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@@ -57,9 +57,21 @@ function blast_nucleotide_form($form, &$form_state) {
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// Upload a file as an alternative to enter a query sequence
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$form['#attributes']['enctype'] = 'multipart/form-data';
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$form['query']['UPLOAD'] = array(
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- '#prefix' => 'Or upload your query files: ',
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- '#type' => 'file',
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- '#description' => t('The file should be a plain-text FASTA file and not a .doc, .docx, etc. It cannot be greater than 10 Mb in size.'),
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+ '#title' => 'Or upload your own query FASTA: ',
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+ '#type' => 'managed_file',
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+ '#description' => t('The file should be a plain-text FASTA
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+(.fasta, .fna, .fa) file. In other words, it cannot have formatting as is the
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+case with MS Word (.doc, .docx) or Rich Text Format (.rtf). It cannot be greater
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+than %max_size in size. <strong>Don\'t forget to press the Upload button before
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+attempting to submit your BLAST.</strong>',
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+ array(
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+ '%max_size' => round(file_upload_max_size() / 1024 / 1024,1) . 'MB'
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+ )
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+ ),
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+ '#upload_validators' => array(
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+ 'file_validate_extensions' => array('fasta fna fa'),
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+ 'file_validate_size' => array(file_upload_max_size()),
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+ ),
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);
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@@ -82,12 +94,24 @@ function blast_nucleotide_form($form, &$form_state) {
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'#default_value' => 0,
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);
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- // Upload a file as an alternative to enter a query sequence
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+ // Upload a file as an alternative to selecting an existing BLAST database
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$form['#attributes']['enctype'] = 'multipart/form-data';
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$form['DB']['DBUPLOAD'] = array(
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- '#prefix' => 'Or upload your own dataset: ',
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- '#type' => 'file',
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- '#description' => t('The file should be a plain-text FASTA file and not a .doc, .docx, etc. It cannot be greater than 10 Mb in size.'),
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+ '#title' => 'Or upload your own dataset: ',
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+ '#type' => 'managed_file',
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+ '#description' => t('The file should be a plain-text FASTA
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+(.fasta, .fna, .fa) file. In other words, it cannot have formatting as is the
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+case with MS Word (.doc, .docx) or Rich Text Format (.rtf). It cannot be greater
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+than %max_size in size. <strong>Don\'t forget to press the Upload button before
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+attempting to submit your BLAST.</strong>',
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+ array(
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+ '%max_size' => round(file_upload_max_size() / 1024 / 1024,1) . 'MB'
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+ )
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+ ),
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+ '#upload_validators' => array(
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+ 'file_validate_extensions' => array('fasta fna fa'),
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+ 'file_validate_size' => array(file_upload_max_size()),
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+ ),
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);
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// ALGORITHM PARAMETERS
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@@ -223,47 +247,53 @@ function blast_nucleotide_form($form, &$form_state) {
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*/
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function blast_nucleotide_form_validate($form, &$form_state) {
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- // Validate FASTA seq in textfield
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- $fastaSeq = $form_state['input']['FASTA'];
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- if (isset($fastaSeq)) {
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- if (_validateFasta($fastaSeq)){
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- form_set_error('nBLAST', t('Error: Failed to read the Blast query: Wrong format provided for FASTA nucleotide sequence'));
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+ // Validate Query
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+ //----------------
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+ // @todo: We are currently not validating uploaded files are valid FASTA.
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+ // First check to see if we have an upload & if so then validate it.
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+ $file = file_load($form_state['values']['UPLOAD']);
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+ // If the $file is populated then this is a newly uploaded, temporary file.
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+ if (is_object($file)) {
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+ $form_state['qFlag'] = 'upQuery';
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+ $form_state['upQuery_path'] = drupal_realpath($file->uri);
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+ }
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+ // Otherwise there was no file uploaded.
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+ // Check if there was a query sequence entered in the texfield.
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+ elseif (!empty($form_state['input']['FASTA'])) {
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+ // Check to ensure that the query sequence entered is valid FASTA.
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+ if (_validateFasta($form_state['input']['FASTA'])){
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+ form_set_error('nBLAST', t('You need to provide a valid FASTA sequence
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+for the query.'));
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}
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else {
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$form_state['qFlag'] = 'seqQuery';
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}
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}
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-
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- // Validate query upload
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- $upQuery = file_save_upload('UPLOAD', array('file_validate_extensions' => array('txt fasta fa fna')), FILE_EXISTS_RENAME);
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- if ($upQuery) {
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- $upQuery_uri = $upQuery->uri;
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- $form_state['upQuery_path'] = drupal_realpath($upQuery_uri);
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- $upQuery_content = file_get_contents($form_state['upQuery_path']);
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- if (_validateFasta($upQuery_content)){
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- form_set_error('nBLAST', t('Error: Failed to upload the Blast query: Wrong format provided for FASTA nucleotide sequence'));
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- }
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- else {
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- $form_state['qFlag'] = 'upQuery';
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- }
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+ // Otherwise they didn't enter a query!!
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+ else {
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+ form_set_error('nBLAST', t('You must either enter a FASTA sequence in the
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+text field or upload one of your own.'));
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}
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- // Validate blast database upload
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- $upDB = file_save_upload('DBUPLOAD', array('file_validate_extensions' => array('txt fasta fa fna')), FILE_EXISTS_RENAME);
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- if ($upDB) {
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- $upDB_uri = $upDB->uri;
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- $form_state['upDB_path'] = drupal_realpath($upDB_uri);
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- $upDB_content = file_get_contents($form_state['upDB_path']);
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- if (_validateFasta($upDB_content)){
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- form_set_error('DB', t('Error: Failed to upload the Blast subject sequence file: Wrong format provided for FASTA nucleotide sequence'));
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- }
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- else {
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- $form_state['dbFlag'] = 'upQuery';
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- }
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+ // Validate Database
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+ //-------------------
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+ // @todo: We are currently not validating uploaded files are valid FASTA.
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+ // First check to see if we have an upload & if so then validate it.
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+ $file = file_load($form_state['values']['DBUPLOAD']);
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+ // If the $file is populated then this is a newly uploaded, temporary file.
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+ if (is_object($file)) {
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+ $form_state['dbFlag'] = 'upDB';
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+ $form_state['upDB_path'] = drupal_realpath($file->uri);
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}
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- else {
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+ // Otherwise there was no file uploaded
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+ // Check if there was a database choosen from the list instead
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+ elseif (!empty($form_state['values']['SELECT_DB'])) {
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$form_state['dbFlag'] = 'blastdb';
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}
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+ // Otherwise they didn't select a database!!
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+ else {
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+ form_set_error('DB', t('You must either choose a database from the list or upload one of your own.'));
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+ }
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}
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@@ -274,6 +304,8 @@ function blast_nucleotide_form_validate($form, &$form_state) {
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*/
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function blast_nucleotide_form_submit($form, &$form_state) {
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+ $error = FALSE;
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+
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$eVal = $form_state['values']['eVal'];
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$trgtKey = $form_state['values']['maxTarget'];
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@@ -358,17 +390,28 @@ function blast_nucleotide_form_submit($form, &$form_state) {
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}
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// If the BLAST database was uploaded then use it to run the BLAST
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- if ( $form_state['dbFlag'] == 'upQuery') {
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+ if ( $form_state['dbFlag'] == 'upDB') {
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// Since we only support using the -db flag (not -subject) we need to create a
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// blast database for the FASTA uploaded.
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// NOTE: We can't support subject because we need to generate the ASN.1+ format
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// to provide multiple download type options from the same BLAST
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$blastdb_with_path = $form_state['upDB_path'];
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- system("makeblastdb -in $blastdb_with_path -dbtype nucl -parse_seqids");
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-
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- //$blast_subj_cmd = "blastn -query $query -subject $subjectSeq -out sites/default/files/$subSeqOut.blastn.html -evalue $eVal -word_size $wordSize -gapopen $gapOpen -gapextend $gapExtend -penalty $penalty -reward $reward -num_alignments 100 -html";
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- //system($blast_subj_cmd);
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+ $result = NULL;
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+ exec("makeblastdb -in $blastdb_with_path -dbtype nucl -parse_seqids 2>&1", $result);
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+
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+ // Check that the BLAST database was made correctly.
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+ $result = implode('<br />', $result);
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+ if (preg_match('/Error/', $result)) {
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+ drupal_set_message('Unable to generate a BLAST database from your uploaded
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+FASTA sequence. Please check that your file is a valid FASTA file and that if
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+your sequence headers include pipes (i.e.: | ) they adhere to '
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+. l('NCBI standards.', 'http://www.ncbi.nlm.nih.gov/books/NBK21097/table/A632/?report=objectonly', array('attributes' => array('target' => '_blank'))),
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+ 'error'
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+ );
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+
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+ $error = TRUE;
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+ }
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}
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// Otherwise, we are using one of the website provided BLAST databases so form the
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@@ -406,8 +449,10 @@ function blast_nucleotide_form_submit($form, &$form_state) {
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// Redirect to the BLAST results page
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drupal_goto("blast/report/$job_id");
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}
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- else {
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- $dbfile_uploaded_msg = ($form_state['dbFlag'] == 'upQuery') ? 'The BLAST database was submitted via user upload.' : 'Existing BLAST Database was chosen';
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+ // We check if $error is set to TRUE because if so then the error has already
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+ // been reported.
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+ elseif (!$error) {
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+ $dbfile_uploaded_msg = ($form_state['dbFlag'] == 'upDB') ? 'The BLAST database was submitted via user upload.' : 'Existing BLAST Database was chosen';
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tripal_report_error(
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'blast_ui',
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TRIPAL_ERROR,
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Lacey Sanderson