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gut expression form
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@bradfordcondon
bradfordcondon committed Dec 13, 2017
1 parent bd0b42e commit 5d739ea
Showing 1 changed file with 104 additions and 102 deletions.
206 changes: 104 additions & 102 deletions tripal_analysis_expression/includes/TripalImporter/tripal_expression_data_loader.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -109,23 +109,6 @@ class tripal_expression_data_loader extends TripalImporter{
'#options' => $organisms,
];

// At this time the analysis module has the extra fields.
// These fields do not appear to do anything for the analysis module.
// The following three form fields prevent an error form appearing
// when the expression biomaterial is submitted.
$form['removed'] = [
'#type' => 'value',
'#default_value' => '',
];
$form['num_new'] = [
'#type' => 'value',
'#default_value' => '',
];
$form['analysis_type'] = [
'#type' => 'value',
'#default_value' => '',
];

//protocols, assays, etc go here

$form['experimental_design'] = [
Expand Down Expand Up @@ -154,16 +137,18 @@ class tripal_expression_data_loader extends TripalImporter{
'#value' => $contacts,
];

$lt_message = tripal_set_message(t('If the biomaterial provider is not present in the dropdown list, ') . l(t('add a new contact.'), 'bio_data/add') . t(' A biomaterial provider is not required.'), TRIPAL_INFO, ['return_html' => TRUE]);
//TODO: WE DONT USE THIS (BUT WE SHOULD)

$form['experimental_design']['biosourceprovider_id'] = [
'#title' => t('Biomaterial Provider'),
'#type' => 'select',
'#empty_value' => '',
'#description' => t('The contact who provided the biomaterial. If the biomaterial is already') . (' present in the database, the biomaterial provider selected here will') . (' overwrite the biomaterial provider set for the biomaterial in the database.'),
'#options' => $form['choose_contact']['#value'],
'#suffix' => $lt_message,
];
// $lt_message = tripal_set_message(t('If the biomaterial provider is not present in the dropdown list, ') . l(t('add a new contact.'), 'bio_data/add') . t(' A biomaterial provider is not required.'), TRIPAL_INFO, ['return_html' => TRUE]);

// $form['experimental_design']['biosourceprovider_id'] = [
// '#title' => t('Biomaterial Provider'),
// '#type' => 'select',
// '#empty_value' => '',
// '#description' => t('The contact who provided the biomaterial. If the biomaterial is already') . (' present in the database, the biomaterial provider selected here will') . (' overwrite the biomaterial provider set for the biomaterial in the database.'),
// '#options' => $form['choose_contact']['#value'],
// '#suffix' => $lt_message,
// ];

$lt_message = tripal_set_message(t('If the array design does not appear in this list, ') . l(t('add a new arraydesign.'), 'bio_data/add') . t(' If an array design is not selected, then a generic array design will be created for the analysis.'), TRIPAL_INFO, ['return_html' => TRUE]);

Expand All @@ -176,79 +161,91 @@ class tripal_expression_data_loader extends TripalImporter{
'#options' => $arraydesigns,
'#suffix' => $lt_message,
];
//
$form['experimental_design']['acquisition_details'] = [
'#title' => t('Acquisition Details'),
'#type' => 'fieldset',
'#description' => t('This represents the quantification technique. In the case of a microarray, it is scanning, in the case of a sequencer, it is sequencing. The output of this process is a digitial image of an array for a microarray or a set of digital images or nucleotide base calls for a sequencer.'),
'#collapsible' => TRUE,
'#collapsed' => TRUE,
'#weight' => 1,
];

$form['experimental_design']['acquisition_details']['acquisitiondate'] = [
'#type' => 'date',
'#title' => t('Date Acquisition Run'),
'#description' => t('If no date is provided, then the current date will be used.'),
'#required' => TRUE,
'#default_value' => [
'year' => $year,
'month' => $month,
'day' => $day,
],
];
//TODO: WE DONT USE THIS (BUT WE SHOULD)

$form['experimental_design']['acquisition_details']['acquisition_uri'] = [
'#type' => 'textfield',
'#title' => t('Acquisition URI'),
'#description' => t('URI location that describes the acquisition.'),
];
//
// $form['experimental_design']['acquisition_details'] = [
// '#title' => t('Acquisition Details'),
// '#type' => 'fieldset',
// '#description' => t('This represents the quantification technique. In the case of a microarray, it is scanning, in the case of a sequencer, it is sequencing. The output of this process is a digitial image of an array for a microarray or a set of digital images or nucleotide base calls for a sequencer.'),
// '#collapsible' => TRUE,
// '#collapsed' => FALSE,
// '#weight' => 1,
// ];

// $form['experimental_design']['acquisition_details']['acquisitiondate'] = [
// '#type' => 'date',
// '#title' => t('Date Acquisition Run'),
// '#description' => t('If no date is provided, then the current date will be used.'),
// '#required' => TRUE,
// '#default_value' => [
// 'year' => $year,
// 'month' => $month,
// 'day' => $day,
// ],
// ];

//TODO: WE DONT USE THIS (BUT WE SHOULD)

// $form['experimental_design']['acquisition_details']['acquisition_uri'] = [
// '#type' => 'textfield',
// '#title' => t('Acquisition URI'),
// '#description' => t('URI location that describes the acquisition.'),
// ];

$lt_message = tripal_set_message(t('If the acquisition protocol is not present in the dropdown list, ') . l(t('add a new protocol.'), 'bio_data/add') . t(' An acquisition protocol is not required.'), TRIPAL_INFO, ['return_html' => TRUE]);

$acquisitions = tripal_get_protocol_select_options(FALSE, 'Acquisition Protocol');

$form['experimental_design']['acquisition_details']['acquisition_protocol_id'] = [
'#title' => t('Acquisition Protocol'),
'#type' => 'select',
'#description' => t('The protocol associated with this acquisition.'),
'#options' => $acquisitions,
'#suffix' => $lt_message,
];
//TODO: WE DONT USE THIS (BUT WE SHOULD)

//
// $form['experimental_design']['acquisition_details']['acquisition_protocol_id'] = [
// '#title' => t('Acquisition Protocol'),
// '#type' => 'select',
// '#description' => t('The protocol associated with this acquisition.'),
// '#options' => $acquisitions,
// '#suffix' => $lt_message,
// ];

$form['experimental_design']['quantification_details'] = [
'#title' => t('Quantification Details'),
'#type' => 'fieldset',
'#description' => t(' Quantification is the transformation of an image or set of sequences to numeric expression data. This typically involves statistical procedures.'),
'#collapsible' => TRUE,
'#collapsed' => TRUE,
'#collapsed' => FALSE,
'#weight' => 1,
];
$form['experimental_design']['quantification_details']['quantificationunits'] = [
'#type' => 'textfield',
'#title' => t('Units'),
'#description' => t('The units associated with the loaded values (ie, FPKM, RPKM, raw counts).'),
];

$form['experimental_design']['quantification_details']['quantificationdate'] = [
'#type' => 'date',
'#title' => t('Date Quantification Run'),
'#description' => t('If no date is provided, then the current date will be used.'),
'#required' => TRUE,
'#default_value' => [
'year' => $year,
'month' => $month,
'day' => $day,
],
];

$form['experimental_design']['quantification_details']['quantification_uri'] = [
'#type' => 'textfield',
'#title' => t('Quantification URI'),
'#description' => t('URI location that describes the quantification.'),
];

$lt_message = tripal_set_message(t('If the quantification operator is not present in the dropdown list, ') . l(t('add a new contact.'), 'bio_data/add') . t('A quantication operator is not required.'), TRIPAL_INFO, ['return_html' => TRUE]);
//TODO: WE DONT USE THIS (BUT WE SHOULD)

// $form['experimental_design']['quantification_details']['quantificationdate'] = [
// '#type' => 'date',
// '#title' => t('Date Quantification Run'),
// '#description' => t('If no date is provided, then the current date will be used.'),
// '#required' => TRUE,
// '#default_value' => [
// 'year' => $year,
// 'month' => $month,
// 'day' => $day,
// ],
// ];


//TODO: WE DONT USE THIS (BUT WE SHOULD)

// $form['experimental_design']['quantification_details']['quantification_uri'] = [
// '#type' => 'textfield',
// '#title' => t('Quantification URI'),
// '#description' => t('URI location that describes the quantification.'),
// ];
//
// $lt_message = tripal_set_message(t('If the quantification operator is not present in the dropdown list, ') . l(t('add a new contact.'), 'bio_data/add') . t('A quantication operator is not required.'), TRIPAL_INFO, ['return_html' => TRUE]);

// Obtain the list of contacts from the chado contact table.
$sql = 'SELECT
Expand All @@ -266,26 +263,30 @@ class tripal_expression_data_loader extends TripalImporter{
'#value' => $contacts,
];

$form['experimental_design']['quantification_details']['quantification_operator_id'] = [
'#title' => t('Quantification Operator'),
'#type' => 'select',
'#empty_value' => '',
'#description' => t('The quantification operator. If the operator does not appear in this list, ') . l(t('add a new contact.'), 'bio_data/add') . t(' An operator is not required.'),
'#options' => $form['choose_contact']['#value'],
'#suffix' => $lt_message,
];

$lt_message = tripal_set_message(t('If the quantification protocol is not present in the dropdown list, ') . l(t('add a new protocol.'), 'bio_data/add') . t(' A quantification protocol is not required.'), TRIPAL_INFO, ['return_html' => TRUE]);

$quantifications = tripal_get_protocol_select_options(FALSE, 'Quantification Protocol');

$form['experimental_design']['quantification_details']['quantification_protocol_id'] = [
'#title' => t('Quantification Protocol'),
'#type' => 'select',
'#description' => t('The protocol associated with this quantification.'),
'#options' => $quantifications,
'#suffix' => $lt_message,
];
//TODO: WE DONT USE THIS (BUT WE SHOULD)
//
// $form['experimental_design']['quantification_details']['quantification_operator_id'] = [
// '#title' => t('Quantification Operator'),
// '#type' => 'select',
// '#empty_value' => '',
// '#description' => t('The quantification operator. If the operator does not appear in this list, ') . l(t('add a new contact.'), 'bio_data/add') . t(' An operator is not required.'),
// '#options' => $form['choose_contact']['#value'],
// '#suffix' => $lt_message,
// ];


//TODO: WE DONT USE THIS (BUT WE SHOULD)
// $lt_message = tripal_set_message(t('If the quantification protocol is not present in the dropdown list, ') . l(t('add a new protocol.'), 'bio_data/add') . t(' A quantification protocol is not required.'), TRIPAL_INFO, ['return_html' => TRUE]);
//
// $quantifications = tripal_get_protocol_select_options(FALSE, 'Quantification Protocol');

// $form['experimental_design']['quantification_details']['quantification_protocol_id'] = [
// '#title' => t('Quantification Protocol'),
// '#type' => 'select',
// '#description' => t('The protocol associated with this quantification.'),
// '#options' => $quantifications,
// '#suffix' => $lt_message,
// ];

$form['filetype'] = [
'#type' => 'radios',
Expand Down Expand Up @@ -369,14 +370,15 @@ class tripal_expression_data_loader extends TripalImporter{
$analysis_id = $arguments['analysis_id'];
$feature_uniquenames = $arguments['feature_uniquenames'];
$arraydesign_id = $arguments['arraydesign_id'];
$acquisitiondate = $arguments['acquisitiondate'];
$create_biosamples = $arguments['create_biosamples'];
$quantificationdate = $arguments['quantificationdate'];

$quantificationunits = $arguments['quantificationunits'];

//missing
$assaydate = '';//$arguments['assaydate'];
$contact_id = '';//$arguments['contact_id'];
// $acquisitiondate = $arguments['acquisitiondate'];
// $create_biosamples = $arguments['create_biosamples'];
// $quantificationdate = $arguments['quantificationdate'];
//
//$record = ['table' => 'analysis', 'id' => $node->analysis_id];
//
Expand Down

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