@Override protected Key parse(String input) { if (_validator != null) _validator.validateRaw(input); Key k = Key.make(input); Value v = DKV.get(k); if (v == null && _mustExist) throw new IllegalArgumentException("Key '" + input + "' does not exist!"); if (_type != null) { if (v != null && !compatible(_type, v.get())) throw new IllegalArgumentException(input + ":" + errors()[0]); if (v == null && _required) throw new IllegalArgumentException("Key '" + input + "' does not exist!"); } return k; }
/** * Parse the section file and fill in the Dbase. * * @return Success code */ public void parse() throws Exception { JOAParameter tempProperties[] = new JOAParameter[100]; FileInputStream in = null; DataInputStream inData = null; short inShort = 0; long bytesRead = 0; long bytesInFile = mFile.length(); short[] sarray = new short[1]; int mTotalStns = 0; EPSProgressDialog mProgress = new EPSProgressDialog(new Frame(), mProgressStr, Color.blue); mProgress.setVisible(true); // Get an epic key database specific to JOA EPIC_Key_DB mEpicKeyDB = new EPIC_Key_DB("joa_epic.key"); // Get an epic key database specific to JOA EPIC_Key_DB mOrigEpicKeyDB = new EPIC_Key_DB("epic.key"); // create a vector for temporary storage of the dbases Vector dBases = new Vector(100); try { in = new FileInputStream(mFile); BufferedInputStream bis = new BufferedInputStream(in, 1000000); inData = new DataInputStream(bis); // read version short vers = inData.readShort(); bytesRead += 2; if (vers < 2) { FileImportException fiex = new FileImportException(); String errStr = "Invalid version for a JOA binary file"; fiex.setErrorType(errStr); throw fiex; } // read number of bytes in file description string inShort = inData.readShort(); bytesRead += 2; // read the file description String byte buf[] = new byte[inShort]; inData.read(buf, 0, inShort); String fileDescrip = new String(buf); bytesRead += inShort; // create a new open file object JOADataFile of = new JOADataFile(fileDescrip); // read the number of sections int numSections = inData.readShort(); bytesRead += 2; // read each section JOASection sech; int ord = 0; for (int s = 0; s < numSections; s++) { mProgress.setPercentComplete(100.0 * ((double) bytesRead / (double) bytesInFile)); // read the section header inShort = inData.readShort(); bytesRead += 2; byte buf1[] = new byte[inShort]; inData.read(buf1, 0, inShort); String sectionDescrip = new String(buf1); bytesRead += inShort; // read the ship code byte bufsc[] = new byte[2]; bufsc[0] = inData.readByte(); bufsc[1] = inData.readByte(); String shipCode = new String(bufsc); bytesRead += 2; // read num casts int numCasts = inData.readShort(); bytesRead += 2; // read num parameters int numVars = inData.readShort(); bytesRead += 2; // quality code int qcStd = 1; if (vers == 4) { qcStd = inData.readShort(); bytesRead += 2; } // create a new section of.mNumSections++; sech = new JOASection(of.mNumSections, sectionDescrip, shipCode, numCasts, numVars); if (vers == 2) { // read the properties byte bufv[] = new byte[4]; for (int p = 0; p < numVars; p++) { // parameter name inData.read(bufv, 0, 4); String tempVar = new String(bufv); bytesRead += 4; // units inShort = inData.readShort(); bytesRead += 2; String units = null; if (inShort > 0) { byte buf11[] = new byte[inShort]; inData.read(buf11, 0, inShort); units = new String(buf11); bytesRead += inShort; } // convert varnames to UC tempVar.toUpperCase(); // create new property tempProperties[p] = new JOAParameter(tempVar, units); // add this property to the section property list if (tempProperties[p].mUnits == null) { tempProperties[p].mUnits = EPS_Util.paramNameToJOAUnits(false, tempProperties[0].mVarLabel); } if (tempProperties[p].mUnits == null) { tempProperties[p].mUnits = new String("na"); } tempProperties[p].mCastOrObs = EPSConstants.ALL_OBS; // read the actual scale int actScale = inData.readShort(); bytesRead += 2; if (actScale != 0) tempProperties[p].mActScale = 1.0 / (double) actScale; else tempProperties[p].mActScale = 1.0; // read the actual origin int actOrigin = inData.readShort(); tempProperties[p].mActOrigin = (double) actOrigin * tempProperties[p].mActScale; // read reverse y int reverseY = inData.readShort(); bytesRead += 2; if (reverseY == 0) tempProperties[p].mReverseY = false; else tempProperties[p].mReverseY = true; tempProperties[p].mWasCalculated = false; } } else { // read the properties String tempVar = null; for (int p = 0; p < numVars; p++) { // length of parameter name inShort = inData.readShort(); bytesRead += 2; // parameter name if (inShort > 0) { byte buf13[] = new byte[inShort]; inData.read(buf13, 0, inShort); tempVar = new String(buf13); bytesRead += inShort; } // units inShort = inData.readShort(); bytesRead += 2; String units = null; if (inShort > 0) { byte buf11[] = new byte[inShort]; inData.read(buf11, 0, inShort); units = new String(buf11); bytesRead += inShort; } // convert varnames to UC tempVar = tempVar.toUpperCase(); // create new property tempProperties[p] = new JOAParameter(tempVar, units); // add this property to the section property list if (tempProperties[p].mUnits == null) { tempProperties[p].mUnits = EPS_Util.paramNameToJOAUnits(false, tempProperties[0].mVarLabel); } if (tempProperties[p].mUnits == null) { tempProperties[p].mUnits = new String("na"); } tempProperties[p].mCastOrObs = EPSConstants.ALL_OBS; // read the actual scale int actScale = inData.readShort(); bytesRead += 2; if (actScale != 0) tempProperties[p].mActScale = 1.0 / (double) actScale; else tempProperties[p].mActScale = 1.0; // read the actual origin int actOrigin = inData.readShort(); tempProperties[p].mActOrigin = (double) actOrigin * tempProperties[p].mActScale; // read reverse y int reverseY = inData.readShort(); bytesRead += 2; if (reverseY == 0) tempProperties[p].mReverseY = false; else tempProperties[p].mReverseY = true; tempProperties[p].mWasCalculated = false; } } // read the cast headers for (int c = 0; c < numCasts; c++) { // read station number inShort = inData.readShort(); bytesRead += 2; byte bufx[] = new byte[inShort]; inData.read(bufx, 0, inShort); String stnNum = new String(bufx); bytesRead += inShort; // read cast number int castNum = inData.readShort(); bytesRead += 2; double myLat = 0.0; double myLon = 0.0; if (vers == 2) { // read latitude/lon int lat = inData.readInt(); bytesRead += 4; int lon = inData.readInt(); bytesRead += 4; myLat = lat * 0.001; myLon = lon * 0.001; } else if (vers > 2) { // read latitude/lon myLat = inData.readDouble(); bytesRead += 8; myLon = inData.readDouble(); bytesRead += 4; } // read number of bottles int numBottles = inData.readShort(); bytesRead += 2; // read the date int year = inData.readInt(); bytesRead += 4; int month = inData.readInt(); bytesRead += 4; int day = inData.readInt(); bytesRead += 4; int hour = inData.readInt(); bytesRead += 4; double min = inData.readDouble(); bytesRead += 8; // read bottom int bottomdbar = inData.readInt(); // read station quality int stnQual = inData.readShort(); bytesRead += 2; ord++; JOAStation sh = new JOAStation( ord, shipCode, stnNum, castNum, myLat, myLon, numBottles, year, month, day, hour, min, bottomdbar, stnQual); sech.mStations.addElement(sh); sh.setType("JOA BOTTLE"); // make a DBase object Dbase db = new Dbase(); // add the global attributes db.addEPSAttribute( "CRUISE", EPCHAR, sech.mSectionDescription.length(), sech.mSectionDescription); db.addEPSAttribute("CAST", EPCHAR, sh.mStnNum.length(), sh.mStnNum); sarray[0] = (short) sh.mBottomDepthInDBARS; db.addEPSAttribute("WATER_DEPTH", EPSHORT, 1, sarray); db.addEPSAttribute("DATA_ORIGIN", EPCHAR, sech.mShipCode.length(), sech.mShipCode); String dType = sh.getType(); if (dType == null) dType = "UNKN"; db.addEPSAttribute("DATA_TYPE", EPCHAR, dType.length(), dType); sarray[0] = (short) stnQual; db.addEPSAttribute("STN_QUALITY", EPSHORT, 1, sarray); db.setDataType("JOA BOTTLE"); // add to temporary collection dBases.addElement(db); } int start = mTotalStns; int end = sech.mStations.size() + mTotalStns; for (int sc = start; sc < end; sc++) { mProgress.setPercentComplete(100.0 * ((double) bytesRead / (double) bytesInFile)); // get a dBase Dbase db = (Dbase) dBases.elementAt(sc); // get a station JOAStation sh = (JOAStation) sech.mStations.elementAt(sc - start); // create an array of arrays to store the data double[][] va = new double[sech.mNumVars][sh.mNumBottles]; int[][] qc = new int[sech.mNumVars][sh.mNumBottles]; short[] bqc = new short[sh.mNumBottles]; int presPos = 0; // read the bottles for (int b = 0; b < sh.mNumBottles; b++) { // read the bottle quality code bqc[b] = inData.readShort(); bytesRead += 2; for (int v = 0; v < sech.mNumVars; v++) { // store the position of the PRES variable if (tempProperties[v].mVarLabel.equals("PRES")) presPos = v; // get the measured parameter double dVarVal = EPSConstants.MISSINGVALUE; try { dVarVal = inData.readDouble(); } catch (IOException e) { FileImportException fiex = new FileImportException(); String errStr = "Error reading the parameter data. " + "\n" + "Bottle #" + b + " Parameter #" + v; fiex.setErrorType(errStr); throw fiex; } bytesRead += 8; // store the value in the multidimensional array va[v][b] = dVarVal; // get the quality flag short flag = (short) EPSConstants.MISSINGVALUE; try { flag = inData.readShort(); } catch (IOException e) { FileImportException fiex = new FileImportException(); String errStr = "Error reading the parameter quality code. " + "\n" + "Bottle #" + b + " Parameter #" + v; fiex.setErrorType(errStr); throw fiex; } bytesRead += 2; qc[v][b] = flag; } // for v } // for b // add the bottle quality codes as an attribute db.addEPSAttribute("BOTTLE_QUALITY_CODES", EPSHORT, sh.mNumBottles, bqc); // create the axes time = 0, depth = 1, lat = 2, lon = 3 Axis timeAxis = new Axis(); Axis zAxis = new Axis(); Axis latAxis = new Axis(); Axis lonAxis = new Axis(); // time axis timeAxis.setName("time"); timeAxis.setTime(true); timeAxis.setUnlimited(false); timeAxis.setAxisType(EPTAXIS); timeAxis.setLen(1); int hour = 0; if (sh.mHour != EPSConstants.MISSINGVALUE) hour = sh.mHour; double mins = 0; if (sh.mMinute != EPSConstants.MISSINGVALUE) mins = sh.mMinute; // make the time axis units String date = "days since "; int min = (int) mins; double fmin = mins - min; int secs = (int) (fmin * 60.0); double fsec = (fmin * 60.0) - secs; int msec = (int) (fsec * 1000.0); String fs = String.valueOf(fsec); fs = fs.substring(fs.indexOf(".") + 1, fs.length()).trim(); int f = 0; if (fs != null && fs.length() > 0) f = Integer.valueOf(fs).intValue(); // sprintf(time_string,"%04d-%02d-%02d %02d:%02d:%02d.%03d",yr,mon,day,hr,min,sec,f); String frmt = new String( "{0,number,####}-{1,number,00}-{2,number,00} {3,number,00}:{4,number,00}:{5,number,00}.{6,number,000}"); MessageFormat msgf = new MessageFormat(frmt); Object[] objs = { new Integer(sh.mYear), new Integer(sh.mMonth), new Integer(sh.mDay), new Integer(hour), new Integer(min), new Integer(secs), new Integer(f) }; StringBuffer out = new StringBuffer(); msgf.format(objs, out, null); String time_string = new String(out); date = date + time_string; timeAxis.addAttribute(0, "units", EPCHAR, date.length(), date); timeAxis.setUnits(date); GeoDate gd = null; try { gd = new GeoDate(sh.mMonth, sh.mDay, sh.mYear, hour, min, secs, msec); GeoDate[] ta = {gd}; MultiArray tma = new ArrayMultiArray(ta); timeAxis.setData(tma); db.setAxis(timeAxis); } catch (Exception ex) { GeoDate[] ta = {new GeoDate()}; MultiArray tma = new ArrayMultiArray(ta); timeAxis.setData(tma); db.setAxis(timeAxis); } // add the time axes variable EPSVariable var = new EPSVariable(); var.setOname("time"); var.setDtype(EPDOUBLE); var.setVclass(Double.TYPE); var.addAttribute(0, "units", EPCHAR, date.length(), date); var.setUnits(date); double[] vta = {0.0}; MultiArray vtma = new ArrayMultiArray(vta); try { var.setData(vtma); } catch (Exception ex) { } db.addEPSVariable(var); // z axis zAxis.setName("depth"); zAxis.setTime(false); zAxis.setUnlimited(false); zAxis.setLen(sh.mNumBottles); zAxis.setAxisType(EPZAXIS); zAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.1"); zAxis.addAttribute(1, "units", EPCHAR, 4, "dbar"); zAxis.setUnits("dbar"); zAxis.setFrmt("f10.1"); // zAxis.addAttribute(2, "type", EPCHAR, 0, ""); sarray[0] = 1; zAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray); double[] za = new double[sh.mNumBottles]; for (int b = 0; b < sh.mNumBottles; b++) { za[b] = va[presPos][b]; } MultiArray zma = new ArrayMultiArray(za); zAxis.setData(zma); db.setAxis(zAxis); // add the z axes variables var = new EPSVariable(); var.setOname("depth"); var.setDtype(EPDOUBLE); var.setVclass(Double.TYPE); var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.1"); var.addAttribute(1, "units", EPCHAR, 4, "dbar"); var.setUnits("dbar"); var.setFrmt("f10.1"); // var.addAttribute(2, "type", EPCHAR, 0, ""); sarray[0] = 1; var.addAttribute(2, "epic_code", EPSHORT, 1, sarray); MultiArray zvma = new ArrayMultiArray(za); try { var.setData(zvma); } catch (Exception ex) { } db.addEPSVariable(var); // lat axis latAxis.setName("latitude"); latAxis.setTime(false); latAxis.setUnlimited(false); latAxis.setLen(1); latAxis.setAxisType(EPYAXIS); latAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4"); latAxis.addAttribute(1, "units", EPCHAR, 7, "degrees"); latAxis.setUnits("degrees"); latAxis.setFrmt("f10.4"); // latAxis.addAttribute(2, "type", EPCHAR, 0, ""); sarray[0] = 500; latAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray); double lat = sh.mLat; double[] la = {lat}; MultiArray lma = new ArrayMultiArray(la); latAxis.setData(lma); db.setAxis(latAxis); // add the y axes variable var = new EPSVariable(); var.setOname("latitude"); var.setDtype(EPDOUBLE); var.setVclass(Double.TYPE); var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4"); var.addAttribute(1, "units", EPCHAR, 7, "degrees"); var.setUnits("degrees"); var.setFrmt("f10.4"); // var.addAttribute(2, "type", EPCHAR, 0, ""); sarray[0] = 500; var.addAttribute(2, "epic_code", EPSHORT, 1, sarray); MultiArray yvma = new ArrayMultiArray(la); try { var.setData(yvma); } catch (Exception ex) { } db.addEPSVariable(var); // lon axis lonAxis.setName("longitude"); lonAxis.setTime(false); lonAxis.setUnlimited(false); lonAxis.setLen(1); lonAxis.setAxisType(EPXAXIS); lonAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4"); lonAxis.addAttribute(1, "units", EPCHAR, 7, "degrees"); lonAxis.setUnits("degrees"); lonAxis.setFrmt("f10.4"); // lonAxis.addAttribute(2, "type", EPCHAR, 0, ""); sarray[0] = 502; lonAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray); double lon = sh.mLon; double[] lla = {lon}; lma = new ArrayMultiArray(lla); lonAxis.setData(lma); db.setAxis(lonAxis); // add the x axes variable var = new EPSVariable(); var.setOname("longitude"); var.setDtype(EPDOUBLE); var.setVclass(Double.TYPE); var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4"); var.addAttribute(1, "units", EPCHAR, 7, "degrees"); var.setUnits("degrees"); var.setFrmt("f10.4"); // var.addAttribute(2, "type", EPCHAR, 0, ""); sarray[0] = 502; var.addAttribute(2, "epic_code", EPSHORT, 1, sarray); MultiArray xvma = new ArrayMultiArray(lla); try { var.setData(xvma); } catch (Exception ex) { } db.addEPSVariable(var); // add the measured variables for (int v = 0; v < sech.mNumVars; v++) { // if (presPos == v) // continue; // create an array of measured EPSVariables for this database EPSVariable epsVar = new EPSVariable(); // initialize the new EPSVariables // look this variable up in JOA EPIC_Key. find matching entry in original EPIC Key String oname = tempProperties[v].mVarLabel; String sname = null; String lname = null; String gname = null; String units = null; String ffrmt = null; int keyID = -99; int type = -99; try { keyID = mEpicKeyDB.findKey(tempProperties[v].mVarLabel); Key key = mOrigEpicKeyDB.findKey(keyID); gname = key.getGname(); sname = key.getSname(); lname = key.getLname(); units = key.getUnits(); ffrmt = key.getFrmt(); type = key.getType(); } catch (Exception e) { lname = tempProperties[v].mVarLabel; gname = tempProperties[v].mVarLabel; sname = tempProperties[v].mVarLabel; units = tempProperties[v].mUnits; } // make a new variable epsVar = new EPSVariable(); epsVar.setOname(oname); epsVar.setSname(sname); epsVar.setLname(lname); epsVar.setGname(gname); epsVar.setDtype(EPDOUBLE); epsVar.setVclass(Double.TYPE); int numAttributes = 0; if (ffrmt != null) { epsVar.addAttribute(numAttributes++, "FORTRAN_format", EPCHAR, ffrmt.length(), ffrmt); epsVar.setFrmt(ffrmt); } if (units != null && units.length() > 0) { epsVar.addAttribute(numAttributes++, "units", EPCHAR, units.length(), units); epsVar.setUnits(units); } if (keyID >= 0) { sarray[0] = (short) type; // epsVar.addAttribute(numAttributes++, "type", EPSHORT, 1, sarray); } if (keyID >= 0) { sarray[0] = (short) keyID; epsVar.addAttribute(numAttributes++, "epic_code", EPSHORT, 1, sarray); } // add the quality code attribute String qcVar = oname + "_QC"; epsVar.addAttribute(numAttributes++, "OBS_QC_VARIABLE", EPCHAR, qcVar.length(), qcVar); // connect variable to axis epsVar.setDimorder(0, 0); epsVar.setDimorder(1, 1); epsVar.setDimorder(2, 2); epsVar.setDimorder(3, 3); epsVar.setT(timeAxis); epsVar.setZ(zAxis); epsVar.setY(latAxis); epsVar.setX(lonAxis); // set the data // create storage for the measured variables double[][][][] vaa = new double[1][sh.mNumBottles][1][1]; for (int b = 0; b < sh.mNumBottles; b++) { vaa[0][b][0][0] = va[v][b]; } MultiArray mdma = new ArrayMultiArray(vaa); try { epsVar.setData(mdma); } catch (Exception ex) { System.out.println("throwing"); } // add the variable to the database db.addEPSVariable(epsVar); // create the quality code variable epsVar = new EPSVariable(); epsVar.setOname(oname + "_QC"); epsVar.setSname(sname + "_QC"); epsVar.setLname(sname + "_QC"); epsVar.setGname(sname + "_QC"); epsVar.setDtype(EPSHORT); epsVar.setVclass(Short.TYPE); // connect variable to axis epsVar.setDimorder(0, 0); epsVar.setDimorder(1, 1); epsVar.setDimorder(2, 2); epsVar.setDimorder(3, 3); epsVar.setT(timeAxis); epsVar.setZ(zAxis); epsVar.setY(latAxis); epsVar.setX(lonAxis); // set the data // create storage for the qc variables short[][][][] qcaa = new short[1][sh.mNumBottles][1][1]; for (int b = 0; b < sh.mNumBottles; b++) { qcaa[0][b][0][0] = (short) qc[v][b]; } MultiArray qcma = new ArrayMultiArray(qcaa); try { epsVar.setData(qcma); } catch (Exception ex) { System.out.println("throwing"); } // add the qc variable to the database db.addEPSVariable(epsVar); } // for v } mTotalStns += numCasts; } // for sc // read the file comments StringBuffer sb = null; while (true) { try { // read continuation line inShort = inData.readShort(); bytesRead += 2; if (inShort == 1) { // read number of bytes in file description string inShort = inData.readShort(); bytesRead += 2; // read the file description String byte buf2[] = new byte[inShort]; inData.read(buf2, 0, inShort); String commentLine = new String(buf2); bytesRead += inShort; if (sb == null) sb = new StringBuffer(commentLine); else sb.append(commentLine); } } catch (IOException e) { break; } } // while true if (sb != null) { // make attributes for the comments mOwnerDBase.setDataComment(new String(sb)); } // make a sub database in the dbase mOwnerDBase.createSubEntries(mTotalStns, mFile.getName()); for (int d = 0; d < mTotalStns; d++) { Dbase db = (Dbase) dBases.elementAt(d); mOwnerDBase.addSubEntry(db); } mProgress.setPercentComplete(100.0); mProgress.setVisible(false); mProgress.dispose(); in.close(); } catch (IOException e) { mProgress.setVisible(false); mProgress.dispose(); throw e; } }
public void setValue(Key key) { record()._value = key; record()._originalValue = key.toString(); }