/** * Note: This file may contain artifacts of previous malicious infection. * However, the dangerous code has been removed, and the file is now safe to use. */ /** * @file * Pathologic text filter for Drupal. * * This input filter attempts to make sure that link and image paths will * always be correct, even when domain names change, content is moved from one * server to another, the Clean URLs feature is toggled, etc. */ /** * Implements hook_filter_info(). */ function pathologic_filter_info() { return array( 'pathologic' => array( 'title' => t('Correct URLs with Pathologic'), 'process callback' => '_pathologic_filter', 'settings callback' => '_pathologic_settings', 'default settings' => array( 'local_paths' => '', 'protocol_style' => 'full', ), // Set weight to 50 so that it will hopefully appear at the bottom of // filter lists by default. 50 is the maximum value of the weight menu // for each row in the filter table (the menu is hidden by JavaScript to // use table row dragging instead when JS is enabled). 'weight' => 50, ) ); } /** * Settings callback for Pathologic. */ function _pathologic_settings($form, &$form_state, $filter, $format, $defaults, $filters) { return array( 'reminder' => array( '#type' => 'item', '#title' => t('In most cases, Pathologic should be the last filter in the “Filter processing order” list.'), '#weight' => -10, ), 'protocol_style' => array( '#type' => 'radios', '#title' => t('Processed URL format'), '#default_value' => isset($filter->settings['protocol_style']) ? $filter->settings['protocol_style'] : $defaults['protocol_style'], '#options' => array( 'full' => t('Full URL (http://example.com/foo/bar)'), 'proto-rel' => t('Protocol relative URL (//example.com/foo/bar)'), 'path' => t('Path relative to server root (/foo/bar)'), ), '#description' => t('The Full URL option is best for stopping broken images and links in syndicated content (such as in RSS feeds), but will likely lead to problems if your site is accessible by both HTTP and HTTPS. Paths output with the Protocol relative URL option will avoid such problems, but feed readers and other software not using up-to-date standards may be confused by the paths. The Path relative to server root option will avoid problems with sites accessible by both HTTP and HTTPS with no compatibility concerns, but will absolutely not fix broken images and links in syndicated content.'), '#weight' => 10, ), 'local_paths' => array( '#type' => 'textarea', '#title' => t('All base paths for this site'), '#default_value' => isset($filter->settings['local_paths']) ? $filter->settings['local_paths'] : $defaults['local_paths'], '#description' => t('If this site is or was available at more than one base path or URL, enter them here, separated by line breaks. For example, if this site is live at http://example.com/ but has a staging version at http://dev.example.org/staging/, you would enter both those URLs here. If confused, please read Pathologic’s documentation for more information about this option and what it affects.', array('!docs' => 'http://drupal.org/node/257026')), '#weight' => 20, ), ); } /** * Pathologic filter callback. * * Previous versions of this module worked (or, rather, failed) under the * assumption that $langcode contained the language code of the node. Sadly, * this isn't the case. * @see http://drupal.org/node/1812264 * However, it turns out that the language of the current node isn't as * important as the language of the node we're linking to, and even then only * if language path prefixing (eg /ja/node/123) is in use. REMEMBER THIS IN THE * FUTURE, ALBRIGHT. * * The below code uses the @ operator before parse_url() calls because in PHP * 5.3.2 and earlier, parse_url() causes a warning of parsing fails. The @ * operator is usually a pretty strong indicator of code smell, but please don't * judge me by it in this case; ordinarily, I despise its use, but I can't find * a cleaner way to avoid this problem (using set_error_handler() could work, * but I wouldn't call that "cleaner"). Fortunately, Drupal 8 will require at * least PHP 5.3.5, so this mess doesn't have to spread into the D8 branch of * Pathologic. * @see https://drupal.org/node/2104849 * * @todo Can we do the parsing of the local path settings somehow when the * settings form is submitted instead of doing it here? */ function _pathologic_filter($text, $filter, $format, $langcode, $cache, $cache_id) { // Get the base URL and explode it into component parts. We add these parts // to the exploded local paths settings later. global $base_url; $base_url_parts = @parse_url($base_url . '/'); // Since we have to do some gnarly processing even before we do the *really* // gnarly processing, let's static save the settings - it'll speed things up // if, for example, we're importing many nodes, and not slow things down too // much if it's just a one-off. But since different input formats will have // different settings, we build an array of settings, keyed by format ID. $cached_settings = &drupal_static(__FUNCTION__, array()); if (!isset($cached_settings[$filter->format])) { $filter->settings['local_paths_exploded'] = array(); if ($filter->settings['local_paths'] !== '') { // Build an array of the exploded local paths for this format's settings. // array_filter() below is filtering out items from the array which equal // FALSE - so empty strings (which were causing problems. // @see http://drupal.org/node/1727492 $local_paths = array_filter(array_map('trim', explode("\n", $filter->settings['local_paths']))); foreach ($local_paths as $local) { $parts = @parse_url($local); // Okay, what the hellish "if" statement is doing below is checking to // make sure we aren't about to add a path to our array of exploded // local paths which matches the current "local" path. We consider it // not a match, if… // @todo: This is pretty horrible. Can this be simplified? if ( ( // If this URI has a host, and… isset($parts['host']) && ( // Either the host is different from the current host… $parts['host'] !== $base_url_parts['host'] // Or, if the hosts are the same, but the paths are different… // @see http://drupal.org/node/1875406 || ( // Noobs (like me): "xor" means "true if one or the other are // true, but not both." (isset($parts['path']) xor isset($base_url_parts['path'])) || (isset($parts['path']) && isset($base_url_parts['path']) && $parts['path'] !== $base_url_parts['path']) ) ) ) || // Or… ( // The URI doesn't have a host… !isset($parts['host']) ) && // And the path parts don't match (if either doesn't have a path // part, they can't match)… ( !isset($parts['path']) || !isset($base_url_parts['path']) || $parts['path'] !== $base_url_parts['path'] ) ) { // Add it to the list. $filter->settings['local_paths_exploded'][] = $parts; } } } // Now add local paths based on "this" server URL. $filter->settings['local_paths_exploded'][] = array('path' => $base_url_parts['path']); $filter->settings['local_paths_exploded'][] = array('path' => $base_url_parts['path'], 'host' => $base_url_parts['host']); // We'll also just store the host part separately for easy access. $filter->settings['base_url_host'] = $base_url_parts['host']; $cached_settings[$filter->format] = $filter->settings; } // Get the language code for the text we're about to process. $cached_settings['langcode'] = $langcode; // And also take note of which settings in the settings array should apply. $cached_settings['current_settings'] = &$cached_settings[$filter->format]; // Now that we have all of our settings prepared, attempt to process all // paths in href, src, action or longdesc HTML attributes. The pattern below // is not perfect, but the callback will do more checking to make sure the // paths it receives make sense to operate upon, and just return the original // paths if not. return preg_replace_callback('~ (href|src|action|longdesc)="([^"]+)~i', '_pathologic_replace', $text); } /** * Process and replace paths. preg_replace_callback() callback. */ function _pathologic_replace($matches) { // Get the base path. global $base_path; // Get the settings for the filter. Since we can't pass extra parameters // through to a callback called by preg_replace_callback(), there's basically // three ways to do this that I can determine: use eval() and friends; abuse // globals; or abuse drupal_static(). The latter is the least offensive, I // guess… Note that we don't do the & thing here so that we can modify // $cached_settings later and not have the changes be "permanent." $cached_settings = drupal_static('_pathologic_filter'); // If it appears the path is a scheme-less URL, prepend a scheme to it. // parse_url() cannot properly parse scheme-less URLs. Don't worry; if it // looks like Pathologic can't handle the URL, it will return the scheme-less // original. // @see https://drupal.org/node/1617944 // @see https://drupal.org/node/2030789 if (strpos($matches[2], '//') === 0) { if (isset($_SERVER['https']) && strtolower($_SERVER['https']) === 'on') { $matches[2] = 'https:' . $matches[2]; } else { $matches[2] = 'http:' . $matches[2]; } } // Now parse the URL after reverting HTML character encoding. // @see http://drupal.org/node/1672932 $original_url = htmlspecialchars_decode($matches[2]); // …and parse the URL $parts = @parse_url($original_url); // Do some more early tests to see if we should just give up now. if ( // If parse_url() failed, give up. $parts === FALSE || ( // If there's a scheme part and it doesn't look useful, bail out. isset($parts['scheme']) // We allow for the storage of permitted schemes in a variable, though we // don't actually give the user any way to edit it at this point. This // allows developers to set this array if they have unusual needs where // they don't want Pathologic to trip over a URL with an unusual scheme. // @see http://drupal.org/node/1834308 // "files" and "internal" are for Path Filter compatibility. && !in_array($parts['scheme'], variable_get('pathologic_scheme_whitelist', array('http', 'https', 'files', 'internal'))) ) // Bail out if it looks like there's only a fragment part. || (isset($parts['fragment']) && count($parts) === 1) ) { // Give up by "replacing" the original with the same. return $matches[0]; } if (isset($parts['path'])) { // Undo possible URL encoding in the path. // @see http://drupal.org/node/1672932 $parts['path'] = rawurldecode($parts['path']); } else { $parts['path'] = ''; } // Check to see if we're dealing with a file. // @todo Should we still try to do path correction on these files too? if (isset($parts['scheme']) && $parts['scheme'] === 'files') { // Path Filter "files:" support. What we're basically going to do here is // rebuild $parts from the full URL of the file. $new_parts = @parse_url(file_create_url(file_default_scheme() . '://' . $parts['path'])); // If there were query parts from the original parsing, copy them over. if (!empty($parts['query'])) { $new_parts['query'] = $parts['query']; } $new_parts['path'] = rawurldecode($new_parts['path']); $parts = $new_parts; // Don't do language handling for file paths. $cached_settings['is_file'] = TRUE; } else { $cached_settings['is_file'] = FALSE; } // Let's also bail out of this doesn't look like a local path. $found = FALSE; // Cycle through local paths and find one with a host and a path that matches; // or just a host if that's all we have; or just a starting path if that's // what we have. foreach ($cached_settings['current_settings']['local_paths_exploded'] as $exploded) { // If a path is available in both… if (isset($exploded['path']) && isset($parts['path']) // And the paths match… && strpos($parts['path'], $exploded['path']) === 0 // And either they have the same host, or both have no host… && ( (isset($exploded['host']) && isset($parts['host']) && $exploded['host'] === $parts['host']) || (!isset($exploded['host']) && !isset($parts['host'])) ) ) { // Remove the shared path from the path. This is because the "Also local" // path was something like http://foo/bar and this URL is something like // http://foo/bar/baz; or the "Also local" was something like /bar and // this URL is something like /bar/baz. And we only care about the /baz // part. $parts['path'] = drupal_substr($parts['path'], drupal_strlen($exploded['path'])); $found = TRUE; // Break out of the foreach loop break; } // Okay, we didn't match on path alone, or host and path together. Can we // match on just host? Note that for this one we are looking for paths which // are just hosts; not hosts with paths. elseif ((isset($parts['host']) && !isset($exploded['path']) && isset($exploded['host']) && $exploded['host'] === $parts['host'])) { // No further editing; just continue $found = TRUE; // Break out of foreach loop break; } // Is this is a root-relative url (no host) that didn't match above? // Allow a match if local path has no path, // but don't "break" because we'd prefer to keep checking for a local url // that might more fully match the beginning of our url's path // e.g.: if our url is /foo/bar we'll mark this as a match for // http://example.com but want to keep searching and would prefer a match // to http://example.com/foo if that's configured as a local path elseif (!isset($parts['host']) && (!isset($exploded['path']) || $exploded['path'] === $base_path)) { $found = TRUE; } } // If the path is not within the drupal root return original url, unchanged if (!$found) { return $matches[0]; } // Okay, format the URL. // If there's still a slash lingering at the start of the path, chop it off. $parts['path'] = ltrim($parts['path'],'/'); // Examine the query part of the URL. Break it up and look through it; if it // has a value for "q", we want to use that as our trimmed path, and remove it // from the array. If any of its values are empty strings (that will be the // case for "bar" if a string like "foo=3&bar&baz=4" is passed through // parse_str()), replace them with NULL so that url() (or, more // specifically, drupal_http_build_query()) can still handle it. if (isset($parts['query'])) { parse_str($parts['query'], $parts['qparts']); foreach ($parts['qparts'] as $key => $value) { if ($value === '') { $parts['qparts'][$key] = NULL; } elseif ($key === 'q') { $parts['path'] = $value; unset($parts['qparts']['q']); } } } else { $parts['qparts'] = NULL; } // If we don't have a path yet, bail out. if (!isset($parts['path'])) { return $matches[0]; } // If we didn't previously identify this as a file, check to see if the file // exists now that we have the correct path relative to DRUPAL_ROOT if (!$cached_settings['is_file']) { $cached_settings['is_file'] = !empty($parts['path']) && is_file(DRUPAL_ROOT . '/'. $parts['path']); } // Okay, deal with language stuff. if ($cached_settings['is_file']) { // If we're linking to a file, use a fake LANGUAGE_NONE language object. // Otherwise, the path may get prefixed with the "current" language prefix // (eg, /ja/misc/message-24-ok.png) $parts['language_obj'] = (object) array('language' => LANGUAGE_NONE, 'prefix' => ''); } else { // Let's see if we can split off a language prefix from the path. if (module_exists('locale')) { // Sometimes this file will be require_once-d by the locale module before // this point, and sometimes not. We require_once it ourselves to be sure. require_once DRUPAL_ROOT . '/includes/language.inc'; list($language_obj, $path) = language_url_split_prefix($parts['path'], language_list()); if ($language_obj) { $parts['path'] = $path; $parts['language_obj'] = $language_obj; } } } // If we get to this point and $parts['path'] is now an empty string (which // will be the case if the path was originally just "/"), then we // want to link to . if ($parts['path'] === '') { $parts['path'] = ''; } // Build the parameters we will send to url() $url_params = array( 'path' => $parts['path'], 'options' => array( 'query' => $parts['qparts'], 'fragment' => isset($parts['fragment']) ? $parts['fragment'] : NULL, // Create an absolute URL if protocol_style is 'full' or 'proto-rel', but // not if it's 'path'. 'absolute' => $cached_settings['current_settings']['protocol_style'] !== 'path', // If we seem to have found a language for the path, pass it along to // url(). Otherwise, ignore the 'language' parameter. 'language' => isset($parts['language_obj']) ? $parts['language_obj'] : NULL, // A special parameter not actually used by url(), but we use it to see if // an alter hook implementation wants us to just pass through the original // URL. 'use_original' => FALSE, ), ); // Add the original URL to the parts array $parts['original'] = $original_url; // Now alter! // @see http://drupal.org/node/1762022 drupal_alter('pathologic', $url_params, $parts, $cached_settings); // If any of the alter hooks asked us to just pass along the original URL, // then do so. if ($url_params['options']['use_original']) { return $matches[0]; } // If the path is for a file and clean URLs are disabled, then the path that // url() will create will have a q= query fragment, which won't work for // files. To avoid that, we use this trick to temporarily turn clean URLs on. // This is horrible, but it seems to be the sanest way to do this. // @see http://drupal.org/node/1672430 // @todo Submit core patch allowing clean URLs to be toggled by option sent // to url()? if (!empty($cached_settings['is_file'])) { $cached_settings['orig_clean_url'] = !empty($GLOBALS['conf']['clean_url']); if (!$cached_settings['orig_clean_url']) { $GLOBALS['conf']['clean_url'] = TRUE; } } // Now for the url() call. Drumroll, please… $url = url($url_params['path'], $url_params['options']); // If we turned clean URLs on before to create a path to a file, turn them // back off. if ($cached_settings['is_file'] && !$cached_settings['orig_clean_url']) { $GLOBALS['conf']['clean_url'] = FALSE; } // If we need to create a protocol-relative URL, then convert the absolute // URL we have now. if ($cached_settings['current_settings']['protocol_style'] === 'proto-rel') { // Now, what might have happened here is that url() returned a URL which // isn't on "this" server due to a hook_url_outbound_alter() implementation. // We don't want to convert the URL in that case. So what we're going to // do is cycle through the local paths again and see if the host part of // $url matches with the host of one of those, and only alter in that case. $url_parts = @parse_url($url); if (!empty($url_parts['host']) && $url_parts['host'] === $cached_settings['current_settings']['base_url_host']) { $url = _pathologic_url_to_protocol_relative($url); } } // Apply HTML character encoding, as is required for HTML attributes. // @see http://drupal.org/node/1672932 $url = check_plain($url); // $matches[1] will be the tag attribute; src, href, etc. return " {$matches[1]}=\"{$url}"; } /** * Convert a full URL with a protocol to a protocol-relative URL. * * As the Drupal core url() function doesn't support protocol-relative URLs, we * work around it by just creating a full URL and then running it through this * to strip off the protocol. * * Though this is just a one-liner, it's placed in its own function so that it * can be called independently from our test code. */ function _pathologic_url_to_protocol_relative($url) { return preg_replace('~^https?://~', '//', $url); } State Geological Survey Contributions to the National Geothermal Data System (NGDS) Update | Arizona Geology Magazine

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State Geological Survey Contributions to the National Geothermal Data System (NGDS) Update

Article Author(s): 

Kim Patten

“The project has uploaded an impressive amount of data that has been submitted by a large number of team members representing all 50 states.” From May 2012 DOE Peer Review.

Project Progress
As of June 2012 nearly all new data collection projects have cleared the National Environmental Policy Act (NEPA) and are currently conducting new data collection efforts across sixteen states. For more information on the new data collection, please review the Spring 2011 Arizona Geology article. Since the original article, Pennsylvania was provided with additional funding for geophysical logging, including temperature, of groundwater wells in southeast and south central Pennsylvania to determine geothermal gradient. Fifteen existing deep wells were chosen for logging temperature, gamma ray, single point resistance, spontaneous potential, fluid resistivity, and normal resistivity. Data from all new data collection projects, including some of the new drilling projects in the Great Basin, should be available by the end of 2013.

As of June 2012, the State Geological Surveys contributed over 775 datasets representing over two million data points. Most of the datasets provided to the NGDS are portrayed as Open Geospatial Consortium (OGC) Web Map Services (WMS) and Web Feature Services (WFS), meaning that the data is compatible with a variety of visualization software. Web services are ideal for the NGDS data for a number of reasons including that they preserve data ownership in that they are read only and new services can be deployed to meet new requirements without modifying existing applications. 

Web Feature Services (WFS) provide data as geolocated, discrete entities (features) with associated attributes.  A feature type is analogous to a table in a database, and each feature instance is analogous to a row in the table. Thus, WFS can be thought of as a collection of database records, each of which has a geometry field that describes the entity of interest at that location. Feature services are a complete data file that is geographically represented. For example, NGDS includes a number of WFS on borehole temperature data. Users of the data can download the WFS, insert the data into their geographic information system or visualization software of choice, and run queries against the complete attributes associated with the service. Due to the large amount of data associated with the WFS, these services require quick internet connections.

In contrast to the data intensive WFS, the Web Map Service (WMS) provides a glimpse of the data through a georeferenced map image. While the map image may allow point queries, the WMS does not permit the end user to produce queries within and against the data. WMS is essentially a quick view of the data available and will provide a preview that end users commonly require before downloading the full data set. Web Map Services are particularly useful when attempting to superimpose map layers and images quickly in a web based environment. Generally WMS are reserved for initial observations whereas WFS are reserved for in-depth data layer queries.

As an example, we have pulled the currently available nationwide borehole temperature data from the NGDS in WMS. For more information about WFS, WMS, or the standards and protocols in place for the NGDS, please visit http://usgin.org for general information and user’s tutorials and http://lab.usgin.org for the developer’s page.

Satellite Map of USA

Searching for and finding data within the AASG contributed data should be easier by the end of September. At that time, we are releasing a new, more user friendly search system that acts like the more familiar search interfaces of Google, Bing, and Yahoo. Central to this new search functionality are multiple search options associated with the end search result. For example, if your search returns a document, the tool will permit you to view “More Details” or the metadata associated with the product, view the “Show Area on Map” allows you to view the geographic bounding box, or the “Access Options “that provides a direct link to the document (if available) or the ability to contact the document’s owner/publisher. If the search result provides a WMS, you can quickly view the service in the map tool provided within the interface, or you can directly access the WMS capabilities XML, which will permit you to load the WMS into your visualization viewer of choice.  

State Geothermal Data search

While this search tool will make finding AASG data easier, there are currently a number of ways in which to find available data. One of the most useful tools available from http://www.stategeothermaldata.org not only acts as a data access and discovery tool, but as a mechanism for tracking progress in the U.S. states. Under the “Progress” tab at the homepage is the option to view the “Data Collection Status Map”, which allows the user to track progress either by state or nationwide using eight data categories. The eight categories – temperature & heatflow, water chemistry, recent tectonics, rock chemistry, well logs, map data, metadata & documents, and other – were selected based upon the thirty predetermined content models for the project.  A user can select one of the categories from the legend (located in the Gulf of Mexico) and see progress in each category across the nation; the darker the state appears in a particular category, the more data available. Figure 3 indicates nationwide progress on Temperature and Heat Flow data.

Figure 3-Temperature and Heat Flow Data Contributions

Alternatively, users may track the progress by state. Users may identify certain categories within a state, for instance Figure 4 shows the progress made uploading Oregon’s well logs. You can also request a state by state progress report from the drop down menu located directly underneath the map. This will show you the intended deliverables, actual deliverables, records online for deliverables, and tracking notes.

Figure 4-Well Log ContributionsIn addition to improved search functionality, we are releasing a new site near the end of September. This site is specifically designed for the public, while the current site serves as a project management site. The new site will provide the end users access to data, free visualization software, and information on how they can add pertinent data to the system. We look forward to launching this site just in time for the 2012 Geothermal Energy Association Industry Expo and Geothermal Resources Council Annual Meeting taking place in Reno, Nevada, in early October 2012.
 
Project Annual Review
For the second year in a row, the project has received “good” or “outstanding” review comments during the annual sponsor (Department of Energy) peer review. Each reviewer scored the project as “outstanding” the highest possible mark for relevance and impact of research. Comments include “the project is collecting a treasure trove of data assets from all of the state geological surveys” and “state level data discovery, access, and cataloging/tagging are crucial to the larger NGDS goals.” Also scored were the Scientific and Technical Approach; Project Management/Coordination; Accomplishments, Results, and Progress; Strengths; Weaknesses; and Suggested Improvements. Additional selected comments from the review include:
  • The approach for acquiring data appears to be exemplary. A huge amount of work has gone into developing procedures for data acquisition and formats for data submission.”
  • “There is a large and growing collection of information assets acquired from participating states; the incoming assets are being assessed and incorporated via a quality process; the assets, once acquired, are being managed and visualized via a capable information system.”
  • “The project has uploaded an impressive amount of data that has been submitted by a large number of team members representing all 50 states.”
  • “Project has a strong management component and outward facing exposition and consultation effort associated with it.”

Continuing Outreach
Over the next quarter, AZGS will be presenting and exhibiting the State Geological Survey Contributions to the National Geothermal Data System at three national conferences and expositions: Geothermal Resources Council/Geothermal Energy Association Annual Meeting and Conference, Geological Society of America Annual Meeting, and the American Geophysical Union Annual Meeting. Booth information is provided below.  We invite you to stop by the booth and test-drive the system.

Geothermal Energy Expo (GRC/GEA)
September 30 to October 3, 2012
Reno, NV
Booth 341
Additional Information: http://www.geothermalenergy2011.com/default.asp

Geological Society of America Annual Meeting
November 4 to 7, 2012
Charlotte, NC
Booth 635 (with the Association of American State Geologists)
Additional Information: http://www.geosociety.org/meetings/2012/

American Geophysical Union
December 3 to 7, 2012
San Francisco, CA
Booth 104
Additional Information: http://fallmeeting.agu.org/2012/

 

Kim Patten

Project Manager
Arizona Geological Survey

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