From c6cd044c640b0a681350c675bc2b6637a3a8513b Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Wed, 24 Aug 2011 12:09:03 -0400 Subject: [PATCH 01/16] Hack to fix field ordering Javascript was implicitly ordering based on the key when doing a for ... in loop, while the code was written assuming ordering based on the order inserted. Added a new array fieldOrderList which stores the order that the ids should be printed in. --- htdocs/dqgui_step1.js | 30 +++++++++++++----------------- htdocs/query_gui_data_loader.php | 6 +++++- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/htdocs/dqgui_step1.js b/htdocs/dqgui_step1.js index 203a2ebf781..b7338c0b744 100644 --- a/htdocs/dqgui_step1.js +++ b/htdocs/dqgui_step1.js @@ -55,7 +55,7 @@ function purgeCategory(type, categoryId){ //REMOTING FUNCTIONS ------------------------------------------------------------- //loadFieldsByRemote is called by the iframe page to load fields -function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake){ +function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake,fieldOrderList){ var oFieldsCell=document.getElementById(type+"SelectCell"); //Set the cacheability flag @@ -108,22 +108,17 @@ function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake){ var currentLongestString=0; var cellWidth=0; var totalWidth=0; - for(var i in remoteFieldData){ - //Calculate the cell sizing information so that fields don't wrap. - if(loopcounter%8==0 && loopcounter!=0){ - cellWidth=(currentLongestString*8+30); - totalWidth+=cellWidth+10; - oCell.style.width=cellWidth+'px'; - oRow.appendChild(oCell); - oCell=document.createElement("TD"); - oCell.setAttribute("valign","top"); - currentLongestString=0; - } - - //Create the field row - if(loopcounter%8!=0){ - var oBR=document.createElement("BR"); - oCell.appendChild(oBR); + //for(var i in remoteFieldData){ + for(var x = 0;x < fieldOrderList.length; x++) { + // HACK: using x, and then assigning i = fieldOrderList[x] is easier than rewriting + // the code to use fieldOrderList[i] everywhere, since this was changed from remoteFieldData + // to fieldOrderList + i = fieldOrderList[x]; + if(loopcounter%3==0 && loopcounter!=0) { + oBody.appendChild(oRow); + oRow = document.createElement("TR"); + oRow.style.fontSize="80%"; + oRow.style.width="100%"; } //create the checkbox and assign the event handler @@ -147,6 +142,7 @@ function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake){ } loopcounter++; } + oBody.appendChild(oRow); //Finalize cell and table sizing. cellWidth=(currentLongestString*8+30); diff --git a/htdocs/query_gui_data_loader.php b/htdocs/query_gui_data_loader.php index d31955a4b35..4fe054000c4 100644 --- a/htdocs/query_gui_data_loader.php +++ b/htdocs/query_gui_data_loader.php @@ -54,7 +54,7 @@ case 'fields': // field list loading $remoteLoaderFunction = 'loadFieldsByRemote'; - $remoteLoaderArgs = "\"$_GET[type]\", \"$_GET[cat_id]\", remoteFieldData, $caching_enabled"; + $remoteLoaderArgs = "\"$_GET[type]\", \"$_GET[cat_id]\", remoteFieldData, $caching_enabled, false, fieldOrderList"; $query = "SELECT parameter_type.ParameterTypeID, Name, Description, parameter_type.Type, ParameterTypeCategoryID FROM parameter_type, parameter_type_category_rel WHERE parameter_type.ParameterTypeID=parameter_type_category_rel.ParameterTypeID AND parameter_type.Queryable=1 AND parameter_type_category_rel.ParameterTypeCategoryID='$_GET[cat_id]'"; $DB->select($query, $results); @@ -95,6 +95,9 @@ } $script.= "];\n"; } + foreach($sortable as $id => $name) { + $script .= "fieldOrderList.push($id);\n"; + } break; case "saveQuery": @@ -419,6 +422,7 @@ function treeToExpression(&$expression, &$tree, &$conditionals, $parentID=null) qrGroupsNesting = new Array; qrSelectedFields = new Array; qrUsedCategories = new Array; +fieldOrderList = []; // new Array; From 59612e1d2bf1721ef890efe78de6d75aad6d5cd8 Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Thu, 25 Aug 2011 10:39:16 -0400 Subject: [PATCH 02/16] Insert columns from parameter_session too, so that MRI session ids get inserted to the quat table --- tools/quat.php | 27 ++++++++++++++++++++++++--- 1 file changed, 24 insertions(+), 3 deletions(-) diff --git a/tools/quat.php b/tools/quat.php index 2982135eb4c..92378b92145 100644 --- a/tools/quat.php +++ b/tools/quat.php @@ -107,6 +107,7 @@ // run the create table statement $createSQL = "CREATE TABLE $nextTableName (SessionID int not null primary key, $createSQL)"; + $insertSQL = "INSERT INTO $nextTableName (SessionID) SELECT DISTINCT SessionID FROM flag f JOIN parameter_type pt ON (f.Test_name=pt.SourceFrom) WHERE pt.CurrentGUITable='$nextTableName' UNION select DISTINCT SessionID FROM parameter_session ps JOIN parameter_type pt ON (pt.ParameterTypeID=ps.ParameterTypeID) WHERE pt.CurrentGUITable='$nextTableName'"; $quatTableCounter++; $nextTableName = $quatTableBasename . $quatTableCounter; $result = $db->run($createSQL); @@ -164,9 +165,9 @@ function GetSelectStatement($parameterType, $field=NULL) { switch($parameterType['SourceFrom']) { case 'files': if($field == null) { - $field = "FileID"; + $field = "File"; } - $query = "SELECT $field AS Value FROM files JOIN session as S ON (s.ID=files.SessionID) WHERE OutputType='$parameterType[SourceField]'"; + $query = "SELECT $field AS Value FROM files JOIN session as S ON (s.ID=files.SessionID) WHERE OutputType='$parameterType[SourceCondition]'"; break; case 'parameter_file': @@ -245,7 +246,27 @@ function GetSelectStatement($parameterType, $field=NULL) { foreach($parameterTypes AS $parameterType) { if($parameterType['CurrentGUITable'] != null) { print "Updating $parameterType[Name], memory: " . memory_get_usage() . " bytes\n"; - $db->run("UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID AND flag.CommentID NOT LIKE 'DDE%') WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND flag.CommentID NOT LIKE 'DDE%' AND s.ID=quat_table_2.SessionID)"); + if(strpos($parameterType['Name'], "vineland") !== FALSE || + strpos($parameterType['Name'], "EARLI") !== FALSE || + strpos($parameterType['Name'], "adi") !== FALSE || + strpos($parameterType['Name'], "csbs") !== FALSE || + strpos($parameterType['Name'], "aosi") !== FALSE + ) { + continue; + } + switch($parameterType['SourceFrom']) { + case 'session': + case 'candidate': + case 'parameter_session': + print "UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID) WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND s.ID=$parameterType[CurrentGUITable].SessionID)"; + $db->run("UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID) WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND s.ID=$parameterType[CurrentGUITable].SessionID)"); + //exit(-1); + break; + default: + print "UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID AND flag.CommentID NOT LIKE 'DDE%') WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND flag.CommentID NOT LIKE 'DDE%' AND s.ID=$parameterType[CurrentGUITable].SessionID)"; + $db->run("UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID AND flag.CommentID NOT LIKE 'DDE%') WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND flag.CommentID NOT LIKE 'DDE%' AND s.ID=$parameterType[CurrentGUITable].SessionID)"); + break; + } //$db->run("UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " WHERE $parameterType[CurrentGUITable].SessionID=s.ID)"); } } From c8964f820d9fb101ab90569ba496391903905c06 Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Mon, 29 Aug 2011 15:49:21 -0400 Subject: [PATCH 03/16] Added debug statements and insert admin and validity --- tools/data_dictionary_builder.php | 41 +++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/tools/data_dictionary_builder.php b/tools/data_dictionary_builder.php index a0d3461ea66..50b71fd89ad 100644 --- a/tools/data_dictionary_builder.php +++ b/tools/data_dictionary_builder.php @@ -98,6 +98,7 @@ //delete all 'Instrument' entries from parameter_type $DB->run("delete from parameter_type where ParameterTypeID in ($instrumentParameterTypeIDString)"); +print "Cleared data from BVL instruments\n"; //Instruments with excessively wordy names. Entries are OPTIONAL //It would be really nice to have a table_names.Abbreviation field, but messy to change the names *everywhere*. @@ -120,11 +121,13 @@ +print "Reading instruments\n"; //Read the ip_output.txt staging file. $fp=fopen("ip_output.txt","r"); $data=fread($fp, filesize("ip_output.txt")); fclose($fp); +print "Parsing instruments\n"; $instruments=explode("{-@-}",trim($data)); //process all HTML_QuickForm Elements found in ip_output.txt @@ -143,6 +146,7 @@ switch($bits[0]){ case "table": $table=$bits[1]; + print "At $table\n"; break; case "title": @@ -158,6 +162,7 @@ //for HTML_QuickForm versions of standard HTML Form Elements... default: +continue; // jump straight to validity for debugging if($bits[0]=="select"){ $bits[0]=enumizeOptions($bits[3], $table, $bits[1]); } else if($bits[0]=="textarea"){ @@ -172,6 +177,7 @@ $bits[0]="varchar(255)"; } +print "Inserting $table $bits[1]\n"; $parameterCount++; $bits[2]=htmlspecialchars($bits[2]); //find values to insert @@ -188,6 +194,41 @@ $error=$DB->insert("parameter_type_category_rel",array("ParameterTypeID"=>$paramId, "ParameterTypeCategoryID"=>$catId)); } } + + if(empty($table)) continue; +print "Inserting validity for $table\n"; + // Insert validity + $Name = (array_key_exists($table, $abbreviations) ? $abbreviations[$table] : $table ) . "_Validity"; + $ParameterTypeID = array_key_exists($Name, $parameter_types) ? $parameter_types[$Name] : ''; + $error=$DB->insert("parameter_type", + array('ParameterTypeID'=>$ParameterTypeID, + 'Name'=>$Name, + 'Type'=>'enum(\'Questionable\', \'Invalid\', \'Valid\')', + 'Description'=>"Validity of $table", + 'SourceField'=>'Validity', 'SourceFrom'=>$table, 'CurrentGUITable'=>'quat_table_' . ceil(($parameterCount - 0.5) / 150), 'Queryable'=>'1')); + if($ParameterTypeID === '') { + $paramId= $DB->lastInsertID; + } else { + $paramId = $ParameterTypeID; + } + $error=$DB->insert("parameter_type_category_rel",array("ParameterTypeID"=>$paramId, "ParameterTypeCategoryID"=>$catId)); + // Insert administration +print "Inserting administration for $table\n"; + $Name = (array_key_exists($table, $abbreviations) ? $abbreviations[$table] : $table ) . "_Administration"; + $ParameterTypeID = array_key_exists($Name, $parameter_types) ? $parameter_types[$Name] : ''; + $error=$DB->insert("parameter_type", + array('ParameterTypeID'=>$ParameterTypeID, + 'Name'=>$Name, + 'Type'=>'enum(\'None\', \'Partial\', \'All\')', + 'Description'=>"Administration for $table", + 'SourceField'=>'Administration', 'SourceFrom'=>$table, 'CurrentGUITable'=>'quat_table_' . ceil(($parameterCount - 0.5) / 150), 'Queryable'=>'1')); + if($ParameterTypeID === '') { + $paramId= $DB->lastInsertID; + } else { + $paramId = $ParameterTypeID; + } + $error=$DB->insert("parameter_type_category_rel",array("ParameterTypeID"=>$paramId, "ParameterTypeCategoryID"=>$catId)); + // Insert examiner } //Print completion info message From c82e167d9bcfd4e392250b864765239d1d90fbcf Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Mon, 29 Aug 2011 15:50:14 -0400 Subject: [PATCH 04/16] Added support for Admin and Validity from flag table --- tools/quat.php | 23 +++++++++++++++++++---- 1 file changed, 19 insertions(+), 4 deletions(-) diff --git a/tools/quat.php b/tools/quat.php index 92378b92145..7c007a2eada 100644 --- a/tools/quat.php +++ b/tools/quat.php @@ -107,7 +107,7 @@ // run the create table statement $createSQL = "CREATE TABLE $nextTableName (SessionID int not null primary key, $createSQL)"; - $insertSQL = "INSERT INTO $nextTableName (SessionID) SELECT DISTINCT SessionID FROM flag f JOIN parameter_type pt ON (f.Test_name=pt.SourceFrom) WHERE pt.CurrentGUITable='$nextTableName' UNION select DISTINCT SessionID FROM parameter_session ps JOIN parameter_type pt ON (pt.ParameterTypeID=ps.ParameterTypeID) WHERE pt.CurrentGUITable='$nextTableName'"; + $insertSQL = "INSERT INTO $nextTableName (SessionID) SELECT DISTINCT SessionID FROM flag f JOIN parameter_type pt ON (f.Test_name=pt.SourceFrom) JOIN session s ON (s.ID=f.SessionID) JOIN candidate c ON (c.CandID=s.CandID) WHERE pt.CurrentGUITable='$nextTableName' AND c.Active='Y' AND c.Cancelled='N' AND s.Active='Y' AND s.Cancelled='N' AND c.CenterID IN (2, 3, 4, 5) AND s.Current_stage <> 'Recycling Bin' UNION select DISTINCT SessionID FROM parameter_session ps JOIN parameter_type pt ON (pt.ParameterTypeID=ps.ParameterTypeID) JOIN session s ON (ps.SessionID=s.ID) JOIN candidate c ON (c.CandID=s.CandID) WHERE pt.CurrentGUITable='$nextTableName' AND c.Active='Y' AND c.Cancelled='N' AND s.Active='Y' AND s.Cancelled='N' AND c.CenterID IN (2, 3, 4, 5) AND s.Current_stage <> 'Recycling Bin'"; $quatTableCounter++; $nextTableName = $quatTableBasename . $quatTableCounter; $result = $db->run($createSQL); @@ -119,6 +119,7 @@ $createSQL = ""; $columnCount = 0; print "Finished creating $nextTableName: " . memory_get_usage() . "\n"; +if($quatTableCounter > 2) break; } } @@ -221,7 +222,7 @@ function GetSelectStatement($parameterType, $field=NULL) { if($field == null) { $field = "s.$parameterType[SourceField] Value"; } - $query = "SELECT $field AS Value FROM session s LEFT JOIN psc USING (CenterID)"; + $query = "SELECT $field AS Value FROM session s LEFT JOIN psc USING (CenterID) WHERE 1=1"; break; case 'mri_acquisition_dates': @@ -234,9 +235,15 @@ function GetSelectStatement($parameterType, $field=NULL) { //for behavioural instrument data default: if($field == null) { - $field = "`$parameterType[SourceFrom]`.`$parameterType[SourceField]`"; + if($parameterType['SourceField'] == 'Administration' || + $parameterType['SourceField'] == 'Validity' || + $parameterType['SourceField'] == 'Data_entry') { + $field = "`flag`.`$parameterType[SourceField]`"; + } else { + $field = "`$parameterType[SourceFrom]`.`$parameterType[SourceField]`"; + } } - $query = "SELECT $field AS Value FROM session s JOIN flag ON (s.ID=flag.SessionID) LEFT JOIN feedback_bvl_thread USING (CommentID) CROSS JOIN $parameterType[SourceFrom] LEFT JOIN candidate ON (s.CandID = candidate.CandID) WHERE flag.Administration<>'None' AND flag.CommentID=$parameterType[SourceFrom].CommentID AND (feedback_bvl_thread.Status IS NULL OR feedback_bvl_thread.Status='closed' OR feedback_bvl_thread.Status='comment')"; + $query = "SELECT $field AS Value FROM session s JOIN flag ON (s.ID=flag.SessionID) LEFT JOIN feedback_bvl_thread USING (CommentID) CROSS JOIN $parameterType[SourceFrom] LEFT JOIN candidate ON (s.CandID = candidate.CandID) WHERE flag.Administration IN ('All', 'Partial') AND flag.Data_entry='Complete' AND flag.CommentID=$parameterType[SourceFrom].CommentID AND (feedback_bvl_thread.Status IS NULL OR feedback_bvl_thread.Status='closed' OR feedback_bvl_thread.Status='comment')"; break; } return $query; @@ -250,6 +257,12 @@ function GetSelectStatement($parameterType, $field=NULL) { strpos($parameterType['Name'], "EARLI") !== FALSE || strpos($parameterType['Name'], "adi") !== FALSE || strpos($parameterType['Name'], "csbs") !== FALSE || + strpos($parameterType['Name'], "fyi") !== FALSE || + strpos($parameterType['Name'], "head_measurements_subject") !== FALSE || + strpos($parameterType['Name'], "i3") !== FALSE || + strpos($parameterType['Name'], "ibq_r") !== FALSE || + strpos($parameterType['Name'], "m_chat_proband") !== FALSE || + strpos($parameterType['Name'], "med_psych_hist") !== FALSE || strpos($parameterType['Name'], "aosi") !== FALSE ) { continue; @@ -257,6 +270,8 @@ function GetSelectStatement($parameterType, $field=NULL) { switch($parameterType['SourceFrom']) { case 'session': case 'candidate': + case 'psc': + case 'parameter_candidate'; case 'parameter_session': print "UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID) WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND s.ID=$parameterType[CurrentGUITable].SessionID)"; $db->run("UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID) WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND s.ID=$parameterType[CurrentGUITable].SessionID)"); From 2a13cdfdbbce8f920cca0f1996be7bbea4038072 Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Mon, 29 Aug 2011 16:07:12 -0400 Subject: [PATCH 05/16] Add support for examiner field to DQG --- tools/data_dictionary_builder.php | 14 ++++++++++---- tools/quat.php | 10 ++++++++-- 2 files changed, 18 insertions(+), 6 deletions(-) diff --git a/tools/data_dictionary_builder.php b/tools/data_dictionary_builder.php index 50b71fd89ad..b04c5e7d479 100644 --- a/tools/data_dictionary_builder.php +++ b/tools/data_dictionary_builder.php @@ -140,9 +140,9 @@ $paramId=""; $bits=explode("{@}",trim($item)); //exclude Examiners, since their answer options do not exist in ip_output.txt - if(ereg("^Examiner", $bits[1])){ - continue; - } + //if(ereg("^Examiner", $bits[1])){ + // continue; + // switch($bits[0]){ case "table": $table=$bits[1]; @@ -162,7 +162,13 @@ //for HTML_QuickForm versions of standard HTML Form Elements... default: -continue; // jump straight to validity for debugging +//continue; // jump straight to validity for debugging + if(ereg("^Examiner", $bits[1])) { + // Treat examiner specially, since it's a select box but we need + // to treat it as a varchar. derive_timepoint_variables will derive + // the name from the examiner id + $bits[0] = "varchar(255)"; +} else continue; if($bits[0]=="select"){ $bits[0]=enumizeOptions($bits[3], $table, $bits[1]); } else if($bits[0]=="textarea"){ diff --git a/tools/quat.php b/tools/quat.php index 7c007a2eada..9de5acc8d98 100644 --- a/tools/quat.php +++ b/tools/quat.php @@ -239,11 +239,17 @@ function GetSelectStatement($parameterType, $field=NULL) { $parameterType['SourceField'] == 'Validity' || $parameterType['SourceField'] == 'Data_entry') { $field = "`flag`.`$parameterType[SourceField]`"; - } else { + } else if($parameterType['SourceField'] == 'Examiner') + $field = "e.`full_name`"; + else { $field = "`$parameterType[SourceFrom]`.`$parameterType[SourceField]`"; } } - $query = "SELECT $field AS Value FROM session s JOIN flag ON (s.ID=flag.SessionID) LEFT JOIN feedback_bvl_thread USING (CommentID) CROSS JOIN $parameterType[SourceFrom] LEFT JOIN candidate ON (s.CandID = candidate.CandID) WHERE flag.Administration IN ('All', 'Partial') AND flag.Data_entry='Complete' AND flag.CommentID=$parameterType[SourceFrom].CommentID AND (feedback_bvl_thread.Status IS NULL OR feedback_bvl_thread.Status='closed' OR feedback_bvl_thread.Status='comment')"; + if($parameterType['SourceField'] == 'Examiner') + $query = "SELECT $field AS Value FROM session s JOIN flag ON (s.ID=flag.SessionID) LEFT JOIN feedback_bvl_thread USING (CommentID) CROSS JOIN $parameterType[SourceFrom] LEFT JOIN candidate ON (s.CandID = candidate.CandID) LEFT JOIN examiners e ON (e.examinerID=$parameterType[SourceFrom].Examiner) WHERE flag.Administration IN ('All', 'Partial') AND flag.Data_entry='Complete' AND flag.CommentID=$parameterType[SourceFrom].CommentID AND (feedback_bvl_thread.Status IS NULL OR feedback_bvl_thread.Status='closed' OR feedback_bvl_thread.Status='comment')"; + else { + $query = "SELECT $field AS Value FROM session s JOIN flag ON (s.ID=flag.SessionID) LEFT JOIN feedback_bvl_thread USING (CommentID) CROSS JOIN $parameterType[SourceFrom] LEFT JOIN candidate ON (s.CandID = candidate.CandID) WHERE flag.Administration IN ('All', 'Partial') AND flag.Data_entry='Complete' AND flag.CommentID=$parameterType[SourceFrom].CommentID AND (feedback_bvl_thread.Status IS NULL OR feedback_bvl_thread.Status='closed' OR feedback_bvl_thread.Status='comment')"; + } break; } return $query; From 2a615ad2b1358d6278e88b67f3930304c394cfdf Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Tue, 30 Aug 2011 13:16:33 -0400 Subject: [PATCH 06/16] Stop skipping instruments that was added for debugging --- tools/data_dictionary_builder.php | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/tools/data_dictionary_builder.php b/tools/data_dictionary_builder.php index b04c5e7d479..ec9b1285b2e 100644 --- a/tools/data_dictionary_builder.php +++ b/tools/data_dictionary_builder.php @@ -139,10 +139,6 @@ foreach($items AS $item){ $paramId=""; $bits=explode("{@}",trim($item)); - //exclude Examiners, since their answer options do not exist in ip_output.txt - //if(ereg("^Examiner", $bits[1])){ - // continue; - // switch($bits[0]){ case "table": $table=$bits[1]; @@ -168,8 +164,7 @@ // to treat it as a varchar. derive_timepoint_variables will derive // the name from the examiner id $bits[0] = "varchar(255)"; -} else continue; - if($bits[0]=="select"){ + } else if($bits[0]=="select"){ $bits[0]=enumizeOptions($bits[3], $table, $bits[1]); } else if($bits[0]=="textarea"){ $bits[0]="text"; From 4b693488d144d7c1ee7eb73b72932deaf8ade526 Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Tue, 30 Aug 2011 13:18:45 -0400 Subject: [PATCH 07/16] Added IBIS's derive timepoint variables script --- tools/new_derive_timepoints.php | 162 ++++++++++++++++++++++++++++++++ 1 file changed, 162 insertions(+) create mode 100644 tools/new_derive_timepoints.php diff --git a/tools/new_derive_timepoints.php b/tools/new_derive_timepoints.php new file mode 100644 index 00000000000..b7ad58179af --- /dev/null +++ b/tools/new_derive_timepoints.php @@ -0,0 +1,162 @@ + 'MRI_Native_T1_File', + 't2w' => 'MRI_Native_T2_File', + ); + $ParameterTypeIDs = array(); + + // Delete old values, and populate array of ParameterTypeIDs + foreach($FileTypes as $type => $parameter_type) { + $ParameterTypeIDs[$type] = $db->pselectOne("SELECT ParameterTypeID FROM parameter_type WHERE Name=:parametertype", array('parametertype' => $parameter_type)); + if(empty($ParameterTypeIDs[$type])) { + print "Error: missing parameterTypeID for $parameter_type\n"; + exit(-1); + } + $ParameterTypeIDs[$type . '_QC'] = $db->pselectOne("SELECT ParameterTypeID FROM parameter_type WHERE Name=:parametertype", array('parametertype' => $parameter_type . '_QC')); + if(empty($ParameterTypeIDs[$type . '_QC'])) { + print "Error: missing parameterTypeID for $parameter_type" . "_QC\n"; + exit(-1); + } + $db->delete('parameter_session', array('ParameterTypeID'=>$ParameterTypeIDs[$type])); + $db->delete('parameter_session', array('ParameterTypeID'=>$ParameterTypeIDs[$type . '_QC'])); + + //} + + //foreach($FileTypes as $type => $parameter_type) { + // Get the files, but only the selected ones. This (theoretically) + // ensures only 1 per SessionID + $sessions = $db->pselect("SELECT SessionID, File, QCStatus FROM files f + JOIN parameter_file pf USING(FileID) + JOIN parameter_type pt USING(ParameterTypeID) + WHERE File like '%$type%' + AND pt.Name='Selected' AND COALESCE(pf.Value, '') <> '' AND File NOT LIKE '%phantom%' AND (f.QCStatus = 'Pass' OR f.QCStatus IS NULL)", array()); + + foreach($sessions as $row) { + $val = array(); + print "Inserting $row[SessionID]\n"; + $val['SessionID']=$row['SessionID']; + $val['Value'] = $row['File']; + $val['ParameterTypeID'] = $ParameterTypeIDs[$type]; + $val['InsertTime'] = time(); + $db->insert("parameter_session", $val); + + print "Inserting $row[SessionID] QC Status\n"; + $val['Value'] = $row['QCStatus']; + $val['ParameterTypeID'] = $ParameterTypeIDs[$type . '_QC']; + $db->insert("parameter_session", $val); + } + + // TEMPORARY: DELETE files with multiples selected, so quat + // doesn't die. These files should be fixed. + + $duplisessions = $db->pselect("select SessionID, Value, count(*) from parameter_session WHERE ParameterTypeID=" . $ParameterTypeIDs[$type] . " GROUP BY SessionID, ParameterTypeID HAVING COUNT(*) > 1", array()); + foreach ($duplisessions as $row) { + print "Deleting $row[SessionID]\n"; + $db->delete('parameter_session', array('SessionID' => $row['SessionID'])); + } + } +} + +function DeriveRadiologicalReviewStatus() { + global $db; + $PTIDs = array('SAS', 'SAS2', 'PVS', 'PVS2'); + $sessions = $db->pselect("SELECT * FROM session join flag on (session.ID=flag.SessionID) JOIN final_radiological_review USING(CommentID) WHERE Active='Y' and Cancelled='N'", array()); + foreach ($PTIDs as $type) { + $PTID = $db->pselectOne("SELECT ParameterTypeID FROM parameter_type WHERE Name=:parametertype", array('parametertype' => 'Final_Radiological_Review_' . $type)); + if(!is_numeric($PTID)) { + print "Error finding ParameterTypeID for $PTID\n"; + return -1; + } + foreach($sessions as $row) { + $val['SessionID'] = $row['SessionID']; + switch($row[$type]) { + case '0': + $val['Value'] = 'None'; + break; + case '1': + $val['Value'] = 'Minimal'; + break; + case '2': + $val['Value'] = 'Mild'; + break; + case '3': + $val['Value'] = 'Moderate'; + break; + case '4': + $val['Value'] = 'Marked'; + break; + default: + $val['Value'] = 'Not Answered'; + break; + } + $val['ParameterTypeID'] = $PTID; + $val['InsertTime'] = time(); + print "Inserting $val[SessionID], $val[Value]\n"; + $db->insert("parameter_session", $val); + } + } +} +function DeriveCohort() { + global $db; + $sessions = $db->pselect("SELECT ID, SubprojectID FROM session WHERE Active='Y' and Cancelled='N'", array()); + $PTID = $db->pselectOne("SELECT ParameterTypeID FROM parameter_type WHERE Name=:parametertype", + array('parametertype' => 'Cohort')); + foreach($sessions as $row) { + if(!is_numeric($PTID)) { + print "Error finding ParameterTypeID for cohort\n"; + return -1; + } + $val['SessionID'] = $row['ID']; + switch($row['SubprojectID']) { + case 1: + $val['Value'] = '6 month recruit'; + break; + case 2: + $val['Value'] = '12 month recruit'; + break; + case 3: + $val['Value'] = 'Control'; + break; + default: + $val['Value'] = 'Unknown'; + break; + } + $val['ParameterTypeID'] = $PTID; + $val['InsertTime'] = time(); + print "Inserting $val[SessionID], $val[Value]\n"; + $db->insert("parameter_session", $val); + } +} + + +MRI_Find_And_Insert_Selected(); + +DeriveRadiologicalReviewStatus(); +DeriveCohort(); +?> From 0c60330b6d5a43f1a4e1e6dea9494532b1c6b5ad Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Wed, 31 Aug 2011 16:39:46 -0400 Subject: [PATCH 08/16] Fixed bug where JS side caching wasn't working since DQG-Cosmetic changes --- htdocs/dqgui_step1.js | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/htdocs/dqgui_step1.js b/htdocs/dqgui_step1.js index b7338c0b744..b1a952391c3 100644 --- a/htdocs/dqgui_step1.js +++ b/htdocs/dqgui_step1.js @@ -108,12 +108,25 @@ function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake,fieldOrder var currentLongestString=0; var cellWidth=0; var totalWidth=0; - //for(var i in remoteFieldData){ - for(var x = 0;x < fieldOrderList.length; x++) { + + if(cache) { + iterator = remoteFieldData; + } else { + iterator = fieldOrderList; + } + for(var x = 0;x < iterator.length; x++) { // HACK: using x, and then assigning i = fieldOrderList[x] is easier than rewriting // the code to use fieldOrderList[i] everywhere, since this was changed from remoteFieldData - // to fieldOrderList - i = fieldOrderList[x]; + // to fieldOrderList. + // If working with cached data, use the old way. + if(cache) { + if(remoteFieldData[x] === undefined) continue; + i = x; + } else { + i = fieldOrderList[x]; + } + + if(loopcounter%3==0 && loopcounter!=0) { oBody.appendChild(oRow); oRow = document.createElement("TR"); From ddd9b3d8428391ecf9ce78ee3abc0c303773a495 Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Thu, 1 Sep 2011 14:07:31 -0400 Subject: [PATCH 09/16] Fix so that DQG doesn't show blank rows --- htdocs/query_gui_data_loader.php | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/htdocs/query_gui_data_loader.php b/htdocs/query_gui_data_loader.php index 4fe054000c4..a2f4f8de175 100644 --- a/htdocs/query_gui_data_loader.php +++ b/htdocs/query_gui_data_loader.php @@ -46,8 +46,9 @@ $DB->select($query, $results); foreach($results AS $row) { - $script .= "remoteFieldData.push({id:".$row['ParameterTypeCategoryID'].",name:\"".$row['Name']."\"});\n"; - // $script .= "remoteFieldData[".$row['ParameterTypeCategoryID']."]=\"$row[Name]\";\n"; + if ((!is_null($row['Name']))&&(!preg_match('/Array/',$row['Name']))) { + $script .= "remoteFieldData.push({id:".$row['ParameterTypeCategoryID'].",name:\"".$row['Name']."\"});\n"; + } } break; @@ -262,7 +263,8 @@ // add the selected tables $query .= join(', ', $selectedTables); - $query .= " WHERE "; + //$query .= " WHERE "; + $query .= " WHERE COALESCE(" . join(', ', $selectedFields) . ") IS NOT NULL AND "; // if there are more than one table involved, join them if(count($selectedTables) > 1) { From 9e55acbb5071e6fc99c3a52525ee1c1ecd7cf1d3 Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Wed, 24 Aug 2011 11:04:43 -0400 Subject: [PATCH 10/16] Fixed table so that it uses rows instead of
This results in useful scrolling in the DQG --- htdocs/dqgui_step1.js | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/htdocs/dqgui_step1.js b/htdocs/dqgui_step1.js index b1a952391c3..ad425c1ce42 100644 --- a/htdocs/dqgui_step1.js +++ b/htdocs/dqgui_step1.js @@ -94,6 +94,7 @@ function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake,fieldOrder //Create the table that will hold all the field checkboxes var oTable=document.createElement("TABLE"); oTable.border=0; + oTable.style.width="100%"; oFieldsContainerDiv.appendChild(oTable); var oBody=document.createElement("TBODY"); oTable.appendChild(oBody); @@ -133,6 +134,8 @@ function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake,fieldOrder oRow.style.fontSize="80%"; oRow.style.width="100%"; } + oCell=document.createElement("TD"); + oCell.setAttribute("valign","top"); //create the checkbox and assign the event handler var oCheckbox=addNewElement("INPUT", type+"SelectCheckbox", "checkbox"); @@ -141,28 +144,28 @@ function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake,fieldOrder if(stepNumber==1){ oCheckbox.onclick=addFieldToSelected; } + //Check the box off if it is already selected if(stepNumber==1 && selectedFields[i]){ oCheckbox.checked=true; } - oCell.appendChild(oCheckbox); //create the text node var tText=document.createTextNode(remoteFieldData[i][1]); + + oCell.appendChild(oCheckbox); oCell.appendChild(tText); - if(remoteFieldData[i][1].length > currentLongestString){ - currentLongestString=remoteFieldData[i][1].length; - } + + oRow.appendChild(oCell); + + + loopcounter++; } oBody.appendChild(oRow); //Finalize cell and table sizing. - cellWidth=(currentLongestString*8+30); - totalWidth+=cellWidth+10; - oCell.style.width=cellWidth+'px'; - oRow.appendChild(oCell); - oTable.width=totalWidth; + oTable.width="100%"; } From 5bb0c9d08635a1fa1ea779bd536a2f714b9af512 Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Tue, 23 Aug 2011 10:47:28 -0400 Subject: [PATCH 11/16] Bug fix so default active tab is define variable, not save/load --- htdocs/dqgui_core.js | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/htdocs/dqgui_core.js b/htdocs/dqgui_core.js index b04a4029bad..f583b0070ff 100644 --- a/htdocs/dqgui_core.js +++ b/htdocs/dqgui_core.js @@ -51,6 +51,10 @@ function initialize(){ sendRemoteDataQuery("query_gui_data_loader.php?mode=categories"); sendRemoteDataQuery("query_gui_data_loader.php?mode=listQueries"); + // Make sure the front end active div matches the backend. + // If it's uninitialized explicitly, for some reason the front end seems to default + // to 3, while the backend defaults to 1. + setStepDiv(stepNumber); } @@ -260,4 +264,4 @@ function getEventTarget(mozTarget, ieTarget){ } else { return ieTarget; } -} \ No newline at end of file +} From 6d287b8c454a0a1c4cf89f82ab1515ef37750e2e Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Fri, 9 Sep 2011 15:05:27 -0400 Subject: [PATCH 12/16] Added fancy highlighting to DQG using jQuery --- htdocs/JS/jquery-1.4.2.min.js | 154 ++++++++++++++++++++++++++++++++++ htdocs/dqgui_core.js | 23 +++++ htdocs/dqgui_step1.js | 50 +++++------ htdocs/main.css | 12 +++ htdocs/query_gui.php | 1 + 5 files changed, 210 insertions(+), 30 deletions(-) create mode 100644 htdocs/JS/jquery-1.4.2.min.js diff --git a/htdocs/JS/jquery-1.4.2.min.js b/htdocs/JS/jquery-1.4.2.min.js new file mode 100644 index 00000000000..7c243080233 --- /dev/null +++ b/htdocs/JS/jquery-1.4.2.min.js @@ -0,0 +1,154 @@ +/*! 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diff --git a/htdocs/dqgui_core.js b/htdocs/dqgui_core.js index f583b0070ff..75b0fca51a7 100644 --- a/htdocs/dqgui_core.js +++ b/htdocs/dqgui_core.js @@ -265,3 +265,26 @@ function getEventTarget(mozTarget, ieTarget){ return ieTarget; } } + +function setJQueryClickHandlers() { + $('.fieldsSelectCell').unbind('click').click(function(e) { + e.stopPropagation(); + cellId = $(this).attr('id'); + + if(cellId.indexOf("Cell") >= 0) { + // Clicked on table cell + //alert('Clicked on table cell'); + if($(this).hasClass("selected")) { + addFieldToSelected(cellId.replace("Cell", ""), false) + } else { + addFieldToSelected(cellId.replace("Cell", ""), true) + } + } /* else if (cellId.indexOf("fieldsSelect_") >= 0) { + // Clicked on checkbox + alert('Clicked on checkbox'); + } */ + }); +} +$(document).ready(function() { + setJQueryClickHandlers(); +}); diff --git a/htdocs/dqgui_step1.js b/htdocs/dqgui_step1.js index ad425c1ce42..bda78f60a00 100644 --- a/htdocs/dqgui_step1.js +++ b/htdocs/dqgui_step1.js @@ -136,13 +136,19 @@ function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake,fieldOrder } oCell=document.createElement("TD"); oCell.setAttribute("valign","top"); + oCell.setAttribute("class",type+"SelectCell fieldsSelect"); + oCell.setAttribute("id",type+"SelectCell_" + remoteFieldData[i][0]); + oCell.setAttribute("title",remoteFieldData[i][2]); //create the checkbox and assign the event handler var oCheckbox=addNewElement("INPUT", type+"SelectCheckbox", "checkbox"); oCheckbox.id=type+"Select_"+remoteFieldData[i][0]; oCheckbox.setAttribute("title",remoteFieldData[i][2]); + oCheckbox.setAttribute("class",type+"SelectCheckbox fieldsSelect"); if(stepNumber==1){ - oCheckbox.onclick=addFieldToSelected; + // handled by jQuery on fieldSelectCell + + //oCheckbox.onclick=addFieldToSelected; } //Check the box off if it is already selected @@ -166,46 +172,28 @@ function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake,fieldOrder //Finalize cell and table sizing. oTable.width="100%"; + setJQueryClickHandlers(); } function loadCategoriesByRemote(categories){ -categoryNames = new Array(); -for (var i=0; i < categories.length; i++) { -categoryNames[categories[i].id] = categories[i].name; -}; + categoryNames = new Array(); + for (var i=0; i < categories.length; i++) { + categoryNames[categories[i].id] = categories[i].name; + }; var selects=["fieldCategorySelect","conditionalCategorySelect"]; for(var i in selects){ var oFieldCategorySelect=document.getElementById(selects[i]); -for (var i=0; i < categories.length; i++) { -oCategoryOption=document.createElement("OPTION"); -oCategoryOption.value=categories[i].id; -oCategoryOption.appendChild(document.createTextNode(categories[i].name)); -oFieldCategorySelect.appendChild(oCategoryOption); -}; + for (var i=0; i < categories.length; i++) { + oCategoryOption=document.createElement("OPTION"); + oCategoryOption.value=categories[i].id; + oCategoryOption.appendChild(document.createTextNode(categories[i].name)); + oFieldCategorySelect.appendChild(oCategoryOption); + }; } } -/* - -//loadCategoriesByRemote populates the category select drop down via the remote loader page -function loadCategoriesByRemote(categories){ - categoryNames=categories; - var selects=["fieldCategorySelect","conditionalCategorySelect"]; - for(var i in selects){ - var oFieldCategorySelect=document.getElementById(selects[i]); - for(var cat_id in categories){ - oCategoryOption=document.createElement("OPTION"); - oCategoryOption.value=cat_id; - oCategoryOption.appendChild(document.createTextNode(categories[cat_id])); - oFieldCategorySelect.appendChild(oCategoryOption); - } - } -} - -*/ - //FIELD SELECTING/UNSELECTING FUNCTIONS ------------------------------------------------ //checkAllFields adds/removes all the fields to the selected fields box @@ -238,6 +226,7 @@ function addFieldToSelected(fieldId, status, checkall){ } //If the box is checked then add the field if(status==true){ + $("#fieldsSelectCell_" + fieldId).addClass("selected"); var coll=document.getElementsByTagName("INPUT"); for(var i=0; i + From 777fe7457ded1f1872403f91625ee0ae4ee23141 Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Mon, 3 Oct 2011 12:26:02 -0400 Subject: [PATCH 13/16] Removed basic/Advanced mode and gave jQuery highlighting treatment to Define Population --- htdocs/dqgui_core.js | 18 ++++++++++-------- htdocs/dqgui_step2.js | 19 +++++++++++++++++++ htdocs/query_gui.php | 10 +++++----- 3 files changed, 34 insertions(+), 13 deletions(-) diff --git a/htdocs/dqgui_core.js b/htdocs/dqgui_core.js index 75b0fca51a7..9669223b631 100644 --- a/htdocs/dqgui_core.js +++ b/htdocs/dqgui_core.js @@ -42,7 +42,7 @@ var fieldData=new Array(); //The field information, loaded by remote. [id]=[id var selectedFields = new Array(); //The array of fields the user has selected. [id]=true/false; -var currentMode = "Basic"; // either Basic or Advanced +var currentMode = "Advanced"; // either Basic or Advanced //INITIALIZATION --------------------------------------------------------- //Initialize function for the page run on body load. @@ -267,22 +267,24 @@ function getEventTarget(mozTarget, ieTarget){ } function setJQueryClickHandlers() { - $('.fieldsSelectCell').unbind('click').click(function(e) { + $('.fieldsSelectCell,.conditionalsSelectCell').unbind('click').click(function(e) { e.stopPropagation(); cellId = $(this).attr('id'); if(cellId.indexOf("Cell") >= 0) { // Clicked on table cell //alert('Clicked on table cell'); + if(cellId.indexOf("conditional") >= 0) { + addToSelected = checkConditionalField; + } else { + addToSelected = addFieldToSelected; + } if($(this).hasClass("selected")) { - addFieldToSelected(cellId.replace("Cell", ""), false) + addToSelected(cellId.replace("Cell", ""), false) } else { - addFieldToSelected(cellId.replace("Cell", ""), true) + addToSelected(cellId.replace("Cell", ""), true) } - } /* else if (cellId.indexOf("fieldsSelect_") >= 0) { - // Clicked on checkbox - alert('Clicked on checkbox'); - } */ + } }); } $(document).ready(function() { diff --git a/htdocs/dqgui_step2.js b/htdocs/dqgui_step2.js index 33dd83bf428..99d84981a41 100644 --- a/htdocs/dqgui_step2.js +++ b/htdocs/dqgui_step2.js @@ -15,12 +15,31 @@ function addCheckedConditionals(){ for(var fieldId in categoryFields[conditionalsActiveCategoryId]){ var oCheckbox=document.getElementById("conditionalsSelect_"+fieldId); if(oCheckbox.checked){ + $('#conditionalsSelectCell_' + fieldId).removeClass("selected"); addConditionalToSelected(fieldId); oCheckbox.checked=false; } } } +function checkConditionalField(fieldId, status) { + if(!fieldId || fieldId.type == "click") { + var fieldId = this.id; + } + + var prefix = fieldId.split("_", 1); + fieldId = fieldId.substr(prefix[0].length+1); + if(status == null) { + var status = this.checked; + } + if(status == true) { + $('#conditionalsSelectCell_' + fieldId).addClass("selected"); + $('#conditionalsSelect_' + fieldId).attr('checked', 'checked'); + } else { + $('#conditionalsSelect_' + fieldId).removeAttr('checked'); + $('#conditionalsSelectCell_' + fieldId).removeClass("selected"); + } +} function addConditionalToSelected(fieldId){ var id=selectedConditionals.length; //Get the target group id diff --git a/htdocs/query_gui.php b/htdocs/query_gui.php index af012760eca..6e948865aa6 100644 --- a/htdocs/query_gui.php +++ b/htdocs/query_gui.php @@ -41,11 +41,11 @@ - + - +
Define VariablesDefine Population Download Spreadsheet   Save/Load QueryGo to Advanced Mode
@@ -131,9 +131,9 @@ - - - + + +
From a51c188a703f04ae44f205d0d542ed33dbc7314f Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Tue, 4 Oct 2011 10:04:36 -0400 Subject: [PATCH 14/16] Unescape HTML encoded strings before displaying in DQG. Also, explicitly set character encoding to UTF-8 when encoding. Together, these should fix the display issues that were happening with descriptions that had special characters in them. --- htdocs/dqgui_core.js | 9 +++++++++ htdocs/dqgui_step1.js | 9 ++++++--- htdocs/query_gui_data_loader.php | 2 +- 3 files changed, 16 insertions(+), 4 deletions(-) diff --git a/htdocs/dqgui_core.js b/htdocs/dqgui_core.js index 9669223b631..3b6403ea145 100644 --- a/htdocs/dqgui_core.js +++ b/htdocs/dqgui_core.js @@ -266,6 +266,15 @@ function getEventTarget(mozTarget, ieTarget){ } } +function decodeHTMLEntities(s) { + // Return javascript string with HTML entities decoded into their + // real characters by creating a textarea, setting the innerHTML, + // then returning the parsed value. + var t = document.createElement('textarea'); + t.innerHTML = s; + return t.value; +} + function setJQueryClickHandlers() { $('.fieldsSelectCell,.conditionalsSelectCell').unbind('click').click(function(e) { e.stopPropagation(); diff --git a/htdocs/dqgui_step1.js b/htdocs/dqgui_step1.js index bda78f60a00..fe0088093b3 100644 --- a/htdocs/dqgui_step1.js +++ b/htdocs/dqgui_step1.js @@ -138,12 +138,14 @@ function loadFieldsByRemote(type, catId, remoteFieldData, cache, fake,fieldOrder oCell.setAttribute("valign","top"); oCell.setAttribute("class",type+"SelectCell fieldsSelect"); oCell.setAttribute("id",type+"SelectCell_" + remoteFieldData[i][0]); - oCell.setAttribute("title",remoteFieldData[i][2]); + oCell.setAttribute("title", decodeHTMLEntities(remoteFieldData[i][2])); + + //oCell.setAttribute("title",remoteFieldData[i][2]); //create the checkbox and assign the event handler var oCheckbox=addNewElement("INPUT", type+"SelectCheckbox", "checkbox"); oCheckbox.id=type+"Select_"+remoteFieldData[i][0]; - oCheckbox.setAttribute("title",remoteFieldData[i][2]); + oCheckbox.setAttribute("title",decodeHTMLEntities(remoteFieldData[i][2])); oCheckbox.setAttribute("class",type+"SelectCheckbox fieldsSelect"); if(stepNumber==1){ // handled by jQuery on fieldSelectCell @@ -295,10 +297,11 @@ function addRow(id, columnData){ if(i==0){ newCell.appendChild(document.createTextNode(categoryNames[columnData[3]])); } else { - newCell.appendChild(document.createTextNode(columnData[i])); + newCell.appendChild(document.createTextNode(decodeHTMLEntities(columnData[i]))); } newCell.style.borderBottom="1px black solid"; newRow.appendChild(newCell); + } return newRow; } diff --git a/htdocs/query_gui_data_loader.php b/htdocs/query_gui_data_loader.php index a2f4f8de175..be58d355e21 100644 --- a/htdocs/query_gui_data_loader.php +++ b/htdocs/query_gui_data_loader.php @@ -90,7 +90,7 @@ $data[] = $rawdata[$id]; } foreach($data AS $result){ - $script.= "remoteFieldData[".$result['ParameterTypeID']."]=[".$result['ParameterTypeID'].", \"".$result['Name']."\", \"".htmlentities($result['Description'])."\", ".$result['ParameterTypeCategoryID'].", \"".$result['Type']."\""; + $script.= "remoteFieldData[".$result['ParameterTypeID']."]=[".$result['ParameterTypeID'].", \"".$result['Name']."\", \"".htmlentities($result['Description'], ENT_COMPAT | ENT_HTML401, 'UTF-8')."\", ".$result['ParameterTypeCategoryID'].", \"".$result['Type']."\""; if(!empty($result['Values'])){ $script.= ", [".$result['Values']."]"; } From 7bdaced44d5a13209e8ef69f84138388a8eacf6e Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Wed, 25 Jan 2012 11:39:55 -0500 Subject: [PATCH 15/16] Removed quat scripts from cosmetic branch --- tools/new_derive_timepoints.php | 162 -------------------------------- tools/quat.php | 54 ++--------- 2 files changed, 6 insertions(+), 210 deletions(-) delete mode 100644 tools/new_derive_timepoints.php diff --git a/tools/new_derive_timepoints.php b/tools/new_derive_timepoints.php deleted file mode 100644 index b7ad58179af..00000000000 --- a/tools/new_derive_timepoints.php +++ /dev/null @@ -1,162 +0,0 @@ - 'MRI_Native_T1_File', - 't2w' => 'MRI_Native_T2_File', - ); - $ParameterTypeIDs = array(); - - // Delete old values, and populate array of ParameterTypeIDs - foreach($FileTypes as $type => $parameter_type) { - $ParameterTypeIDs[$type] = $db->pselectOne("SELECT ParameterTypeID FROM parameter_type WHERE Name=:parametertype", array('parametertype' => $parameter_type)); - if(empty($ParameterTypeIDs[$type])) { - print "Error: missing parameterTypeID for $parameter_type\n"; - exit(-1); - } - $ParameterTypeIDs[$type . '_QC'] = $db->pselectOne("SELECT ParameterTypeID FROM parameter_type WHERE Name=:parametertype", array('parametertype' => $parameter_type . '_QC')); - if(empty($ParameterTypeIDs[$type . '_QC'])) { - print "Error: missing parameterTypeID for $parameter_type" . "_QC\n"; - exit(-1); - } - $db->delete('parameter_session', array('ParameterTypeID'=>$ParameterTypeIDs[$type])); - $db->delete('parameter_session', array('ParameterTypeID'=>$ParameterTypeIDs[$type . '_QC'])); - - //} - - //foreach($FileTypes as $type => $parameter_type) { - // Get the files, but only the selected ones. This (theoretically) - // ensures only 1 per SessionID - $sessions = $db->pselect("SELECT SessionID, File, QCStatus FROM files f - JOIN parameter_file pf USING(FileID) - JOIN parameter_type pt USING(ParameterTypeID) - WHERE File like '%$type%' - AND pt.Name='Selected' AND COALESCE(pf.Value, '') <> '' AND File NOT LIKE '%phantom%' AND (f.QCStatus = 'Pass' OR f.QCStatus IS NULL)", array()); - - foreach($sessions as $row) { - $val = array(); - print "Inserting $row[SessionID]\n"; - $val['SessionID']=$row['SessionID']; - $val['Value'] = $row['File']; - $val['ParameterTypeID'] = $ParameterTypeIDs[$type]; - $val['InsertTime'] = time(); - $db->insert("parameter_session", $val); - - print "Inserting $row[SessionID] QC Status\n"; - $val['Value'] = $row['QCStatus']; - $val['ParameterTypeID'] = $ParameterTypeIDs[$type . '_QC']; - $db->insert("parameter_session", $val); - } - - // TEMPORARY: DELETE files with multiples selected, so quat - // doesn't die. These files should be fixed. - - $duplisessions = $db->pselect("select SessionID, Value, count(*) from parameter_session WHERE ParameterTypeID=" . $ParameterTypeIDs[$type] . " GROUP BY SessionID, ParameterTypeID HAVING COUNT(*) > 1", array()); - foreach ($duplisessions as $row) { - print "Deleting $row[SessionID]\n"; - $db->delete('parameter_session', array('SessionID' => $row['SessionID'])); - } - } -} - -function DeriveRadiologicalReviewStatus() { - global $db; - $PTIDs = array('SAS', 'SAS2', 'PVS', 'PVS2'); - $sessions = $db->pselect("SELECT * FROM session join flag on (session.ID=flag.SessionID) JOIN final_radiological_review USING(CommentID) WHERE Active='Y' and Cancelled='N'", array()); - foreach ($PTIDs as $type) { - $PTID = $db->pselectOne("SELECT ParameterTypeID FROM parameter_type WHERE Name=:parametertype", array('parametertype' => 'Final_Radiological_Review_' . $type)); - if(!is_numeric($PTID)) { - print "Error finding ParameterTypeID for $PTID\n"; - return -1; - } - foreach($sessions as $row) { - $val['SessionID'] = $row['SessionID']; - switch($row[$type]) { - case '0': - $val['Value'] = 'None'; - break; - case '1': - $val['Value'] = 'Minimal'; - break; - case '2': - $val['Value'] = 'Mild'; - break; - case '3': - $val['Value'] = 'Moderate'; - break; - case '4': - $val['Value'] = 'Marked'; - break; - default: - $val['Value'] = 'Not Answered'; - break; - } - $val['ParameterTypeID'] = $PTID; - $val['InsertTime'] = time(); - print "Inserting $val[SessionID], $val[Value]\n"; - $db->insert("parameter_session", $val); - } - } -} -function DeriveCohort() { - global $db; - $sessions = $db->pselect("SELECT ID, SubprojectID FROM session WHERE Active='Y' and Cancelled='N'", array()); - $PTID = $db->pselectOne("SELECT ParameterTypeID FROM parameter_type WHERE Name=:parametertype", - array('parametertype' => 'Cohort')); - foreach($sessions as $row) { - if(!is_numeric($PTID)) { - print "Error finding ParameterTypeID for cohort\n"; - return -1; - } - $val['SessionID'] = $row['ID']; - switch($row['SubprojectID']) { - case 1: - $val['Value'] = '6 month recruit'; - break; - case 2: - $val['Value'] = '12 month recruit'; - break; - case 3: - $val['Value'] = 'Control'; - break; - default: - $val['Value'] = 'Unknown'; - break; - } - $val['ParameterTypeID'] = $PTID; - $val['InsertTime'] = time(); - print "Inserting $val[SessionID], $val[Value]\n"; - $db->insert("parameter_session", $val); - } -} - - -MRI_Find_And_Insert_Selected(); - -DeriveRadiologicalReviewStatus(); -DeriveCohort(); -?> diff --git a/tools/quat.php b/tools/quat.php index 9de5acc8d98..2982135eb4c 100644 --- a/tools/quat.php +++ b/tools/quat.php @@ -107,7 +107,6 @@ // run the create table statement $createSQL = "CREATE TABLE $nextTableName (SessionID int not null primary key, $createSQL)"; - $insertSQL = "INSERT INTO $nextTableName (SessionID) SELECT DISTINCT SessionID FROM flag f JOIN parameter_type pt ON (f.Test_name=pt.SourceFrom) JOIN session s ON (s.ID=f.SessionID) JOIN candidate c ON (c.CandID=s.CandID) WHERE pt.CurrentGUITable='$nextTableName' AND c.Active='Y' AND c.Cancelled='N' AND s.Active='Y' AND s.Cancelled='N' AND c.CenterID IN (2, 3, 4, 5) AND s.Current_stage <> 'Recycling Bin' UNION select DISTINCT SessionID FROM parameter_session ps JOIN parameter_type pt ON (pt.ParameterTypeID=ps.ParameterTypeID) JOIN session s ON (ps.SessionID=s.ID) JOIN candidate c ON (c.CandID=s.CandID) WHERE pt.CurrentGUITable='$nextTableName' AND c.Active='Y' AND c.Cancelled='N' AND s.Active='Y' AND s.Cancelled='N' AND c.CenterID IN (2, 3, 4, 5) AND s.Current_stage <> 'Recycling Bin'"; $quatTableCounter++; $nextTableName = $quatTableBasename . $quatTableCounter; $result = $db->run($createSQL); @@ -119,7 +118,6 @@ $createSQL = ""; $columnCount = 0; print "Finished creating $nextTableName: " . memory_get_usage() . "\n"; -if($quatTableCounter > 2) break; } } @@ -166,9 +164,9 @@ function GetSelectStatement($parameterType, $field=NULL) { switch($parameterType['SourceFrom']) { case 'files': if($field == null) { - $field = "File"; + $field = "FileID"; } - $query = "SELECT $field AS Value FROM files JOIN session as S ON (s.ID=files.SessionID) WHERE OutputType='$parameterType[SourceCondition]'"; + $query = "SELECT $field AS Value FROM files JOIN session as S ON (s.ID=files.SessionID) WHERE OutputType='$parameterType[SourceField]'"; break; case 'parameter_file': @@ -222,7 +220,7 @@ function GetSelectStatement($parameterType, $field=NULL) { if($field == null) { $field = "s.$parameterType[SourceField] Value"; } - $query = "SELECT $field AS Value FROM session s LEFT JOIN psc USING (CenterID) WHERE 1=1"; + $query = "SELECT $field AS Value FROM session s LEFT JOIN psc USING (CenterID)"; break; case 'mri_acquisition_dates': @@ -235,21 +233,9 @@ function GetSelectStatement($parameterType, $field=NULL) { //for behavioural instrument data default: if($field == null) { - if($parameterType['SourceField'] == 'Administration' || - $parameterType['SourceField'] == 'Validity' || - $parameterType['SourceField'] == 'Data_entry') { - $field = "`flag`.`$parameterType[SourceField]`"; - } else if($parameterType['SourceField'] == 'Examiner') - $field = "e.`full_name`"; - else { - $field = "`$parameterType[SourceFrom]`.`$parameterType[SourceField]`"; - } - } - if($parameterType['SourceField'] == 'Examiner') - $query = "SELECT $field AS Value FROM session s JOIN flag ON (s.ID=flag.SessionID) LEFT JOIN feedback_bvl_thread USING (CommentID) CROSS JOIN $parameterType[SourceFrom] LEFT JOIN candidate ON (s.CandID = candidate.CandID) LEFT JOIN examiners e ON (e.examinerID=$parameterType[SourceFrom].Examiner) WHERE flag.Administration IN ('All', 'Partial') AND flag.Data_entry='Complete' AND flag.CommentID=$parameterType[SourceFrom].CommentID AND (feedback_bvl_thread.Status IS NULL OR feedback_bvl_thread.Status='closed' OR feedback_bvl_thread.Status='comment')"; - else { - $query = "SELECT $field AS Value FROM session s JOIN flag ON (s.ID=flag.SessionID) LEFT JOIN feedback_bvl_thread USING (CommentID) CROSS JOIN $parameterType[SourceFrom] LEFT JOIN candidate ON (s.CandID = candidate.CandID) WHERE flag.Administration IN ('All', 'Partial') AND flag.Data_entry='Complete' AND flag.CommentID=$parameterType[SourceFrom].CommentID AND (feedback_bvl_thread.Status IS NULL OR feedback_bvl_thread.Status='closed' OR feedback_bvl_thread.Status='comment')"; + $field = "`$parameterType[SourceFrom]`.`$parameterType[SourceField]`"; } + $query = "SELECT $field AS Value FROM session s JOIN flag ON (s.ID=flag.SessionID) LEFT JOIN feedback_bvl_thread USING (CommentID) CROSS JOIN $parameterType[SourceFrom] LEFT JOIN candidate ON (s.CandID = candidate.CandID) WHERE flag.Administration<>'None' AND flag.CommentID=$parameterType[SourceFrom].CommentID AND (feedback_bvl_thread.Status IS NULL OR feedback_bvl_thread.Status='closed' OR feedback_bvl_thread.Status='comment')"; break; } return $query; @@ -259,35 +245,7 @@ function GetSelectStatement($parameterType, $field=NULL) { foreach($parameterTypes AS $parameterType) { if($parameterType['CurrentGUITable'] != null) { print "Updating $parameterType[Name], memory: " . memory_get_usage() . " bytes\n"; - if(strpos($parameterType['Name'], "vineland") !== FALSE || - strpos($parameterType['Name'], "EARLI") !== FALSE || - strpos($parameterType['Name'], "adi") !== FALSE || - strpos($parameterType['Name'], "csbs") !== FALSE || - strpos($parameterType['Name'], "fyi") !== FALSE || - strpos($parameterType['Name'], "head_measurements_subject") !== FALSE || - strpos($parameterType['Name'], "i3") !== FALSE || - strpos($parameterType['Name'], "ibq_r") !== FALSE || - strpos($parameterType['Name'], "m_chat_proband") !== FALSE || - strpos($parameterType['Name'], "med_psych_hist") !== FALSE || - strpos($parameterType['Name'], "aosi") !== FALSE - ) { - continue; - } - switch($parameterType['SourceFrom']) { - case 'session': - case 'candidate': - case 'psc': - case 'parameter_candidate'; - case 'parameter_session': - print "UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID) WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND s.ID=$parameterType[CurrentGUITable].SessionID)"; - $db->run("UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID) WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND s.ID=$parameterType[CurrentGUITable].SessionID)"); - //exit(-1); - break; - default: - print "UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID AND flag.CommentID NOT LIKE 'DDE%') WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND flag.CommentID NOT LIKE 'DDE%' AND s.ID=$parameterType[CurrentGUITable].SessionID)"; - $db->run("UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID AND flag.CommentID NOT LIKE 'DDE%') WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND flag.CommentID NOT LIKE 'DDE%' AND s.ID=$parameterType[CurrentGUITable].SessionID)"); - break; - } + $db->run("UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " AND $parameterType[CurrentGUITable].SessionID=s.ID AND flag.CommentID NOT LIKE 'DDE%') WHERE $parameterType[CurrentGUITable].SessionID=(" . GetSelectStatement($parameterType, "DISTINCT s.ID"). " AND flag.CommentID NOT LIKE 'DDE%' AND s.ID=quat_table_2.SessionID)"); //$db->run("UPDATE $parameterType[CurrentGUITable] SET $parameterType[Name]=(" . GetSelectStatement($parameterType) . " WHERE $parameterType[CurrentGUITable].SessionID=s.ID)"); } } From e7fb929c71abd23ce0d880719efae9b84eb04475 Mon Sep 17 00:00:00 2001 From: Dave MacFarlane Date: Fri, 3 Feb 2012 10:07:27 -0500 Subject: [PATCH 16/16] Moved jquery location so that it's consistent with other branches --- htdocs/{JS => js/jquery}/jquery-1.4.2.min.js | 0 htdocs/query_gui.php | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename htdocs/{JS => js/jquery}/jquery-1.4.2.min.js (100%) diff --git a/htdocs/JS/jquery-1.4.2.min.js b/htdocs/js/jquery/jquery-1.4.2.min.js similarity index 100% rename from htdocs/JS/jquery-1.4.2.min.js rename to htdocs/js/jquery/jquery-1.4.2.min.js diff --git a/htdocs/query_gui.php b/htdocs/query_gui.php index 6e948865aa6..fa0b3514373 100644 --- a/htdocs/query_gui.php +++ b/htdocs/query_gui.php @@ -23,7 +23,7 @@ - +