';

export class TableConnector {

Expand Down
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