Revision 4744
Added by walbridge almost 16 years ago
| src/perl/register-dataset.cgi | ||
|---|---|---|
| 432 | 432 |
debug("NO SUCCESS");
|
| 433 | 433 |
debug("Message is: $docStatus");
|
| 434 | 434 |
push(@errorMessages, $docStatus); |
| 435 |
} else {
|
|
| 436 |
deleteRemovedData(); |
|
| 435 | 437 |
} |
| 436 | 438 |
|
| 437 | 439 |
debug("B3");
|
| 438 | 440 |
} else {
|
| 441 |
debug("M1");
|
|
| 442 |
|
|
| 439 | 443 |
# document is being modified |
| 440 | 444 |
$docid = incrementRevision($FORM::docid); |
| 441 | 445 |
|
| ... | ... | |
| 447 | 451 |
if (! $response) {
|
| 448 | 452 |
push(@errorMessages, $metacat->getMessage()); |
| 449 | 453 |
push(@errorMessages, "Failed while updating.\n"); |
| 450 |
} |
|
| 451 |
|
|
| 454 |
} |
|
| 455 |
|
|
| 456 |
debug("M2, $docid");
|
|
| 452 | 457 |
if (scalar(@errorMessages)) {
|
| 453 |
debug("ErrorMessages defined in modify.");
|
|
| 458 |
debug("Errors defined in modify.");
|
|
| 454 | 459 |
|
| 455 | 460 |
$$templateVars{'docid'} = $FORM::docid;
|
| 456 | 461 |
copyFormToTemplateVars(); |
| ... | ... | |
| 458 | 463 |
$$templateVars{'errorMessages'} = \@errorMessages;
|
| 459 | 464 |
$error = 1; |
| 460 | 465 |
} else {
|
| 466 |
deleteRemovedData(); |
|
| 461 | 467 |
$$templateVars{'docid'} = $docid;
|
| 462 | 468 |
$$templateVars{'cfg'} = $skinName;
|
| 463 | 469 |
} |
| ... | ... | |
| 884 | 890 |
for (my $fileNum = 0; $fileNum <= $FORM::upCount; $fileNum++) {
|
| 885 | 891 |
my $fn = 'upload_' . $fileNum; |
| 886 | 892 |
if (hasContent(param($fn))) {
|
| 887 |
debug("Retrieving metadata for file: $fn");
|
|
| 888 |
($docid, $fileInfo) = fileMetadata($fileNum); |
|
| 889 |
$uploadedFiles{ $docid } = $fileInfo;
|
|
| 893 |
# ignore data which is scheduled for deletion |
|
| 894 |
if (grep {$_ eq ("uploadname_$fileNum")} @FORM::deletefile) {
|
|
| 895 |
debug("Not generating metadata for file scheduled for deletion: $fn");
|
|
| 896 |
} else {
|
|
| 897 |
debug("Retrieving metadata for file: $fn");
|
|
| 898 |
($docid, $fileInfo) = fileMetadata($fileNum); |
|
| 899 |
$uploadedFiles{ $docid } = $fileInfo;
|
|
| 900 |
} |
|
| 890 | 901 |
} |
| 891 | 902 |
} |
| 892 | 903 |
|
| ... | ... | |
| 905 | 916 |
|
| 906 | 917 |
# process an _existing_ data file, which is already within Metacat. |
| 907 | 918 |
if ($fileHash =~ /ondisk/) {
|
| 908 |
my $finfo = $fileHash; |
|
| 909 |
$finfo =~ s/ondisk://g; |
|
| 910 |
($docid, $fileHash) = split(":", $finfo);
|
|
| 919 |
($docid, $fileHash) = datafileInfo($fileHash); |
|
| 911 | 920 |
$outFile = $dataDir . "/" . $docid; |
| 912 | 921 |
} else {
|
| 913 | 922 |
# normalize input filenames; Windows filenames include full paths |
| ... | ... | |
| 960 | 969 |
return ($docid, \%dataInfo); |
| 961 | 970 |
} |
| 962 | 971 |
|
| 972 |
sub datafileInfo {
|
|
| 973 |
my $finfo = shift; |
|
| 974 |
$finfo =~ s/ondisk://g; |
|
| 975 |
return my ($docid, $fileHash) = split (":", $finfo);
|
|
| 976 |
} |
|
| 963 | 977 |
|
| 964 | 978 |
sub processFile {
|
| 965 | 979 |
my $fileName = shift; |
| ... | ... | |
| 1025 | 1039 |
return ($outputName, $digest); |
| 1026 | 1040 |
} |
| 1027 | 1041 |
|
| 1042 |
sub deleteRemovedData {
|
|
| 1043 |
# if we have any associated datafiles which are scheduled for deletion, remove them now |
|
| 1044 |
for (my $delNum = 0; $delNum <= $FORM::delCount; $delNum++) {
|
|
| 1045 |
# need to look up the actual upload number, which is contained in the name |
|
| 1046 |
my $upNum = param("deletefile_$delNum");
|
|
| 1047 |
$upNum =~ s/uploadname_//; |
|
| 1048 |
my $upn = param("upload_$upNum");
|
|
| 1049 |
if (hasContent($upn)) {
|
|
| 1050 |
debug("Deleting upload_$upNum, $upn");
|
|
| 1051 |
if (grep {$_ eq ("uploadname_$upNum")} @FORM::deletefile) {
|
|
| 1052 |
if (param("upload_$upNum") =~ /ondisk/) {
|
|
| 1053 |
debug("got a file which is ondisk, proceeding with deletion");
|
|
| 1054 |
deleteFileData(param("upload_$upNum"));
|
|
| 1055 |
} else {
|
|
| 1056 |
debug("got an old reference, not yet in EML, remove from tempdir");
|
|
| 1057 |
deleteFile(param("uploadname_$upNum"));
|
|
| 1058 |
} |
|
| 1059 |
} else {
|
|
| 1060 |
debug("Name didn't match in deletefile list");
|
|
| 1061 |
} |
|
| 1062 |
} |
|
| 1063 |
} |
|
| 1064 |
} |
|
| 1065 |
|
|
| 1028 | 1066 |
sub deleteFile {
|
| 1029 | 1067 |
my $input = shift; |
| 1030 |
|
|
| 1031 |
if ($input =~ /ondisk/) {
|
|
| 1032 |
my $docid = $input; |
|
| 1033 |
$docid =~ s/ondisk://g; |
|
| 1034 |
# XXX FIXME once ondisk support is enabled |
|
| 1035 |
#my $response = $metacat->delete($docid); |
|
| 1036 |
my $response; |
|
| 1068 |
my $fileName = $tempDir . "/" . $input; |
|
| 1069 |
|
|
| 1070 |
if (-e $fileName) {
|
|
| 1071 |
unlink $fileName or |
|
| 1072 |
debug("Failed to delete file $fileName.");
|
|
| 1073 |
} else {
|
|
| 1074 |
debug("Unable to find file $fileName");
|
|
| 1075 |
} |
|
| 1076 |
if (!-e $fileName) {
|
|
| 1077 |
debug("Successfully deleted $fileName");
|
|
| 1078 |
} |
|
| 1079 |
} |
|
| 1080 |
|
|
| 1081 |
sub deleteFileData {
|
|
| 1082 |
my $input = shift; |
|
| 1083 |
my ($docid, $fileHash) = datafileInfo($input); |
|
| 1084 |
my $metacat = Metacat->new($metacatUrl); |
|
| 1085 |
|
|
| 1086 |
my ($username, $password) = getCredentials(); |
|
| 1087 |
my $response = $metacat->login($username, $password); |
|
| 1088 |
if (!$response) {
|
|
| 1089 |
my $msg = $metacat->getMessage(); |
|
| 1090 |
push(@errorMessages, "Failed to login with credentials for `$username`. Error was $msg"); |
|
| 1091 |
debug("Failed to login with given credentials for username $username, Error is: $msg");
|
|
| 1092 |
} else {
|
|
| 1093 |
$response = $metacat->delete($docid); |
|
| 1037 | 1094 |
if (!$response) {
|
| 1038 | 1095 |
my $msg = $metacat->getMessage(); |
| 1039 |
push(@errorMessages, "Failed to delete existing file. Error was: $msg\n");
|
|
| 1096 |
push(@errorMessages, "Failed to delete existing file. Error was: $msg"); |
|
| 1040 | 1097 |
debug("Delete -- Error is: $msg");
|
| 1041 | 1098 |
} else {
|
| 1042 | 1099 |
debug("Delete -- Success! Removed docid $docid");
|
| 1043 | 1100 |
} |
| 1044 |
} else {
|
|
| 1045 |
my $fileName = $tempDir . "/" . $input; |
|
| 1046 |
|
|
| 1047 |
if (-e $fileName) {
|
|
| 1048 |
unlink $fileName or |
|
| 1049 |
debug("Failed to delete file $fileName.");
|
|
| 1050 |
} else {
|
|
| 1051 |
debug("Unable to find file $fileName");
|
|
| 1052 |
} |
|
| 1053 |
if (!-e $fileName) {
|
|
| 1054 |
debug("Successfully deleted $fileName");
|
|
| 1055 |
} |
|
| 1056 | 1101 |
} |
| 1057 | 1102 |
} |
| 1058 | 1103 |
|
| ... | ... | |
| 1933 | 1978 |
my $node; |
| 1934 | 1979 |
my $tempResult; |
| 1935 | 1980 |
my $tempNode; |
| 1936 |
my $aoCount = 1;
|
|
| 1981 |
my $aoCount = 0;
|
|
| 1937 | 1982 |
my $foundDSO; |
| 1938 | 1983 |
|
| 1939 | 1984 |
# set variable values |
| ... | ... | |
| 2239 | 2284 |
my $temp = findValue($tempNode, "mediumName"); |
| 2240 | 2285 |
if (substr($temp, 0, 5) eq "other") {
|
| 2241 | 2286 |
$$templateVars{'dataMedium'} = substr($temp, 0, 5);
|
| 2242 |
$$templateVars{'dataMediumOther'} = substr($temp, 5);
|
|
| 2287 |
$$templateVars{'dataMediumOther'} = substr($temp, 6);
|
|
| 2243 | 2288 |
} else {
|
| 2244 | 2289 |
$$templateVars{'dataMedium'} = $temp;
|
| 2245 | 2290 |
} |
| ... | ... | |
| 2838 | 2883 |
my $userPass = $FORM::password; |
| 2839 | 2884 |
my $dname = "uid=$userDN,o=$userOrg,dc=ecoinformatics,dc=org"; |
| 2840 | 2885 |
|
| 2841 |
if ($FORM::userLoggedIn eq 'true') {
|
|
| 2842 |
my $session = CGI::Session->load(); |
|
| 2843 |
if (!($session->is_empty || $session->is_expired)) {
|
|
| 2844 |
$dname = $session->param("username");
|
|
| 2845 |
$userPass = $session->param("password");
|
|
| 2846 |
} |
|
| 2886 |
my $session = CGI::Session->load(); |
|
| 2887 |
if (!($session->is_empty || $session->is_expired)) {
|
|
| 2888 |
$dname = $session->param("username");
|
|
| 2889 |
$userPass = $session->param("password");
|
|
| 2847 | 2890 |
} |
| 2848 | 2891 |
|
| 2849 | 2892 |
return ($dname, $userPass); |
| ... | ... | |
| 3016 | 3059 |
} |
| 3017 | 3060 |
|
| 3018 | 3061 |
$emldoc .= EMLStart(); |
| 3019 |
# TODO SCW: make sure this replacement works as expected |
|
| 3020 | 3062 |
$emldoc .= accessElement("true");
|
| 3021 | 3063 |
$emldoc .= $dataElem; |
| 3022 | 3064 |
$emldoc .= EMLEnd(); |
| ... | ... | |
| 3026 | 3068 |
my $newDocid = incrementRevision($docid); |
| 3027 | 3069 |
|
| 3028 | 3070 |
$emldoc =~ s/packageId=\"$docid\"/packageId=\"$newDocid\"/; |
| 3029 |
$response = $metacat->update($newDocid, $emldoc);
|
|
| 3071 |
$response = $metacat->update($docid, $emldoc);
|
|
| 3030 | 3072 |
|
| 3031 | 3073 |
if (! $response) {
|
| 3032 | 3074 |
debug("Error while updating in handleModAccept.");
|
| ... | ... | |
| 3741 | 3783 |
$$templateVars{'taxaCount'} = $taxonCount-1;
|
| 3742 | 3784 |
$$templateVars{'taxaAuth'} = normalizeCD($FORM::taxaAuth);
|
| 3743 | 3785 |
my $deleteCount = 0; |
| 3786 |
|
|
| 3787 |
for (my $i = 0; $i <= scalar(@FORM::deletefile); $i++) {
|
|
| 3788 |
my $delfile = pop(@FORM::deletefile); |
|
| 3789 |
$$templateVars{"deletefile_$deleteCount"} = $delfile;
|
|
| 3790 |
debug(" creating deletefile_$deleteCount = $delfile");
|
|
| 3791 |
$deleteCount++; |
|
| 3792 |
} |
|
| 3793 |
$$templateVars{"delCount"} = $deleteCount;
|
|
| 3744 | 3794 |
for (my $upNum = 0; $upNum <= $FORM::upCount; $upNum++) {
|
| 3745 | 3795 |
my $upn = "upload_$upNum"; |
| 3746 | 3796 |
if (hasContent(param($upn))) {
|
| 3747 |
if (grep {$_ eq ("uploadname_$upNum")} @FORM::deletefile) {
|
|
| 3748 |
deleteFile(param("uploadname_$upNum"));
|
|
| 3749 |
$deleteCount++; |
|
| 3750 |
} else {
|
|
| 3751 |
debug("Processing existing file: $upn");
|
|
| 3752 |
$$templateVars{"upload_$upNum"} = param("upload_$upNum");
|
|
| 3753 |
$$templateVars{"uploadname_$upNum"} = param("uploadname_$upNum");
|
|
| 3754 |
$$templateVars{"uploadtype_$upNum"} = param("uploadtype_$upNum");
|
|
| 3755 |
$$templateVars{"uploadperm_$upNum"} = param("uploadperm_$upNum");
|
|
| 3756 |
} |
|
| 3797 |
debug("Processing existing file: $upn");
|
|
| 3798 |
$$templateVars{"upload_$upNum"} = param("upload_$upNum");
|
|
| 3799 |
$$templateVars{"uploadname_$upNum"} = param("uploadname_$upNum");
|
|
| 3800 |
$$templateVars{"uploadtype_$upNum"} = param("uploadtype_$upNum");
|
|
| 3801 |
$$templateVars{"uploadperm_$upNum"} = param("uploadperm_$upNum");
|
|
| 3757 | 3802 |
} |
| 3758 | 3803 |
} |
| 3759 | 3804 |
|
| ... | ... | |
| 3763 | 3808 |
if (hasContent(param($fn))) {
|
| 3764 | 3809 |
my $fileName = eval "\$FORM::file_$fileNum"; |
| 3765 | 3810 |
debug("Processing file: $fn");
|
| 3766 |
# Upload the file object itself to a temporary file, copy file |
|
| 3767 |
# metadata to form |
|
| 3811 |
# Upload the file object itself to a temporary file, copy file metadata to form |
|
| 3768 | 3812 |
my $fileInfo = processFile($fileName); |
| 3769 | 3813 |
# if we have existing uploads, increment the counter to avoid overwriting |
| 3770 | 3814 |
my $totalFileNum = $fileNum + $FORM::upCount; |
| ... | ... | |
| 3776 | 3820 |
} |
| 3777 | 3821 |
} |
| 3778 | 3822 |
# total uploads are: new uploads - deleted files + original uploads |
| 3779 |
$$templateVars{'upCount'} = $uploadCount - $deleteCount + $FORM::upCount;
|
|
| 3823 |
$$templateVars{'upCount'} = $uploadCount + $FORM::upCount;
|
|
| 3780 | 3824 |
$$templateVars{'methodTitle'} = normalizeCD($FORM::methodTitle);
|
| 3781 | 3825 |
|
| 3782 | 3826 |
my @tempMethodPara; |
| ... | ... | |
| 3787 | 3831 |
$$templateVars{'studyExtentDescription'} = normalizeCD($FORM::studyExtentDescription);
|
| 3788 | 3832 |
$$templateVars{'samplingDescription'} = normalizeCD($FORM::samplingDescription);
|
| 3789 | 3833 |
$$templateVars{'origStateContact'} = $FORM::origState;
|
| 3790 |
|
|
| 3791 | 3834 |
$$templateVars{'modules'} = $modules;
|
| 3792 | 3835 |
$$templateVars{'required'} = $required;
|
| 3793 | 3836 |
$$templateVars{'show'} = $show;
|
| 3794 | 3837 |
$$templateVars{'site'} = $FORM::site;
|
| 3795 |
|
|
| 3796 | 3838 |
$$templateVars{'docid'} = $FORM::docid;
|
| 3797 | 3839 |
|
| 3798 | 3840 |
# Check if the session exists |
| ... | ... | |
| 3800 | 3842 |
if (!($session->is_empty || $session->is_expired)) {
|
| 3801 | 3843 |
$$templateVars{'userLoggedIn'} = 'true';
|
| 3802 | 3844 |
} |
| 3845 |
|
|
| 3846 |
# Errors from validation function. print the errors out using the response template |
|
| 3847 |
if (scalar(@errorMessages)) {
|
|
| 3848 |
debug("Error messages found when confirming data.");
|
|
| 3849 |
$$templateVars{'status'} = 'failure';
|
|
| 3850 |
$$templateVars{'errorMessages'} = \@errorMessages;
|
|
| 3851 |
$error = 1; |
|
| 3852 |
} |
|
| 3803 | 3853 |
|
| 3804 |
if (! $error) {
|
|
| 3854 |
if (!$error) {
|
|
| 3805 | 3855 |
# If no errors, then print out data in confirm Data template |
| 3806 | 3856 |
$$templateVars{'section'} = "Confirm Data";
|
| 3807 | 3857 |
$template->process($templates->{'confirmData'}, $templateVars);
|
| 3808 | 3858 |
|
| 3809 | 3859 |
} else {
|
| 3810 |
# Errors from validation function. print the errors out using the response template |
|
| 3811 |
if (scalar(@errorMessages)) {
|
|
| 3812 |
$$templateVars{'status'} = 'failure';
|
|
| 3813 |
$$templateVars{'errorMessages'} = \@errorMessages;
|
|
| 3814 |
$error = 1; |
|
| 3815 |
} |
|
| 3816 | 3860 |
# Create our HTML response and send it back |
| 3817 |
$$templateVars{'function'} = "submitted";
|
|
| 3818 |
$$templateVars{'section'} = "Submission Status";
|
|
| 3819 |
$template->process($templates->{'response'}, $templateVars);
|
|
| 3861 |
$$templateVars{'function'} = "submitted";
|
|
| 3862 |
$$templateVars{'section'} = "Submission Status";
|
|
| 3863 |
$template->process($templates->{'response'}, $templateVars);
|
|
| 3820 | 3864 |
} |
| 3821 | 3865 |
} |
| 3822 | 3866 |
|
Also available in: Unified diff
Complete implementation of otherEntity editing and deletion, syncronizing changes to EML document. Now all elements which are created by the form can also be edited (Bug #3319). Also prevented associated party duplication on modification.