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Re: No "DATE" field in ASCII table
Jerome,
Both the ASCII output and the NetCDF output for insitu data are
generated in methods inside of las/xml/perl/TMAP/insitu.pl. The method
for ASCII output is called insitu_data(). All of the formatting of the
output is taken care of in this perl method and no scripts or templates
are used. We realized that human readable strings were an important
part of the output after releasing LAS 6.4.0 and included this column in
LAS 6.4.1. I've attached our current las/xml/perl/TMAP/insitu.pl which
should be compatible with your version of LAS. (But make sure you back
up your current version before you replace it!) In any case, you should
see the changes that include the human readable date string.
I hope this helps.
-- Jon
Jerome King wrote:
Hi all!
I have installed the LAS_insitu demo package to display my insitu data
in LAS.
I have modified the TMAPDBI to connect LAS to a MYSQL database.
When I query data and output it in the "ASCII table" format, I get
most of the required fields such as prof_ID, lon, lat, depth, hours
since, and variable.
BUT I don't get a "DATE" filed.
I have double-checked the TMAPDBI and made sure the $tref is being
assigned and I load the TMAPdate module at the beginning.
The only difference between the LAS_insitu_demo database and my
database is the format in which "DATE" is stored as:
My database: 2004-06-29 15:13:53
The LAS-insitu_demo database: 20040629
I think the TMAPDBI was written to take into account several "DATE"
format with the TMAPdate module.
So I am not sure why I am not getting a "DATE" field.
Any ideas?
Thanks a bunch!
Jerome.
#
# $Id: insitu.pl,v 1.15 2005/02/07 19:54:07 mclean Exp $
#
# Code to support insitu data access and visualization methods.
#
use strict;
use LAS;
use TMAPDate;
use TMAPDBI;
use TMAPJGOFS;
use TMAPWODB;
use TMAPDapper;
package LAS::Server::Ferret;
use File::Basename;
use MD5;
use LASNetCDF;
require ("cruise.pl");
sub insitu_property {
my ($self) = @_;
$self->{props}->{style} = "property";
$self->{props}->{outputView} = "";
$self->{props}->{setupScript} = "insitu_property_setup";
my $numVars = scalar @{$self->{vars}};
die "Property/property plot requires two (and only two) variables; found $numVars"
if $numVars != 2;
$self->graphic_2_var;
}
sub insitu_poly_xy {
my ($self) = @_;
$self->{props}->{style} = "poly";
$self->{props}->{outputView} = "xy";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_poly_xt {
my ($self) = @_;
$self->{props}->{style} = "poly";
$self->{props}->{outputView} = "xt";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_poly_yt {
my ($self) = @_;
$self->{props}->{style} = "poly";
$self->{props}->{outputView} = "yt";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_waterfall_xz {
my ($self) = @_;
$self->{props}->{style} = "waterfall";
$self->{props}->{outputView} = "xz";
$self->{props}->{setupScript} = "insitu_setup_stations";
$self->graphic;
}
sub insitu_waterfall_yz {
my ($self) = @_;
$self->{props}->{style} = "waterfall";
$self->{props}->{outputView} = "yz";
$self->{props}->{setupScript} = "insitu_setup_stations";
$self->graphic;
}
sub insitu_waterfall_zt {
my ($self) = @_;
$self->{props}->{style} = "waterfall";
$self->{props}->{outputView} = "zt";
$self->{props}->{setupScript} = "insitu_setup_stations";
$self->graphic;
}
sub insitu_gaussian_xy {
my ($self) = @_;
$self->{props}->{style} = "gaussian";
$self->{props}->{outputView} = "xy";
$self->{props}->{setupScript} = "insitu_setup";
$self->{props}->{no_sampling} = 1;
$self->graphic;
}
sub insitu_gaussian_xz {
my ($self) = @_;
$self->{props}->{style} = "gaussian";
$self->{props}->{outputView} = "xz";
$self->{props}->{setupScript} = "insitu_setup";
$self->{props}->{no_sampling} = 1;
$self->graphic;
}
sub insitu_gaussian_xt {
my ($self) = @_;
$self->{props}->{style} = "gaussian";
$self->{props}->{outputView} = "xt";
$self->{props}->{setupScript} = "insitu_setup";
$self->{props}->{no_sampling} = 1;
$self->graphic;
}
sub insitu_gaussian_yz {
my ($self) = @_;
$self->{props}->{style} = "gaussian";
$self->{props}->{outputView} = "yz";
$self->{props}->{setupScript} = "insitu_setup";
$self->{props}->{no_sampling} = 1;
$self->graphic;
}
sub insitu_gaussian_yt {
my ($self) = @_;
$self->{props}->{style} = "gaussian";
$self->{props}->{outputView} = "yt";
$self->{props}->{setupScript} = "insitu_setup";
$self->{props}->{no_sampling} = 1;
$self->graphic;
}
sub insitu_gaussian_zt {
my ($self) = @_;
$self->{props}->{style} = "gaussian";
$self->{props}->{outputView} = "zt";
$self->{props}->{setupScript} = "insitu_setup";
$self->{props}->{no_sampling} = 1;
$self->graphic;
}
sub insitu_property_depth {
my ($self) = @_;
$self->{props}->{style} = "property_depth";
$self->{props}->{outputView} = "";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_pie_xy {
my ($self) = @_;
$self->{props}->{style} = "pie";
$self->{props}->{outputView} = "xy";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_pie_xz {
my ($self) = @_;
$self->{props}->{style} = "pie";
$self->{props}->{outputView} = "xz";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_pie_xt {
my ($self) = @_;
$self->{props}->{style} = "pie";
$self->{props}->{outputView} = "xt";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_pie_yz {
my ($self) = @_;
$self->{props}->{style} = "pie";
$self->{props}->{outputView} = "yz";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_pie_yt {
my ($self) = @_;
$self->{props}->{style} = "pie";
$self->{props}->{outputView} = "yt";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_pie_zt {
my ($self) = @_;
$self->{props}->{style} = "pie";
$self->{props}->{outputView} = "zt";
$self->{props}->{setupScript} = "insitu_setup";
$self->graphic;
}
sub insitu_pie_station_depth {
my ($self) = @_;
$self->{props}->{style} = "pie";
$self->{props}->{outputView} = "station_depth";
$self->{props}->{setupScript} = "insitu_setup_stations";
$self->graphic;
}
sub insitu_meta_xy{
my ($self) = @_;
$self->insitu_meta("xy");
}
sub insitu_meta_xz {
my ($self) = @_;
$self->insitu_meta("xz");
}
sub insitu_meta_yz {
my ($self) = @_;
$self->insitu_meta("yz");
}
sub insitu_meta {
my ($self, $outputView) = @_;
my $props = $self->{props};
my $var = $self->{vars}->[0];
$props->{dataset_title} = $var->getDataset->getLongName;
$props->{var_title} = $var->getAttribute('name');
$props->{variable_name_0} = 'TAX';
$self->setup_region;
if ($props->{insitu_use_ref_map} eq 'false'){
$props->{insitu_refmap} = 0;
}elsif ($props->{insitu_use_ref_map} eq 'true' || $props->{insitu_use_ref_map} eq 'default'){
$props->{insitu_refmap} = 1;
}
my @args0 = qw(dataset_name_0 variable_name_0 dataset_title var_title);
$self->runJournal('insitu_setup', \@args0, undef, 'insitu_setup', \@args0);
my $xrange = $props->{x_lo} . ':' . $props->{x_hi};
my $yrange = $props->{y_lo} . ':' . $props->{y_hi};
my $zrange = $props->{z_lo} . ':' . $props->{z_hi};
my $comm = "go insitu_meta_" . $outputView . " \"" . $props->{dataset_name_0} . "\" TAX " . $xrange . " " . $yrange . " " . $zrange . " " . "\"$props->{insitu_palette}\"" . " " . "\"$props->{insitu_fill_levels}\"" . " " . "\"$props->{insitu_refmap}\"";
$self->command($comm);
$self->genImage($self->{output_file});
}
sub insitu_tsum{
my ($self) = @_;
my $props = $self->{props};
my $var = $self->{vars}->[0];
$props->{dataset_title} = $var->getDataset->getLongName;
$props->{var_title} = $var->getAttribute('name');
$self->setup_region;
my @args0 = qw(dataset_name_0 variable_name_0 dataset_title var_title);
$self->runJournal('insitu_setup', \@args0, undef, 'insitu_setup', \@args0);
my $xrange = $props->{x_lo} . ':' . $props->{x_hi};
my $yrange = $props->{y_lo} . ':' . $props->{y_hi};
my $comm = "go insitu_tsum" . " \"" . $props->{dataset_name_0} . "\" TAX " . $xrange . " " . $yrange . " " . $props->{ts_bin_size};
$self->command($comm);
$self->genImage($self->{output_file});
}
sub insitu_tave{
my ($self) = @_;
my $props = $self->{props};
my $var = $self->{vars}->[0];
$props->{dataset_title} = $var->getDataset->getLongName;
$props->{var_title} = $var->getAttribute('name');
$self->setup_region;
my @args0 = qw(dataset_name_0 variable_name_0 dataset_title var_title);
$self->runJournal('insitu_setup', \@args0, undef, 'insitu_setup', \@args0);
my $xrange = $props->{x_lo} . ':' . $props->{x_hi};
my $yrange = $props->{y_lo} . ':' . $props->{y_hi};
my $comm = "go insitu_tave" . " \"" . $props->{dataset_name_0} . "\" " . " \"" .$props->{variable_name_0} ."\" " . $xrange . " " . $yrange. " " . $props->{ts_bin_size};
$self->command($comm);
$self->genImage($self->{output_file});
}
sub graphic {
my ($self) = @_;
my $props = $self->{props};
#
# All variables must be from the same dataset
#
my %DsetHash = ();
map { $DsetHash{$_->getURL} = 1 } @{$self->{vars}};
die "Multiple variables must be from same dataset"
if scalar keys %DsetHash > 1;
my $var = $self->{vars}->[0];
$props->{dataset_title} = $var->getDataset->getLongName;
my $size = $props->{size} ? $props->{size} : "0.25";
$self->setWinSize($size);
$self->setup_region;
if(defined($props->{no_sampling})){
my $no_sam = $props->{no_sampling};
$self->command("def symbol no_sampling = `$no_sam`");
}
if ($props->{insitu_use_ref_map} eq 'false'){
$props->{insitu_refmap} = 0;
}elsif ($props->{insitu_use_ref_map} eq 'true' || $props->{insitu_use_ref_map} eq 'default'){
$props->{insitu_refmap} = 1;
}
my @args1 = qw(dataset_name_0 variable_name_0 dataset_title
insitu_fill_levels insitu_palette insitu_refmap
outputView style setupScript db_title
constraint_0 constraint_1 constraint_2 constraint_3
constraint_4 constraint_5 constraint_6 constraint_7);
my @extraArgs = [];
$self->runJournal('insitu_std_gif', \@args1, \@extraArgs);
$self->genImage($self->{output_file});
}
sub graphic_2_var {
my ($self) = @_;
my $props = $self->{props};
#
# All variables must be from the same dataset
#
my %DsetHash = ();
map { $DsetHash{$_->getURL} = 1 } @{$self->{vars}};
die "Multiple variables must be from same dataset"
if scalar keys %DsetHash > 1;
my $var = $self->{vars}->[0];
$props->{dataset_title} = $var->getDataset->getLongName;
my $size = $props->{size} ? $props->{size} : "0.25";
$self->setWinSize($size);
$self->setup_region;
if ($props->{insitu_use_ref_map} eq 'false'){
$props->{insitu_refmap} = 0;
}elsif ($props->{insitu_use_ref_map} eq 'true' || $props->{insitu_use_ref_map} eq 'default'){
$props->{insitu_refmap} = 1;
}
my ($data1,$var1) = getDataAndVarName($self->{vars}->[1]);
$props->{variable_name_1} = $var1;
my @args1 = qw(dataset_name_0 variable_name_0 dataset_title variable_name_1
insitu_fill_levels insitu_palette insitu_refmap
outputView style setupScript db_title
constraint_0 constraint_1 constraint_2 constraint_3
constraint_4 constraint_5 constraint_6 constraint_7);
my @extraArgs = [];
$self->runJournal('insitu_std_gif_2_var', \@args1, \@extraArgs);
$self->genImage($self->{output_file});
}
# Do nothing -- netCDF file has already been created
sub insitu_data_cdf {
my ($self) = @_;
}
#NetCDF file has been created
# - place link in DODS dir
# - return message with DODS URL and instructions
sub insitu_data_dods {
my ($self) = @_;
my $props = $self->{props};
my $output_file = $self->{output_file};
my $LASConfig = &LAS::Server::getConfig;
###my $dods_dir = 'http://ferret.pmel.noaa.gov/cgi-bin/nph-dods/data/WODB_LAS/';
my $dods_dir = $LASConfig->{OPeNDAP_directory};
my $cdf_file = $props->{dataset_name_0};
my $dods_url = $dods_dir.$cdf_file;
open OUT, ">$output_file" or die "Can't open $output_file";
print OUT "<tr><td align = \"left\">\n";
print OUT "OPeNDAP is protocol formerly known as DODS, the Distributed Oceanographic Data System. It is a tool for the sampling and retrieval of remote datasets. Click <a href=\"http://www.unidata.ucar.edu/packages/dods/index.html\";
onClick=\"newwin=window.open('http://www.unidata.ucar.edu/packages/dods/index.html', '', 'menubar=yes,toolbar=yes,resizable=yes,scrollbars=yes'); newwin.focus();return false\">here</a> for more information about OPeNDAP/DODS.<br><br>\n";
print OUT "Copy and paste the following into a Ferret session for OPeNDAP access to the data sample which you requested:<br>\n";
print OUT "use \"".$dods_url."\""."<br><br>\n";
print OUT "OR<br><br>\n";
print OUT "<p>Click on the links below to access OPeNDAP products for the data.<br>\n";
print OUT "\n
<a href=\"$dods_url.html\"\n
onClick=\"newwin=window.open('$dods_url.html', '', 'menubar=yes,toolbar=yes,resizable=yes,scrollbars=yes'); newwin.focus();return false\">Data Request Form</a><br>\n";
print OUT "\n
<a href=\"$dods_url.info\"\n
onClick=\"newwin=window.open('$dods_url.info', '', 'menubar=yes,toolbar=yes,resizable=yes,scrollbars=yes'); newwin.focus();return false\">Information</a><br>\n";
print OUT "\n
<a href=\"$dods_url.dds\"\n
onClick=\"newwin=window.open('$dods_url.dds', '', 'menubar=yes,toolbar=yes,resizable=yes,scrollbars=yes'); newwin.focus();return false\">DDS</a><br>\n";
print OUT "\n
<a href=\"$dods_url.das\"\n
onClick=\"newwin=window.open('$dods_url.das', '', 'menubar=yes,toolbar=yes,resizable=yes,scrollbars=yes'); newwin.focus();return false\">DAS</a><br><br><br></p>\n";
print OUT "</td></tr>\n";
close OUT;
}
sub insitu_data {
my ($self) = @_;
my $props = $self->{props};
my $db = $self->{db};
my $output_file = $self->{output_file};
my $db_type = $db->{config}->{db_type};
open OUT, ">$output_file" or die "Can't open $output_file";
if ($db_type eq 'WODB') {
print OUT "Data from World Ocean Data Base\n";
} elsif ($db_type eq 'JGOFS') {
print OUT "Data from Joint Global Ocean Flux Study\n";
}
print OUT "Output by Live Access Server\n";
print OUT scalar localtime, "\n";
print OUT "\n";
print OUT " Dataset title: ", $props->{dataset_title}, "\n";
print OUT " missing value: ", $db->{config}->{missing}, "\n";
# Display lat/lon/depth/time ranges
my $lon_start = $self->{props}->{x_lo};
my $lon_end = $self->{props}->{x_hi};
my $lat_start = $self->{props}->{y_lo};
my $lat_end = $self->{props}->{y_hi};
my $dep_start = $self->{props}->{z_lo};
my $dep_end = $self->{props}->{z_hi};
my $time_start = $self->{props}->{t_lo};
my $time_end = $self->{props}->{t_hi};
#format metadata values
if($lon_start > 180 && $lon_start < 360) {
my $tmp = 360 - $lon_start;
$lon_start = sprintf("%5.2f",$tmp)."W";
}elsif($lon_start >= 360){
my $tmp = $lon_start - 360;
$lon_start = sprintf("%5.2f",$tmp)."E";
}else{
my $tmp = $lon_start;
$lon_start = sprintf("%5.2f",$tmp)."E";
}
if($lon_end > 180 && $lon_end < 360) {
my $tmp = 360 - $lon_end;
$lon_end = sprintf("%5.2f",$tmp)."W";
}elsif($lon_end >= 360){
my $tmp = $lon_end - 360;
$lon_end = sprintf("%5.2f",$tmp)."E";
}else{
my $tmp = $lon_end;
$lon_end = sprintf("%5.2f",$tmp)."E";
}
if($lat_start < 0){
my $tmp = $lat_start * -1;
$lat_start = sprintf("%4.2f",$tmp)."S";
}else{
my $tmp = $lat_start;
$lat_start = sprintf("%4.2f",$tmp)."N";
}
if($lat_end < 0){
my $tmp = $lat_end * -1;
$lat_end = sprintf("%4.2f",$tmp)."S";
}else{
my $tmp = $lat_end;
$lat_end = sprintf("%4.2f",$tmp)."N";
}
my $day_start = $time_start;
my $day_end = $time_end;
print OUT "Longitude range: $lon_start to $lon_end\n";
print OUT " Latitude range: $lat_start to $lat_end\n";
print OUT " Depth range: $dep_start to $dep_end\n";
print OUT " Time range: $day_start to $day_end\n";
# Here are all the internal variables that all database drivers
# must write into the NetCDF file. Any other variables found
# are data variables.
#
# double trdim(trdim) ;
# double trange(trdim) ;
# double tax(index) ;
# float xax(index) ;
# float yax(index) ;
# float zax(index) ;
# float PROF_ID(index) ;
# float NUMPROFS(dim_one) ;
# float NUMOBS(dim_one) ;
my %varObjects = {};
my %varData = {};
my @varnames = @{$props->{variable_name}};
my $cdf_file = $props->{dataset_name_0};
my $cdf = new LAS::NetCDF($cdf_file);
# Get internal variables we know we'll need
my $prof_id = $cdf->getVariable("PROF_ID");
my $xax = $cdf->getVariable("xax");
my $yax = $cdf->getVariable("yax");
my $zax = $cdf->getVariable("zax");
my $tax = $cdf->getVariable("tax");
# Get all requested variables
foreach my $var (@varnames) {
$varObjects{$var} = $cdf->getVariable($var);
}
my $time_origin = $tax->getAttribute("time_origin");
my $t_origin_object = new TMAP::Date($time_origin);
# Print out some more information that we get from the
# data file.
print OUT " Time origin: $time_origin\n\n";
my @dims = $xax->getDims();
my $index_dim = @dims[0];
my $size = $index_dim->getSize();
# Get data for internal variables we know we'll need
my @prof_ids = $prof_id->getData([0],[$size]);
my @lons = $xax->getData([0],[$size]);
my @lats = $yax->getData([0],[$size]);
my @depths = $zax->getData([0],[$size]);
my @hours = $tax->getData([0],[$size]);
# Get data for all requested variables
foreach my $var (@varnames) {
my $varObj = $varObjects{$var};
@{$varData{$var}} = $varObj->getData([0],[$size]);
}
$cdf->close;
# Format and print the values to OUT
my @date_strings;
foreach my $hrs (@hours){
my $dec_mins = $hrs - int($hrs);
my $mins = int($dec_mins * 60);
my $dec_secs = ($dec_mins * 60) - $mins;
my $secs = int($dec_secs * 60);
my $date = $t_origin_object->addDelta(0,0,0,$hrs,$mins,$secs);
my $date_string = $date->toFerretString;
if (length($date_string) < 12){
$date_string .= " 00:00:00";
}
push(@date_strings,$date_string);
}
my ($line,$prof_id,$lon,$lat,$hrs,$date,$dep,$val) = "";
my ($long_name,$units) = "";
if ($props->{comma_separated}) {
$line = "prof_ID,longitude,latitude,hours since origin,date,depth";
foreach my $var (@varnames) {
my $varObj = $varObjects{$var};
$long_name = $varObj->getAttribute("long_name");
$units = $varObj->getAttribute("units");
$line .= ',' . $long_name;
}
} else {
$line = "prof_ID, lon, lat, hours since, date, depth";
foreach my $var (@varnames) {
my $varObj = $varObjects{$var};
$long_name = sprintf("%14s",$varObj->getAttribute("long_name"));
$units = $varObj->getAttribute("units");
$line .= ',' . $long_name;
}
}
$line .= "\n";
print OUT $line;
for (my $i=0; $i<$size; $i++) {
$line = "";
if ($props->{comma_separated}) {
$prof_id = $prof_ids[$i];
$lon = sprintf("%g",$lons[$i]);
$lat = sprintf("%g",$lats[$i]);
$hrs = sprintf("%g",$hours[$i]);
$date = sprintf("%s",$date_strings[$i]);
$dep = sprintf("%g",$depths[$i]);
$hrs = sprintf("%g",$hours[$i]);
$line = "$prof_id,$lon,$lat,$hrs,$date,$dep";
foreach my $var (@varnames) {
$val = sprintf("%g",$varData{$var}[$i]);
$line .= ',' . $val;
}
} else {
$prof_id = sprintf("%7d",$prof_ids[$i]);
$lon = sprintf("%9.4f",$lons[$i]);
$lat = sprintf("%9.4f",$lats[$i]);
$hrs = sprintf("%12.4f",$hours[$i]);
$date = sprintf("%22s",$date_strings[$i]);
$dep = sprintf("%8.2f",$depths[$i]);
$line = "$prof_id,$lon,$lat,$hrs,$date,$dep";
foreach my $var (@varnames) {
$val = sprintf("%14g",$varData{$var}[$i]);
$line .= ',' . $val;
}
}
$line .= "\n";
print OUT $line;
}
close OUT;
}
#
# $ENV{REQUEST_URI} will look something like this:
#
#/callahan-bin/LASserver.pl?xml=%3C%3Fxml+version%3D%221.0%22%3F%3E%3ClasRequest+package%3D%22%22+href%3D%22file%3Alas.xml%22+%3E%3Clink+match%3D%22%2Flasdata%2Foperations%2Finsitu_profile_list%22+%2F%3E%3Cproperties+%3E%3Cferret+%3E%3Csize+%3E.5%3C%2Fsize%3E%3Cformat+%3Ehtml%3C%2Fformat%3E%3C%2Fferret%3E%3C%2Fproperties%3E%3Cargs+%3E%3Clink+match%3D%22%2Flasdata%2Fdatasets%2Fdapper_pacific_prof_ctd%2Fvariables%2FT_20%22+%2F%3E%3Cregion+%3E%3Crange+low%3D%22204.0%22+type%3D%22x%22+high%3D%22216.0%22+%2F%3E%3Crange+low%3D%22-39.0%22+type%3D%22y%22+high%3D%22-17.0%22+%2F%3E%3Crange+low%3D%220.0%22+type%3D%22z%22+high%3D%22171%22+%2F%3E%3Crange+low%3D%2201-Jan-1983+00%3A00%3A00%22+type%3D%22t%22+high%3D%2231-Oct-1985+23%3A00%3A00%22+%2F%3E%3C%2Fregion%3E%3C%2Fargs%3E%3C%2FlasRequest%3E
#
sub insitu_profile_list {
my ($self) = @_;
my $props = $self->{props};
my $output_file = $self->{output_file};
my $z_lo = $self->{props}->{z_lo};
my $z_hi = $self->{props}->{z_hi};
my $http_host = $ENV{HTTP_HOST};
my $query = $ENV{REQUEST_URI};
# $request is the URL request for the html javascript set_link function
# $next_request is the URL request for Next button (next 100 cruises) on the html page
$query =~ m/(^.+insitu)_profile_list(.+)(%3Cformat....)html(......format%3E)(.+)(%3Cregion.%3E?)(.+)(%3C%2Fregion%3E.+$)/;
my $reqHead = "http://$http_host";;
$reqHead .= "$1"."_single_profile"."$2$3"."gif".$4;
debug("insitu_profile_list: reqhead: $reqHead\n");
my $next_reqHead = "http://$http_host";;
$next_reqHead .= "$1"."_profile_list"."$2$3"."html"."$4";
my $reqFill = $5;
my $reqRegion = "$6";
my $reqOrigRegion = "$7";
my $reqTail = "$8";
$reqFill =~ s/%3Cprofile_list_start\+%3E.+%3C%2Fprofile_list_start%3E//g;
my $reqXRange = "%3Crange+low%3D%22\"+x_lo+\"%22+type%3D%22x%22+high%3D%22\"+x_hi+\"%22+%2F%3E";
my $reqYRange = "%3Crange+low%3D%22\"+y_lo+\"%22+type%3D%22y%22+high%3D%22\"+y_hi+\"%22+%2F%3E";
my $reqTRange = "%3Crange+low%3D%22\"+t_lo+\"%22+type%3D%22t%22+high%3D%22\"+t_hi+\"%22+%2F%3E";
my $reqZRange = "%3Crange+low%3D%22$z_lo%22+type%3D%22z%22+high%3D%22$z_hi%22+%2F%3E";
my $request = "\""."$reqHead"."$reqFill"."$reqRegion"."$reqXRange"."$reqYRange"."$reqZRange"."$reqTRange"."$reqTail"."\"";
# now open the netCDF file and get all the data
my $cdf_file = $props->{dataset_name_0};
my $cdf = new LAS::NetCDF($cdf_file);
my $prof_id = $cdf->getVariable("PROF_ID");
my $xax = $cdf->getVariable("xax");
my $yax = $cdf->getVariable("yax");
my $tax = $cdf->getVariable("tax");
my $time_origin = $tax->getAttribute("time_origin");
my $origin = new TMAP::Date($time_origin);
my $date = new TMAP::Date($time_origin);
my @dims = $xax->getDims();
my $index_dim = @dims[0];
my $size = $index_dim->getSize();
my @prof_ids = $prof_id->getData([0],[$size]);
my @lons = $xax->getData([0],[$size]);
my @lats = $yax->getData([0],[$size]);
my @hours = $tax->getData([0],[$size]);
my $tot_num_profs = scalar @prof_ids;
my ($index,$lon,$lat,$hour,$minute,$second) = (0,0,0,0,0,0);
my $dateString = "dateString";
open OUT, ">$output_file" or die "Can't open $output_file";
print OUT "<html>\n";
print OUT " <head>\n";
print OUT " <script language=\"javascript\">\n";
print OUT " function set_link(lon,lat,date){\n";
print OUT " var x_lo = lon-0.001;\n";
print OUT " var x_hi = lon+0.001;\n";
print OUT " var y_lo = lat-0.001;\n";
print OUT " var y_hi = lat+0.001;\n";
print OUT " var t_lo = date;\n";
print OUT " var t_hi = date;\n";
print OUT " var link = $request\n";
print OUT " var dataWindow = window.open(link);";
print OUT " dataWindow.focus();";
print OUT "}\n";
print OUT " </script>\n";
print OUT " </head>\n";
print OUT " <!-- LAS: Redirect to browser. -->\n";
print OUT " <body>\n";
# if the original list is longer than $max_profs, we want to show the list in parts
# to avoid overloading the browser with a huge list
# if we are at the beginning of the list $props->{profile_list_start} doesn't exist
# if we are in the middle or at the end of the list $props->{profile_list_start} does exist
my $max_profs = 100;
my $prof_count= 0;
my $list_start = 0;
my $list_end = $list_start + $max_profs;
my $next_request = "";
my $next_button_html = "";
if (defined($props->{profile_list_start})){
$list_start = $props->{profile_list_start};
$list_end = $list_start + $max_profs;
}
if($list_end > $tot_num_profs){
$list_end = $tot_num_profs;
}else{
$next_reqHead .= "%3Cprofile_list_start+%3E".$list_end."%3C%2Fprofile_list_start%3E";
$next_request = "$next_reqHead"."$reqFill"."$reqRegion"."$reqOrigRegion"."$reqTail";
my $next_button_amount = "";
if ($list_end + 100 > $tot_num_profs){
$next_button_amount = $tot_num_profs - $list_end;
}else{
$next_button_amount = 100;
}
$next_button_html = "<h2><a href=\"$next_request\">Next $next_button_amount profiles</a></h2>\n";
}
my $real_start = $list_start + 1;
my $real_end = $list_end;
print OUT "<h2>Listing $real_start thru $real_end of $tot_num_profs profiles found in the region selected.</h2>";
if (defined($next_button_html)){
print OUT "$next_button_html";
}
print OUT " <h2>Click on a Profile number to request a plot.</h2>\n";
print OUT <<EOF;
<table width="90%" border=0>
<tr>
<td><div align="center">Profile Number</div></td>
<td>Longitude</td>
<td>Latitude</td>
<td>Time</td>
</tr>
EOF
my $minutes = 0;
for (my $i=$list_start; $i<$list_end; $i++) {
$prof_id = $prof_ids[$i];
$lon = sprintf("%9.4f",$lons[$i]);
$lon =~ s/ //g;
$lat = sprintf("%8.4f",$lats[$i]);
$lat =~ s/ //g;
$hour = int($hours[$i]);
$minutes = ($hours[$i] - $hour) * 60;
$minute = int($minutes);
$second = ($minutes - $minute) * 60;
$date = $origin->addDelta(0,0,0,$hour,$minute,$second);
$dateString = $date->toFerretString();
if ($index != $prof_id) {
print OUT " <tr>\n";
print OUT " <td><div align=\"center\">";
print OUT "<a href=\"javascript:set_link($lon,$lat,\'$dateString\')\">$prof_id</a>";
print OUT "</div></td>\n";
print OUT " <td>$lon</td>\n";
print OUT " <td>$lat</td>\n";
print OUT " <td>$dateString</td>\n";
print OUT " </tr>\n";
$index = $prof_id;
$prof_count++;
}
# last if($prof_count >= $max_profs);
}
print OUT " </table><br>\n";
print OUT " </body>\n";
print OUT "</html>\n";
close OUT;
}
sub insitu_single_profile {
my ($self) = @_;
my $outputView = "xy";
my $props = $self->{props};
my $var = $self->{vars}->[0];
$props->{dataset_title} = $var->getDataset->getLongName;
$props->{var_title} = $var->getAttribute('name');
my @args0 = qw(dataset_name_0 variable_name_0 dataset_title var_title);
$self->runJournal('insitu_setup_single', \@args0, undef, 'insitu_setup_single', \@args0);
my $comm = "go insitu_single" . " \"" . $props->{variable_name_0}."_single\"";
$self->command($comm);
$self->genImage($self->{output_file});
}
############################################################
#
# The rest are internal routines used to generate
# requests for and access the non-NetCDF data.
#
############################################################
sub getVariableConstraint {
my ($self, $constraint) = @_;
my $value = $constraint->getValue;
$value =~ s/\s+//g;
next if (! defined $value || $value eq "");
#
# Let Perl evaluate the validity of the expression for us
#
{
my $lastwarn = $SIG{'__WARN__'};
local($SIG{'__WARN__'}) = sub { $@ = $_[0]};
eval "use strict; $value";
die "Invalid constraint expression: '$value' -- must be a number" if $@;
}
my $var = $constraint->getVariable->getName;
my $op = $constraint->getOp;
my @values = ($var, $op, $value);
return @values;
}
# TODO 06JAN2005 (jm) move database specific formatting to individual DB drivers
# I mean below only three values and 'Always quote non-numeric strings'
sub getTextConstraint {
my ($self,$constraint) = @_;
my @values = $constraint->getValues;
if (scalar @values != 3){
die "Text constraints for JGOFS server must have three and only three values";
}
# Always quote non-numeric strings.
unless ($values[2] =~ /^([+-]?)(?=\d|\.\d)\d*(\.\d*)?([Ee]([+-]?\d+))?$/) {
$values[2] = "\"" . $values[2] . "\"";
}
return @values;
}
# TODO 06JAN2005 Need to test with DB Drivers other than WODB
sub getTextFieldConstraint {
my ($self,$constraint) = @_;
my @values = split(',',$constraint->getValue);
if (scalar @values != 3){
die "Textfield constraints must have three and only three comma separated values, i.e. \"name,operator,value\"\n";
}
return @values;
}
sub getExternalData {
my ($self, $dsetname, $isMetaOnly) = @_;
my $props = $self->{props};
my @regArgs = ($props->{x_lo}, $props->{x_hi},
$props->{y_lo}, $props->{y_hi},
$props->{z_lo}, $props->{z_hi},
$props->{t_lo}, $props->{t_hi});
@regArgs = map { defined($_) ? $_ : 0 } @regArgs;
# In order to enable reuse of existing query results so that a user can look
# at different visualizations without having to download data every time, we
# will generate a data file name below that is based on the database query.
# In the case of data products, rather than visualizations, the qurey results
# must be in the output file that LAS has specified. So we will leave the
# file name alone in this case.
my ($name,$output_path,$suffix) = fileparse($self->{output_file}, '\.(nc|cdf)');
my $output_file = "";
if ( $suffix ) {
$output_file = $self->{output_file};
}
my $DBConfig = $self->{db_config};
my $db_type = $DBConfig->{db_type};
my $db;
if ($db_type eq "mysql") {
debug("Creating new TMAP::DBI::Dataset\n");
$self->{db} = $db = new TMAP::DBI::Dataset($DBConfig);
} elsif ($db_type eq "JGOFS") {
debug("Creating new TMAP::JGOFS::Dataset\n");
$self->{db} = $db = new TMAP::JGOFS::Dataset($DBConfig);
} elsif ($db_type eq "WODB") {
debug("Creating new TMAP::WODB::Dataset\n");
$self->{db} = $db = new TMAP::WODB::Dataset($DBConfig);
} elsif($db_type eq "Dapper"){
$self->{db} = $db = new TMAP::Dapper::Dataset($DBConfig);
} else {
die "getExternalData: Database type \"$db_type\" not recognized.\n";
}
$db->{isMetaOnly} = $isMetaOnly;
my @varnames = @{$props->{variable_name}};
my @vars = @{$self->{vars}};
foreach my $varname (@varnames){
my $var = shift @vars;
$db->setVariableAttributes($varname,$var->getLongName,$var->getAttribute("units"),$DBConfig->{missing});
$var->setURL($output_file);
}
if (defined ($DBConfig->{cruiseID})){
$db->setVariableAttributes($DBConfig->{cruiseID},'CRUISE ID','unitless',$DBConfig->{missing});
}
# Get the longitude domain lo/hi values and do a validity check
my ($lon_domain_lo,$lon_domain_hi) = split(':',$DBConfig->{lon_domain});
if (($lon_domain_hi - $lon_domain_lo) ne 360) {
die "Installation Error: The longitude domain specified by \n<lon_domain> [" . $lon_domain_lo . ":" . $lon_domain_hi . "] must span 360 degrees.\n";
}
$DBConfig->{lon_domain_lo} = $lon_domain_lo;
$DBConfig->{lon_domain_hi} = $lon_domain_hi;
$db->setAxisAttributes("x",$DBConfig->{longitude},"Longitude","degrees_east");
$db->setAxisAttributes("y",$DBConfig->{latitude},"Latitude","degrees_north");
if ($DBConfig->{depth}) {
$db->setAxisAttributes("z",$DBConfig->{depth},"Depth",$DBConfig->{depth_units});
}
# NOTE: The time axis units must be set to 'hours'.
$db->setAxisAttributes("t",$DBConfig->{time},"Time","hours");
my $start = new TMAP::Date($regArgs[6]);
die "Invalid date: $start" if ! $start->isOK;
my $end = new TMAP::Date($regArgs[7]);
die "Invalid date: $end" if ! $end->isOK;
$db->setTimeRange($start,$end);
$db->setTimeOrigin($start);
$db->setTable($DBConfig->{db_table});
$db->addAxisConstraints(@regArgs[0..5], $start->toString, $end->toString);
# Add any user specified constraints
#
my $constraint_num = 0;
my @constraints = $self->{req}->getConstraints;
foreach my $constraint (@constraints){
# Print each constraint to the debug file.
foreach my $key (keys (%{$constraint})){
if(ref($constraint->{$key}) eq 'ARRAY'){
debug("Constraint: $key == array: (",
join(',', @{$constraint->{$key}}), ")\n");
}elsif(ref($constraint->{$key}) eq 'HASH'){
debug("Constraint: $key == hash: (");
while (my ($key,$value) = each %{$constraint->{$key}}) {
debug(", $key=$value");
}
debug(")\n");
}else{
debug("Constraint: $key == $constraint->{$key}\n");
}
}
# Add each constraint using the driver specific method.
my @constraint_values = ();
if (ref($constraint) eq 'LAS::Constraint::Variable'){
@constraint_values = $self->getVariableConstraint($constraint);
} elsif (ref($constraint) eq 'LAS::Constraint::Text'){
@constraint_values = $self->getTextConstraint($constraint);
} elsif (ref($constraint) eq 'LAS::Constraint::TextField'){
@constraint_values = $self->getTextFieldConstraint($constraint);
} else {
die "Unknown constraint type:", ref($constraint);
}
my $constraint_label = $db->addConstraint(@constraint_values);
# A text string description of each constraint is returned and needs
# to be added to the properties for use in labeling the plot
my $constraint_name = "constraint_" . $constraint_num;
$self->{props}->{$constraint_name} = $constraint_label;
$constraint_num++;
}
# For visualization products the output_file has been set to a null string.
# Here we create a new outputfile name based on the database query. This
# will allow multiple visualizations to reuse the same underlying data.
if ($output_file eq "") {
my $queryString = $db->getQueryString();
my $md5 = new MD5;
$md5->reset;
$md5->add($queryString);
my $digest = $md5->digest;
#$digest = unpack("H*", $digest);
$digest = unpack("H*", $digest);
$output_file = $output_path . $digest . ".nc";
my @varnames = @{$props->{variable_name}};
my @vars = @{$self->{vars}};
foreach my $varname (@varnames) {
my $var = shift @vars;
$var->setURL($output_file);
}
}
#
# Only get data if not cached
#
if (! -f $output_file) {
eval {
my $elapsed = "";
debug("getExternalData: calling getData\n");
$db->startTimer();
$db->getData();
$elapsed = $db->getElapsed();
debug("getExternalData: $elapsed secs to get data from the database\n");
$db->writeCDFFile($output_file);
$elapsed = $db->getElapsed();
debug("getExternalData: $elapsed secs to write the CDF file\n");
$db->disconnect();
debug("getExternalData: Finished creating CDF file $output_file\n");
};
if ($@){
debug("getExternalData: data read/write error: $@");
die $@;
}
} else {
debug("getExternalData: Reusing cached data \"$output_file\"\n");
}
$self->{props}->{dataset_title} = $self->{props}->{dataset_name_0};
$self->{props}->{dataset_name_0} = $output_file;
$self->{props}->{db_title} = $DBConfig->{db_title};
#
# Set all of the dataset names to be the same as the netCDF output file
#
my @new_names;
for (@{$props->{dataset_name}}){
push(@new_names, $output_file);
}
$props->{dataset_name} = \@new_names;
debug("getExternalData: Completely finished, returning now.\n");
my $tmp = join(',',@new_names);
}
sub accessDatabase {
my $self = shift;
my $var = $self->{vars}->[0];
my $dsetname = $var->getDataset->getAttribute('url');
# Get the database properties specified in the dataset .xml file.
# A hash of these properties is passed to the individual database drivers
# that use this information to interact with various back end datbases.
$self->{db_config} = {};
$self->{db_config} = &LAS::mergeProperties($self->{db_config},
scalar $var->getDataset->getProperties('database_access'));
$self->{db_config}->{dsetname} = $dsetname;
$self->debugProps('database_access', $self->{db_config});
# Only invoke the getExternalData routine if there is a database type
# specified in the xml. In 'normal' cases, the 'db_type' attribute
# will be empty which means that this is just a normal NetCDF file
# and the call getExternalData is unnecessary.
if ($self->{db_config}->{db_type}) {
$self->{method} = $self->{req}->getOp->getAttribute("method");
debug("method is: ",$self->{method},"\n");
my $isMetaOnly = 0;
if($self->{method} =~ m/insitu_meta_xy/ ||
$self->{method} =~ m/insitu_tsum/ ||
$self->{method} =~ m/insitu_cruise_list/ ||
$self->{method} =~ m/insitu_profile_list/){
$isMetaOnly = 1;
}
my $numvars = scalar @{$self->{vars}};
die "Property/property plot requires two (and only two) variables; found $numvars" if (($self->{method} eq "insitu_property") && $numvars != 2);
eval{
return $self->getExternalData($dsetname, $isMetaOnly);
};
if ($@){
debug("LAS::Server::Ferret accessDatabase: error: $@");
die $@;
}
}
}
1;
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