You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
359 lines
19 KiB
359 lines
19 KiB
<?php
|
|
// turn on warnings and notice during developement
|
|
include('initialize/PhpErrorSettings.inc.php');
|
|
// Project: Web Reference Database (refbase) <http://www.refbase.net>
|
|
// Copyright: Matthias Steffens <mailto:refbase@extracts.de> and the file's
|
|
// original author(s).
|
|
//
|
|
// This code is distributed in the hope that it will be useful,
|
|
// but WITHOUT ANY WARRANTY. Please see the GNU General Public
|
|
// License for more details.
|
|
//
|
|
// File: ./import.php
|
|
// Repository: $HeadURL: file:///svn/p/refbase/code/branches/bleeding-edge/import.php $
|
|
// Author(s): Matthias Steffens <mailto:refbase@extracts.de>
|
|
//
|
|
// Created: 17-Feb-06, 20:57
|
|
// Modified: $Date: 2015-02-16 20:53:19 +0000 (Mon, 16 Feb 2015) $
|
|
// $Author: karnesky $
|
|
// $Revision: 1405 $
|
|
|
|
// Import form that offers to import records from Reference Manager (RIS), CSA Illumina,
|
|
// RefWorks Tagged Format, SciFinder Tagged Format, ISI Web of Science, PubMed MEDLINE, PubMed XML, MODS XML,
|
|
// Endnote Tagged Text, BibTeX or COPAC. Import of the latter five formats is provided via use of bibutils.
|
|
|
|
|
|
// Incorporate some include files:
|
|
include 'includes/header.inc.php'; // include header
|
|
include 'includes/footer.inc.php'; // include footer
|
|
include 'includes/include.inc.php'; // include common functions
|
|
include 'initialize/ini.inc.php'; // include common variables
|
|
|
|
// --------------------------------------------------------------------
|
|
|
|
// START A SESSION:
|
|
// call the 'start_session()' function (from 'include.inc.php') which will also read out available session variables:
|
|
start_session(true);
|
|
|
|
// --------------------------------------------------------------------
|
|
|
|
// Initialize preferred display language:
|
|
// (note that 'locales.inc.php' has to be included *after* the call to the 'start_session()' function)
|
|
include 'includes/locales.inc.php'; // include the locales
|
|
|
|
// --------------------------------------------------------------------
|
|
|
|
// Extract session variables:
|
|
if (isset($_SESSION['errors']))
|
|
{
|
|
$errors = $_SESSION['errors']; // read session variable (only necessary if register globals is OFF!)
|
|
|
|
// Note: though we clear the session variable, the current error message is still available to this script via '$errors':
|
|
deleteSessionVariable("errors"); // function 'deleteSessionVariable()' is defined in 'include.inc.php'
|
|
}
|
|
else
|
|
$errors = array(); // initialize the '$errors' variable in order to prevent 'Undefined variable...' messages
|
|
|
|
if (isset($_SESSION['formVars']))
|
|
{
|
|
$formVars = $_SESSION['formVars']; // read session variable (only necessary if register globals is OFF!)
|
|
|
|
// Remove slashes from parameter values if 'magic_quotes_gpc = On':
|
|
foreach($formVars as $varname => $value)
|
|
$formVars[$varname] = stripSlashesIfMagicQuotes($value); // function 'stripSlashesIfMagicQuotes()' is defined in 'include.inc.php'
|
|
|
|
// Note: though we clear the session variable, the current form variables are still available to this script via '$formVars':
|
|
deleteSessionVariable("formVars"); // function 'deleteSessionVariable()' is defined in 'include.inc.php'
|
|
}
|
|
else
|
|
$formVars = array();
|
|
|
|
// --------------------------------------------------------------------
|
|
|
|
// Initialize preferred display language:
|
|
// (note that 'locales.inc.php' has to be included *after* the call to the 'start_session()' function)
|
|
include 'includes/locales.inc.php'; // include the locales
|
|
|
|
// --------------------------------------------------------------------
|
|
|
|
// If there's no stored message available:
|
|
if (!isset($_SESSION['HeaderString']))
|
|
{
|
|
if (empty($errors)) // provide one of the default messages:
|
|
{
|
|
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable does contain 'allow_batch_import'...
|
|
$HeaderString = "Import records:"; // Provide the default message
|
|
else
|
|
$HeaderString = "Import a record:"; // Provide the default message
|
|
}
|
|
else // -> there were errors validating the user's data input
|
|
$HeaderString = "There were validation errors regarding the data you entered:";
|
|
}
|
|
else // there is already a stored message available
|
|
{
|
|
$HeaderString = $_SESSION['HeaderString']; // extract 'HeaderString' session variable (only necessary if register globals is OFF!)
|
|
|
|
// Note: though we clear the session variable, the current message is still available to this script via '$HeaderString':
|
|
deleteSessionVariable("HeaderString"); // function 'deleteSessionVariable()' is defined in 'include.inc.php'
|
|
}
|
|
|
|
// Adopt the page title & some labels according to the user's permissions:
|
|
if (isset($_SESSION['user_permissions']) AND !preg_match("/allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable does NOT contain 'allow_batch_import'...
|
|
{
|
|
$pageTitle = " -- Import Record"; // adopt page title
|
|
$textEntryFormLabel = "Record"; // adopt the label for the text entry form
|
|
$rowSpan = ""; // adopt table row span parameter
|
|
}
|
|
else
|
|
{
|
|
$pageTitle = " -- Import Records";
|
|
$textEntryFormLabel = "Records";
|
|
$rowSpan = " rowspan=\"2\"";
|
|
}
|
|
|
|
// Extract the view type requested by the user (either 'Mobile', 'Print', 'Web' or ''):
|
|
// ('' will produce the default 'Web' output style)
|
|
if (isset($_REQUEST['viewType']))
|
|
$viewType = $_REQUEST['viewType'];
|
|
else
|
|
$viewType = "";
|
|
|
|
// If there were some errors on submit -> Re-load the data that were submitted by the user:
|
|
if (!empty($errors))
|
|
{
|
|
if (isset($formVars['formType']))
|
|
$formType = $formVars['formType']; // get the form type that was submitted by the user (and which subsequently caused an error)
|
|
else
|
|
$formType = "";
|
|
|
|
// (A) main import form:
|
|
if (isset($formVars['sourceText'])) // '$formVars['sourceText']' may be non-existent in the (unlikely but possible) event that a user calls 'import_modify.php' directly
|
|
$sourceText = $formVars['sourceText'];
|
|
else
|
|
$sourceText = "";
|
|
|
|
if (isset($formVars['importRecordsRadio'])) // 'importRecordsRadio' is only set if user has 'batch_import' permission
|
|
$importRecordsRadio = $formVars['importRecordsRadio'];
|
|
else
|
|
$importRecordsRadio = "";
|
|
|
|
if (isset($formVars['importRecords'])) // 'importRecords' is only set if user has 'batch_import' permission
|
|
$importRecords = $formVars['importRecords'];
|
|
else
|
|
$importRecords = "1";
|
|
|
|
// check whether the user marked the checkbox to skip records with unrecognized data format:
|
|
if (isset($formVars['skipBadRecords']))
|
|
$skipBadRecords = $formVars['skipBadRecords'];
|
|
else
|
|
$skipBadRecords = "";
|
|
|
|
// (B) "Import IDs" form (imports records from PubMed ID, arXiv ID, DOI or OpenURL):
|
|
if (isset($formVars['sourceIDs']))
|
|
$sourceIDs = $formVars['sourceIDs'];
|
|
else
|
|
$sourceIDs = "";
|
|
}
|
|
else // display an empty form (i.e., set all variables to an empty string [""] or their default values, respectively):
|
|
{
|
|
$formType = "";
|
|
|
|
// (A) main import form:
|
|
$sourceText = "";
|
|
$importRecordsRadio = "all";
|
|
$importRecords = "1";
|
|
$skipBadRecords = "";
|
|
|
|
// (B) "Import IDs" form:
|
|
$sourceIDs = "";
|
|
}
|
|
|
|
// Show the login status:
|
|
showLogin(); // (function 'showLogin()' is defined in 'include.inc.php')
|
|
|
|
// (2a) Display header:
|
|
// call the 'displayHTMLhead()' and 'showPageHeader()' functions (which are defined in 'header.inc.php'):
|
|
displayHTMLhead(encodeHTML($officialDatabaseName) . $pageTitle, "index,follow", "Import records into the " . encodeHTML($officialDatabaseName), "", false, "", $viewType, array());
|
|
showPageHeader($HeaderString);
|
|
|
|
// (2b) Start <form> and <table> holding the form elements of the main import form:
|
|
echo "\n<form enctype=\"multipart/form-data\" action=\"import_modify.php\" method=\"POST\">"
|
|
. "\n<input type=\"hidden\" name=\"formType\" value=\"import\">"
|
|
. "\n<input type=\"hidden\" name=\"submit\" value=\"Import\">" // provide a default value for the 'submit' form tag. Otherwise, some browsers may not recognize the correct output format when a user hits <enter> within a form field (instead of clicking the "Import" button)
|
|
. "\n<input type=\"hidden\" name=\"showLinks\" value=\"1\">" // embed '$showLinks=1' so that links get displayed on any 'display details' page
|
|
. "\n<input type=\"hidden\" name=\"showSource\" value=\"1\">"; // for particular formats (e.g., CSA or MEDLINE) original source data will be displayed alongside the parsed data for easier comparison
|
|
|
|
if (isset($errors['badRecords']))
|
|
{
|
|
if ($errors['badRecords'] == "all") // none of the given records had a recognized format
|
|
{
|
|
if (!empty($errors['skipBadRecords']))
|
|
$skipBadRecordsInput = "<br>" . fieldError("skipBadRecords", $errors);
|
|
else
|
|
$skipBadRecordsInput = "";
|
|
}
|
|
elseif ($errors['badRecords'] == "some") // there were at least some records with recognized format but other records could NOT be recognized
|
|
{
|
|
if (!empty($skipBadRecords))
|
|
$skipBadRecordsCheckBoxIsChecked = " checked"; // mark the 'Skip records with unrecognized data format' checkbox
|
|
else
|
|
$skipBadRecordsCheckBoxIsChecked = "";
|
|
|
|
// display the 'Skip records with unrecognized data format' checkbox:
|
|
$skipBadRecordsInput = "<br><input type=\"checkbox\" name=\"skipBadRecords\" value=\"1\"$skipBadRecordsCheckBoxIsChecked title=\"mark this checkbox to omit records with unrecognized data format during import\"> " . fieldError("skipBadRecords", $errors);
|
|
}
|
|
}
|
|
else // all records did have a valid data format -> supress the 'Skip records with unrecognized data format' checkbox
|
|
{
|
|
$skipBadRecordsInput = "";
|
|
}
|
|
|
|
if (!empty($skipBadRecordsInput))
|
|
{
|
|
if ($formType == "importID")
|
|
{
|
|
$skipBadRecordsInputMain = "";
|
|
$skipBadRecordsInputID = $skipBadRecordsInput;
|
|
}
|
|
else // $formType == "import"
|
|
{
|
|
$skipBadRecordsInputMain = $skipBadRecordsInput;
|
|
$skipBadRecordsInputID = "";
|
|
}
|
|
}
|
|
else
|
|
{
|
|
$skipBadRecordsInputMain = "";
|
|
$skipBadRecordsInputID = "";
|
|
}
|
|
|
|
echo "\n<table align=\"center\" border=\"0\" cellpadding=\"0\" cellspacing=\"10\" width=\"95%\" summary=\"This table holds the main import form\">"
|
|
. "\n<tr>\n\t<td width=\"94\" valign=\"top\"><b>" . $textEntryFormLabel . ":</b></td>\n\t<td width=\"10\"> </td>"
|
|
. "\n\t<td colspan=\"3\">" . fieldError("sourceText", $errors) . $skipBadRecordsInputMain . "<textarea name=\"sourceText\" rows=\"6\" cols=\"63\" title=\"paste your records here\">$sourceText</textarea></td>"
|
|
. "\n</tr>";
|
|
|
|
// the code for the next table row is kept a bit more modular than necessary to allow for easy changes in the future
|
|
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable does contain 'allow_batch_import'...
|
|
echo "\n<tr>\n\t<td" . $rowSpan . "> </td>\n\t<td" . $rowSpan . "> </td>";
|
|
|
|
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable does contain 'allow_batch_import'...
|
|
{
|
|
// display a file upload button:
|
|
$uploadButtonLock = "";
|
|
$uploadTitle = $loc["DescriptionFileImport"];
|
|
|
|
echo "\n\t<td width=\"215\" valign=\"top\"" . $rowSpan . ">" . fieldError("uploadFile", $errors) . "<input type=\"file\" name=\"uploadFile\" size=\"17\"$uploadButtonLock title=\"$uploadTitle\"></td>";
|
|
}
|
|
// else
|
|
// {
|
|
// // note that we currently simply hide the upload button if the user doesn't have the 'allow_batch_import' permission (i.e., the two lines below are currently without effect):
|
|
// $uploadButtonLock = " disabled"; // disabling of the upload button doesn't seem to work in all browsers (e.g., it doesn't work in Safari on MacOSX Panther, but does work with Mozilla & Camino) ?:-/
|
|
// $uploadTitle = $loc["NoPermission"] . $loc["NoPermission_ForFileImport"]; // similarily, not all browsers will show title strings for disabled buttons (Safari does, Mozilla & Camino do not)
|
|
//
|
|
// echo "\n\t<td width=\"215\"" . $rowSpan . "> </td>";
|
|
// }
|
|
|
|
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable does contain 'allow_batch_import'...
|
|
{
|
|
if ($importRecordsRadio == "all")
|
|
{
|
|
$importRecordsRadioAllChecked = " checked"; // select the 'All' radio button
|
|
$importRecordsRadioOnlyChecked = "";
|
|
}
|
|
else // $importRecordsRadio == "only"
|
|
{
|
|
$importRecordsRadioAllChecked = "";
|
|
$importRecordsRadioOnlyChecked = " checked"; // select the 'Only' radio button
|
|
}
|
|
|
|
echo "\n\t<td width=\"98\" valign=\"top\"" . $rowSpan . ">Import records:</td>"
|
|
. "\n\t<td valign=\"top\"><input type=\"radio\" name=\"importRecordsRadio\" value=\"all\"$importRecordsRadioAllChecked title=\"choose 'All' if you want to import all records at once\"> All</td>"
|
|
. "\n</tr>"
|
|
. "\n<tr>"
|
|
. "\n\t<td valign=\"top\">" . fieldError("importRecords", $errors) . "<input type=\"radio\" name=\"importRecordsRadio\" value=\"only\"$importRecordsRadioOnlyChecked title=\"choose 'Only' if you just want to import particular records\"> Only: <input type=\"text\" name=\"importRecords\" value=\"$importRecords\" size=\"5\" title=\"enter record number(s): e.g. '1-5 7' imports the first five and the seventh\"></td>";
|
|
}
|
|
// else
|
|
// {
|
|
// echo "\n\t<td colspan=\"2\"> </td>";
|
|
// }
|
|
|
|
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable does contain 'allow_batch_import'...
|
|
echo "\n</tr>";
|
|
|
|
echo "\n<tr>\n\t<td> </td>\n\t<td> </td>";
|
|
|
|
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_import|allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable contains either 'allow_import' or 'allow_batch_import'...
|
|
// adjust the title string for the import button
|
|
{
|
|
$importButtonLock = "";
|
|
$importTitleMain = "press this button to import the given source data";
|
|
$importTitleID = "press this button to fetch & import source data for the given IDs";
|
|
}
|
|
else // Note, that disabling the submit button is just a cosmetic thing -- the user can still submit the form by pressing enter or by building the correct URL from scratch!
|
|
{
|
|
$importButtonLock = " disabled";
|
|
$importTitleMain = "not available since you have no permission to import any records";
|
|
$importTitleID = "not available since you have no permission to import any records";
|
|
}
|
|
|
|
echo "\n\t<td colspan=\"3\">\n\t\t<input type=\"submit\" name=\"submit\" value=\"Import\"$importButtonLock title=\"$importTitleMain\">\n\t</td>"
|
|
. "\n</tr>"
|
|
. "\n</table>"
|
|
. "\n</form>";
|
|
|
|
// (2c) Start <form> and <table> holding the form elements of the "Import IDs" form:
|
|
echo "\n<form action=\"import_modify.php\" method=\"POST\">"
|
|
. "\n<input type=\"hidden\" name=\"formType\" value=\"importID\">"
|
|
. "\n<input type=\"hidden\" name=\"submit\" value=\"Import\">" // provide a default value for the 'submit' form tag. Otherwise, some browsers may not recognize the correct output format when a user hits <enter> within a form field (instead of clicking the "Import" button)
|
|
. "\n<input type=\"hidden\" name=\"showSource\" value=\"1\">"; // in case of the MEDLINE format, original source data will be displayed alongside the parsed data for easier comparison
|
|
|
|
echo "\n<table align=\"center\" border=\"0\" cellpadding=\"0\" cellspacing=\"10\" width=\"95%\" summary=\"This table holds a form to import records via their ID\">"
|
|
. "\n<tr>\n\t<td width=\"94\" valign=\"top\"><b>Import IDs:</b></td>\n\t<td width=\"10\"> </td>"
|
|
. "\n\t<td colspan=\"3\">" . fieldError("sourceIDs", $errors) . $skipBadRecordsInputID . "<input type=\"text\" name=\"sourceIDs\" value=\"$sourceIDs\" size=\"66\" title=\"enter PubMed IDs, arXiv IDs, DOIs or OpenURLs, multiple IDs must be delimited by whitespace\"></td>"
|
|
. "\n</tr>"
|
|
. "\n<tr>\n\t<td> </td>\n\t<td> </td>"
|
|
. "\n\t<td colspan=\"3\">\n\t\t<input type=\"submit\" name=\"submit\" value=\"Import\"$importButtonLock title=\"$importTitleID\">\n\t</td>"
|
|
. "\n</tr>"
|
|
. "\n<tr>\n\t<td align=\"center\" colspan=\"5\"> </td>"
|
|
. "\n</tr>";
|
|
|
|
// (2d) Display a table row with some help text:
|
|
echo "\n<tr>\n\t<td valign=\"top\"><b>Help:</b></td>\n\t<td> </td>"
|
|
. "\n\t<td valign=\"top\" colspan=\"3\">The upper form enables you to import records from "
|
|
. "<a href=\"http://www.endnote.com/\" target=\"top\">Endnote</a> (tagged text or XML), "
|
|
. "<a href=\"http://www.refman.com/\" target=\"top\">Reference Manager</a> (RIS), "
|
|
. "<a href=\"http://www.refworks.com/\" target=\"top\">RefWorks</a>, "
|
|
. "<a href=\"http://en.wikipedia.org/wiki/Bibtex\" target=\"top\">BibTeX</a>, "
|
|
. "<a href=\"http://www.loc.gov/standards/mods/\" target=\"top\">MODS XML</a>, "
|
|
. "<a href=\"http://isiknowledge.com/wos/\" target=\"top\">ISI Web of Science</a>, "
|
|
. "<a href=\"http://www.pubmed.gov/\" target=\"top\">PubMed</a> (MEDLINE or XML), "
|
|
. "<a href=\"" . $importCSArecordsURL . "\" target=\"top\">CSA Illumina</a>, " // '$importCSArecordsURL' is defined in 'ini.inc.php'
|
|
. "<a href=\"http://www.cas.org/SCIFINDER/\" target=\"top\">SciFinder</a> "
|
|
. "and <a href=\"http://www.copac.ac.uk/\" target=\"top\">COPAC</a>."
|
|
. " Please see the <a href=\"http://import.refbase.net/\" target=\"top\">refbase online documentation</a> for more information about the supported formats and any requirements in format structure.</td>"
|
|
. "\n</tr>"
|
|
. "\n<tr>\n\t<td> </td>\n\t<td> </td>"
|
|
. "\n\t<td colspan=\"3\">The lower form allows you to import records via their ID; supported IDs: <a href=\"http://www.pubmed.gov/\" target=\"top\">PubMed</a> <a href=\"http://en.wikipedia.org/wiki/PMID\" target=\"top\">ID (PMID)</a>, <a href=\"http://arxiv.org/\" target=\"top\">arXiv</a> <a href=\"http://arxiv.org/help/arxiv_identifier\" target=\"top\">ID</a>, <a href=\"http://www.doi.org/\" target=\"top\">DOI</a> and <a href=\"http://en.wikipedia.org/wiki/OpenURL\" target=\"top\">OpenURL</a>. Just enter one or more IDs (delimited by whitespace) and press the <em>Import</em> button. Please note that currently you cannot mix different IDs within the same import action, i.e. specify either PubMed IDs or DOIs, etc.</td>"
|
|
. "\n</tr>"
|
|
. "\n</table>"
|
|
. "\n</form>";
|
|
|
|
// --------------------------------------------------------------------
|
|
|
|
// SHOW ERROR IN RED:
|
|
function fieldError($fieldName, $errors)
|
|
{
|
|
if (isset($errors[$fieldName]))
|
|
return "<b><span class=\"warning2\">" . $errors[$fieldName] . "</span></b><br>";
|
|
}
|
|
|
|
// --------------------------------------------------------------------
|
|
|
|
// DISPLAY THE HTML FOOTER:
|
|
// call the 'showPageFooter()' and 'displayHTMLfoot()' functions (which are defined in 'footer.inc.php')
|
|
showPageFooter($HeaderString);
|
|
|
|
displayHTMLfoot();
|
|
|
|
// --------------------------------------------------------------------
|
|
?>
|