[Gmod-tripal-devel] Problems with Views after Tripal update

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[Gmod-tripal-devel] Problems with Views after Tripal update

Michael Dondrup-3
Hi again,

I have observed some more rare glitches after updating from devel to 1.1. I must say that these are quite
seldom use-cases and I am unsure if anyone else has ever used the modules this way, but still it might be useful to
document.
The cases involve:
- creating custom data types and views referencing Feature Node objects
- having these content types and objects from before the update and trying to use them after.

1) I have made custom content types (with CCK) containing
fields referencing Feature Nodes. The filed-widget is set to
autocomplete widget to select feature nodes as you type.
Using the Autocomplete widget after the update
with a feature and saving the content gave an error: "Target ID: Title mismatch. Please check your input."
Being unable to save the content.
Solution: changing the *widget_type* to something else temporarily, saving, and changing *widget_type* back to
autocomplete helped.

1) I have made a view for said content-type containing an exposed filter for the Feature name to be able to filter
entries referencing a given Feature. Entering something
into the filter field, yielded a syntax error: "Syntax error at '.':" (see [1])
… AND ((.name) LIKE ('%my%') …
somehow the filter was looking for the field name in an undefined table.
Assuming, that this might be somehow related to
the Tripal Views Integration ( admin/tripal/views/integration/list ) and edited the "Chado Feature" Drupal View for table 'feature'. (have never edited something here before)
I didn't change any setting but simply saved it with priority '0' (I now have three instances of "Chado Feature" with priorities 10,9,and 0). Indeed this solved the missing table name,
yielding a new error (see [2]):
ERROR: column chado_feature.organism_id does not exist
The table chado_feature has these columns:  vid nid feature_id sync_date

I have tried to remove and add the Field and the filter but to no avail. I cannot remove the field from the datatype, because it contains data already.
 It seems like there is something wrong with my views integration now.

What am I missing here?

Michael









[1] SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.

[2]
• warning: pg_query(): Query failed: ERROR: column chado_feature.organism_id does not exist at character 383 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
       
• user warning: ERROR: column chado_feature.organism_id does not exist at character 383 query: SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((feature.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.








Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway


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Re: [Gmod-tripal-devel] Problems with Views after Tripal update

Michael Dondrup-3
Btw,
here are the exported datatype and view, if somebody is interested.


--- START Content Type ----
$content['type']  = array (
  'name' => 'RNAi',
  'type' => 'rnai_experiment',
  'description' => 'This content allows one to upload and and annotate microscope images.',
  'title_label' => 'Title',
  'body_label' => 'Image Description (free text)',
  'min_word_count' => '10',
  'help' => '<p>Please upload your image and add a description.</p>
',
  'node_options' =>
  array (
    'status' => true,
    'promote' => false,
    'sticky' => false,
    'revision' => false,
  ),
  'language_content_type' => '0',
  'upload' => '0',
  'old_type' => 'rnai_experiment',
  'orig_type' => '',
  'module' => 'node',
  'custom' => '1',
  'modified' => '1',
  'locked' => '0',
  'comment' => '2',
  'comment_default_mode' => '4',
  'comment_default_order' => '1',
  'comment_default_per_page' => '50',
  'comment_controls' => '3',
  'comment_anonymous' => 0,
  'comment_subject_field' => '1',
  'comment_preview' => '1',
  'comment_form_location' => '0',
  'fivestar' => 1,
  'fivestar_stars' => '5',
  'fivestar_labels_enable' => 1,
  'fivestar_label_0' => 'Cancel rating',
  'fivestar_label_1' => 'Poor',
  'fivestar_label_2' => 'Okay',
  'fivestar_label_3' => 'Good',
  'fivestar_label_4' => 'Great',
  'fivestar_label_5' => 'Awesome',
  'fivestar_label_6' => 'Give it @star/@count',
  'fivestar_label_7' => 'Give it @star/@count',
  'fivestar_label_8' => 'Give it @star/@count',
  'fivestar_label_9' => 'Give it @star/@count',
  'fivestar_label_10' => 'Give it @star/@count',
  'fivestar_style' => 'average',
  'fivestar_text' => 'dual',
  'fivestar_title' => 1,
  'fivestar_feedback' => 1,
  'fivestar_unvote' => 0,
  'fivestar_position_teaser' => 'below',
  'fivestar_position' => 'above',
);
$content['groups']  = array (
  0 =>
  array (
    'label' => 'General',
    'group_type' => 'standard',
    'settings' =>
    array (
      'form' =>
      array (
        'style' => 'tabs',
        'description' => '',
      ),
      'display' =>
      array (
        'description' => '',
        5 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'teaser' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'full' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        4 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        2 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        3 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'token' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'label' => 'above',
      ),
    ),
    'weight' => '13',
    'group_name' => 'group_general',
  ),
  1 =>
  array (
    'label' => 'Sample',
    'group_type' => 'standard',
    'settings' =>
    array (
      'form' =>
      array (
        'style' => 'tabs',
        'description' => '<p>Please describe the sample and sample processing here.</p>
',
      ),
      'display' =>
      array (
        'description' => '',
        5 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'teaser' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'full' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        4 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        2 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        3 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'token' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'label' => 'above',
      ),
    ),
    'weight' => '14',
    'group_name' => 'group_sample',
  ),
  2 =>
  array (
    'label' => 'Target description',
    'group_type' => 'standard',
    'settings' =>
    array (
      'form' =>
      array (
        'style' => 'tabs',
        'description' => '<p><strong>Note that the target definition&nbsp;can serve as an estimate only, and can become obsolete,&nbsp;as there might be multiple targets (off-target effects)&nbsp;and imperfect matches.&nbsp;</strong></p>

<p>If possible, choose a target in the <em>Target ID</em> field, as this will be directly linked to the genome database. To achieve a stable and reliable link to the designed target, available&nbsp;sequence types should be prioritized as targets for annotation in the following order:</p>

<ol>
        <li>full length cDNA or mRNA (validated)</li>
        <li>predicted exons with additional evidence (e.g. RNA-seq)</li>
        <li>predicted transcripts with additional evidence</li>
</ol>

<p>Full genes should only be used if the real target sequence is unknown.</p>

<p>It is ok, to leave these&nbsp;fields blank, in case the target should not be disclosed, however that will make tracking targets depend on external sources.</p>

<p>&nbsp;</p>
',
      ),
      'display' =>
      array (
        'description' => '',
        5 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'teaser' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'full' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        4 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        2 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        3 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'token' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'label' => 'above',
      ),
    ),
    'weight' => '15',
    'group_name' => 'group_target',
  ),
  3 =>
  array (
    'label' => 'Fragment description',
    'group_type' => 'standard',
    'settings' =>
    array (
      'form' =>
      array (
        'style' => 'tabs',
        'description' => '<p>Describe the fragment as precise as possible, entering as many fields as possible. The actual target can be derived or reconstructed accurately only based on this information. This information is extremly important in the following scenarios:</p>

<ul>
        <li>The genome annotation changes, resulting in changes of the target</li>
        <li>The genome assembly changes, resulting in changes of the target or the fragment itself (for PCR fragments)</li>
</ul>

<p>&nbsp;</p>
',
      ),
      'display' =>
      array (
        'description' => '',
        5 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'teaser' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'full' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        4 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        2 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        3 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'token' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'label' => 'above',
      ),
    ),
    'weight' => '16',
    'group_name' => 'group_fragment',
  ),
  4 =>
  array (
    'label' => 'Validation',
    'group_type' => 'standard',
    'settings' =>
    array (
      'form' =>
      array (
        'style' => 'tabs',
        'description' => '<p>Please provide an&nbsp;efficacy measurement as well as a link to the validation protocol inside lice-base here.</p>
',
      ),
      'display' =>
      array (
        'description' => '',
        5 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'teaser' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'full' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        4 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        2 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        3 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'token' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'label' => 'above',
      ),
    ),
    'weight' => '17',
    'group_name' => 'group_validation',
  ),
  5 =>
  array (
    'label' => 'Phenotype',
    'group_type' => 'standard',
    'settings' =>
    array (
      'form' =>
      array (
        'style' => 'tabs',
        'description' => '<p>Please describe the observed phenotype here. Please use preferentially the&nbsp;<em>Phenotype CV</em> taxonomy field to annotate phenotypes.&nbsp;</p>

<p><img alt="enlightened" height="20" src="http://lb-test.bccs.uib.no/sites/all/modules/ckeditor/ckeditor/plugins/smiley/images/lightbulb.gif" title="enlightened" width="20" /><strong>Please also annotate missing phenotypes.</strong> This section should be left empty only if the phenotype should not be disclosed.</p>
',
      ),
      'display' =>
      array (
        'description' => '',
        5 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'teaser' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'full' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        4 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        2 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        3 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'token' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'label' => 'above',
      ),
    ),
    'weight' => '18',
    'group_name' => 'group_phenotype',
  ),
  6 =>
  array (
    'label' => 'Upload',
    'group_type' => 'standard',
    'settings' =>
    array (
      'form' =>
      array (
        'style' => 'tabs',
        'description' => '',
      ),
      'display' =>
      array (
        'description' => '',
        5 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'teaser' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'full' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        4 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        2 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        3 =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'token' =>
        array (
          'format' => 'fieldset',
          'exclude' => 0,
        ),
        'label' => 'above',
      ),
    ),
    'weight' => '20',
    'group_name' => 'group_upload',
  ),
);
$content['fields']  = array (
  0 =>
  array (
    'label' => 'Experiment Batch ID',
    'field_name' => 'field_batch_id',
    'type' => 'text',
    'widget_type' => 'autocomplete_widgets_flddata',
    'change' => 'Change basic information',
    'weight' => '14',
    'size' => '60',
    'autocomplete_match' => 'contains',
    'autocomplete_case' => '1',
    'autocomplete_xss' => '0',
    'i18n_flddata' => 0,
    'description' => 'The Batch ID of the Experiment (formerly called Experiment ID). An ID for experiments conducted together.',
    'default_value' =>
    array (
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_general',
    'required' => 1,
    'multiple' => '0',
    'text_processing' => 0,
    'max_length' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'autocomplete_widgets',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '14',
      'parent' => 'group_general',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  1 =>
  array (
    'label' => 'Experiment Contact',
    'field_name' => 'field_experiment_contact',
    'type' => 'userreference',
    'widget_type' => 'userreference_autocomplete',
    'change' => 'Change basic information',
    'weight' => '15',
    'autocomplete_match' => 'contains',
    'size' => '60',
    'reverse_link' => 1,
    'description' => 'The primary experiment contact(s), e.g. a person interested in the results. <b>Please choose only a valid user account (not any name).</b>The account must be registered in Drupal. The users will get a link back to the experiment in their user profile.',
    'default_value' =>
    array (
      0 =>
      array (
        'uid' => NULL,
        '_error_element' => 'default_value_widget][field_experiment_contact][0][uid][uid',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_general',
    'required' => 1,
    'multiple' => '1',
    'referenceable_roles' =>
    array (
      2 => 2,
      3 => 3,
      4 => 4,
    ),
    'referenceable_status' => '',
    'op' => 'Save field settings',
    'module' => 'userreference',
    'widget_module' => 'userreference',
    'columns' =>
    array (
      'uid' =>
      array (
        'type' => 'int',
        'unsigned' => true,
        'not null' => false,
        'index' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '15',
      'parent' => 'group_general',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  2 =>
  array (
    'label' => 'Start Date',
    'field_name' => 'field_start_date',
    'type' => 'datestamp',
    'widget_type' => 'date_popup',
    'change' => 'Change basic information',
    'weight' => '16',
    'default_value' => 'now',
    'default_value2' => 'same',
    'default_value_code' => '',
    'default_value_code2' => '',
    'input_format' => 'j M Y - H:i',
    'input_format_custom' => '',
    'year_range' => '-3:+3',
    'increment' => '1',
    'advanced' =>
    array (
      'label_position' => 'above',
      'text_parts' =>
      array (
        'year' => 0,
        'month' => 0,
        'day' => 0,
        'hour' => 0,
        'minute' => 0,
        'second' => 0,
      ),
    ),
    'label_position' => 'above',
    'text_parts' =>
    array (
    ),
    'description' => 'Enter the date the experiment has been started.',
    'group' => 'group_general',
    'required' => 1,
    'multiple' => '0',
    'repeat' => 0,
    'todate' => '',
    'granularity' =>
    array (
      'year' => 'year',
      'month' => 'month',
      'day' => 'day',
      'hour' => 'hour',
      'minute' => 'minute',
      'second' => 'second',
    ),
    'default_format' => 'medium',
    'tz_handling' => 'none',
    'timezone_db' => '',
    'op' => 'Save field settings',
    'module' => 'date',
    'widget_module' => 'date',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'int',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '16',
      'parent' => 'group_general',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  3 =>
  array (
    'label' => 'End Date',
    'field_name' => 'field_end_date',
    'type' => 'datestamp',
    'widget_type' => 'date_popup',
    'change' => 'Change basic information',
    'weight' => '17',
    'default_value' => 'blank',
    'default_value2' => 'same',
    'default_value_code' => '',
    'default_value_code2' => '',
    'input_format' => 'j M Y - H:i',
    'input_format_custom' => '',
    'year_range' => '-3:+3',
    'increment' => '1',
    'advanced' =>
    array (
      'label_position' => 'above',
      'text_parts' =>
      array (
        'year' => 0,
        'month' => 0,
        'day' => 0,
        'hour' => 0,
        'minute' => 0,
        'second' => 0,
      ),
    ),
    'label_position' => 'above',
    'text_parts' =>
    array (
    ),
    'description' => '',
    'group' => 'group_general',
    'required' => 0,
    'multiple' => '0',
    'repeat' => 0,
    'todate' => '',
    'granularity' =>
    array (
      'year' => 'year',
      'month' => 'month',
      'day' => 'day',
      'hour' => 'hour',
      'minute' => 'minute',
    ),
    'default_format' => 'medium',
    'tz_handling' => 'site',
    'timezone_db' => 'UTC',
    'op' => 'Save field settings',
    'module' => 'date',
    'widget_module' => 'date',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'int',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '17',
      'parent' => 'group_general',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  4 =>
  array (
    'label' => 'Experiment Description',
    'field_name' => 'field_experiment_description',
    'type' => 'text',
    'widget_type' => 'text_textarea',
    'change' => 'Change basic information',
    'weight' => '19',
    'rows' => '3',
    'size' => 60,
    'description' => 'Free text description of the experiment.',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_experiment_description][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_general',
    'required' => 0,
    'multiple' => '0',
    'text_processing' => '0',
    'max_length' => '',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'text',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '19',
      'parent' => 'group_general',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  5 =>
  array (
    'label' => 'Organism',
    'field_name' => 'field_organism',
    'type' => 'nodereference',
    'widget_type' => 'nodereference_autocomplete',
    'change' => 'Change basic information',
    'weight' => '43',
    'autocomplete_match' => 'contains',
    'size' => '60',
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'nid' => NULL,
        '_error_element' => 'default_value_widget][field_organism][0][nid][nid',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_sample',
    'required' => 1,
    'multiple' => '0',
    'referenceable_types' =>
    array (
      'chado_organism' => 'chado_organism',
      'chado_analysis' => 0,
      'blog' => 0,
      'book' => 0,
      'chado_feature' => 0,
      'forum' => 0,
      'chado_library' => 0,
      'page' => 0,
      'panel' => 0,
      'chado_stock' => 0,
      'story' => 0,
      'developmental_stage_cv' => false,
      'cvautocomplete' => false,
      'test_type' => false,
      'new_type' => false,
      'rnai_experiment' => 0,
      'chado_analysis_blast' => false,
      'chado_analysis_interpro' => false,
      'chado_analysis_kegg' => false,
      'chado_analysis_unigene' => false,
      'gallery' => false,
      'gallery_image' => false,
      'in_situ' => false,
      'poll' => false,
    ),
    'advanced_view' => '--',
    'advanced_view_args' => '',
    'op' => 'Save field settings',
    'module' => 'nodereference',
    'widget_module' => 'nodereference',
    'columns' =>
    array (
      'nid' =>
      array (
        'type' => 'int',
        'unsigned' => true,
        'not null' => false,
        'index' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '43',
      'parent' => 'group_sample',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  6 =>
  array (
    'label' => 'Sex',
    'field_name' => 'field_sex',
    'type' => 'text',
    'widget_type' => 'optionwidgets_buttons',
    'change' => 'Change basic information',
    'weight' => '44',
    'description' => 'Enter the sex of the sample organism, if applicable.',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_sample',
    'required' => 1,
    'multiple' => '0',
    'text_processing' => '0',
    'max_length' => '',
    'allowed_values' => 'female
male
both
unknown
',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'optionwidgets',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '44',
      'parent' => 'group_sample',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  7 =>
  array (
    'label' => 'Number of Individuals (Start)',
    'field_name' => 'field_n_individuals_start',
    'type' => 'number_integer',
    'widget_type' => 'number',
    'change' => 'Change basic information',
    'weight' => '45',
    'description' => 'The number of individuals at the start of the experiment.',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_n_individuals_start][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_sample',
    'required' => 0,
    'multiple' => '0',
    'min' => '1',
    'max' => '',
    'prefix' => '',
    'suffix' => '',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'number',
    'widget_module' => 'number',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'int',
        'not null' => false,
        'sortable' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '45',
      'parent' => 'group_sample',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  8 =>
  array (
    'label' => 'Developmental Stage CV',
    'field_name' => 'field_devstage',
    'type' => 'text',
    'widget_type' => 'autocomplete_widgets_cvdata',
    'change' => 'Change basic information',
    'weight' => '46',
    'size' => '60',
    'cv_select' => '23',
    'obsolete' => 0,
    'autocomplete_match' => 'contains',
    'autocomplete_case' => '0',
    'autocomplete_xss' => '0',
    'i18n_flddata' => 0,
    'description' => 'Choose max two developmental stages; first is for start second for harvest. The stages must be specified in order.',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_devstage][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_sample',
    'required' => 1,
    'multiple' => '2',
    'text_processing' => '0',
    'max_length' => '',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'autocomplete_widgets',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '46',
      'parent' => 'group_sample',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  9 =>
  array (
    'label' => 'Sample protocol',
    'field_name' => 'field_sample_protocol',
    'type' => 'nodereference',
    'widget_type' => 'nodereference_autocomplete',
    'change' => 'Change basic information',
    'weight' => '47',
    'autocomplete_match' => 'contains',
    'size' => '60',
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'nid' => NULL,
        '_error_element' => 'default_value_widget][field_sample_protocol][0][nid][nid',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_sample',
    'required' => 0,
    'multiple' => '0',
    'referenceable_types' =>
    array (
      'page' => 'page',
      'chado_analysis' => 0,
      'chado_analysis_blast' => 0,
      'chado_analysis_interpro' => 0,
      'chado_analysis_kegg' => 0,
      'blog' => 0,
      'book' => 0,
      'tripal_bulk_loader' => 0,
      'chado_feature' => 0,
      'forum' => 0,
      'chado_organism' => 0,
      'poll' => 0,
      'chado_project' => 0,
      'rnai_experiment' => 0,
      'story' => 0,
      'chado_analysis_unigene' => false,
      'gallery' => false,
      'gallery_image' => false,
      'in_situ' => false,
      'test_type' => false,
    ),
    'advanced_view' => '--',
    'advanced_view_args' => '',
    'op' => 'Save field settings',
    'module' => 'nodereference',
    'widget_module' => 'nodereference',
    'columns' =>
    array (
      'nid' =>
      array (
        'type' => 'int',
        'unsigned' => true,
        'not null' => false,
        'index' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '47',
      'parent' => 'group_sample',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  10 =>
  array (
    'label' => 'Primary target ID',
    'field_name' => 'field_gene_id',
    'type' => 'nodereference',
    'widget_type' => 'nodereference_autocomplete',
    'change' => 'Change basic information',
    'weight' => '16',
    'autocomplete_match' => 'contains',
    'size' => '60',
    'description' => '<big><b>Please leave this field empty until the genome annotation is complete!</b></big> The primary target sequence <b>from the annotation database</b>. You have to select a valid target sequence (e.g. gene or EST) from the genome annotation. Please use one of the auto-suggest options. If your target doesn\'t show in the auto-select box, leave the field blank.',
    'default_value' =>
    array (
      0 =>
      array (
        'nid' => NULL,
        '_error_element' => 'default_value_widget][field_gene_id][0][nid][nid',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_target',
    'required' => 0,
    'multiple' => '0',
    'referenceable_types' =>
    array (
      'chado_feature' => 'chado_feature',
      'chado_analysis' => 0,
      'chado_analysis_blast' => 0,
      'chado_analysis_interpro' => 0,
      'chado_analysis_kegg' => 0,
      'chado_analysis_unigene' => 0,
      'blog' => 0,
      'book' => 0,
      'forum' => 0,
      'gallery' => 0,
      'gallery_image' => 0,
      'in_situ' => 0,
      'chado_organism' => 0,
      'page' => 0,
      'poll' => 0,
      'rnai_experiment' => 0,
      'story' => 0,
      'test_type' => 0,
    ),
    'advanced_view' => '--',
    'advanced_view_args' => '',
    'op' => 'Save field settings',
    'module' => 'nodereference',
    'widget_module' => 'nodereference',
    'columns' =>
    array (
      'nid' =>
      array (
        'type' => 'int',
        'unsigned' => true,
        'not null' => false,
        'index' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '16',
      'parent' => 'group_target',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  11 =>
  array (
    'label' => 'Gene or target symbol',
    'field_name' => 'field_gene_symbol',
    'type' => 'text',
    'widget_type' => 'text_textfield',
    'change' => 'Change basic information',
    'weight' => '17',
    'rows' => 5,
    'size' => '60',
    'description' => 'Enter the gene symbol here',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_gene_symbol][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_target',
    'required' => 0,
    'multiple' => '1',
    'text_processing' => '0',
    'max_length' => '20',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'text',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'varchar',
        'length' => '20',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '17',
      'parent' => 'group_target',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  12 =>
  array (
    'label' => 'Target type',
    'field_name' => 'field_target_type',
    'type' => 'text',
    'widget_type' => 'autocomplete_widgets_cvdata',
    'change' => 'Change basic information',
    'weight' => '18',
    'size' => '60',
    'cv_select' => '16',
    'obsolete' => 0,
    'autocomplete_match' => 'contains',
    'autocomplete_case' => '0',
    'autocomplete_xss' => '0',
    'i18n_flddata' => 0,
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_target_type][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_target',
    'required' => 0,
    'multiple' => '1',
    'text_processing' => '0',
    'max_length' => '',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'autocomplete_widgets',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '18',
      'parent' => 'group_target',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  13 =>
  array (
    'label' => 'External DBref',
    'field_name' => 'field_ref',
    'type' => 'link',
    'widget_type' => 'link',
    'change' => 'Change basic information',
    'weight' => '19',
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'title' => '',
        'url' => '',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_target',
    'required' => 0,
    'multiple' => '1',
    'validate_url' => 1,
    'url' => 0,
    'title' => 'optional',
    'title_value' => '',
    'enable_tokens' => 0,
    'display' =>
    array (
      'url_cutoff' => '80',
    ),
    'attributes' =>
    array (
      'target' => '_blank',
      'rel' => '',
      'class' => '',
      'title' => '',
    ),
    'op' => 'Save field settings',
    'module' => 'link',
    'widget_module' => 'link',
    'columns' =>
    array (
      'url' =>
      array (
        'type' => 'varchar',
        'length' => 2048,
        'not null' => false,
        'sortable' => true,
      ),
      'title' =>
      array (
        'type' => 'varchar',
        'length' => 255,
        'not null' => false,
        'sortable' => true,
      ),
      'attributes' =>
      array (
        'type' => 'text',
        'size' => 'medium',
        'not null' => false,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '19',
      'parent' => 'group_target',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  14 =>
  array (
    'label' => 'Fragment length',
    'field_name' => 'field_fragment_length',
    'type' => 'number_integer',
    'widget_type' => 'number',
    'change' => 'Change basic information',
    'weight' => '37',
    'description' => 'Enter the fragment length in bases',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_fragment_length][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'min' => '1',
    'max' => '',
    'prefix' => '',
    'suffix' => 'bp',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'number',
    'widget_module' => 'number',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'int',
        'not null' => false,
        'sortable' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '37',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  15 =>
  array (
    'label' => 'Fragment concentration',
    'field_name' => 'field_fragment_concentration',
    'type' => 'number_decimal',
    'widget_type' => 'number',
    'change' => 'Change basic information',
    'weight' => '38',
    'description' => 'Enter the fragment concentration in ng/ul.',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_fragment_concentration][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'min' => '0',
    'max' => '',
    'precision' => '10',
    'scale' => '2',
    'decimal' => '.',
    'prefix' => '',
    'suffix' => 'ng/ul',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'number',
    'widget_module' => 'number',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'numeric',
        'precision' => '10',
        'scale' => '2',
        'not null' => false,
        'sortable' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '38',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  16 =>
  array (
    'label' => 'Sense sequence',
    'field_name' => 'field_ss',
    'type' => 'text',
    'widget_type' => 'text_textarea',
    'change' => 'Change basic information',
    'weight' => '39',
    'rows' => '5',
    'size' => '60',
    'description' => 'The sense sequence with respect to the target.',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_ss][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'text_processing' => '0',
    'max_length' => '',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'text',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '39',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 1,
      ),
      'full' =>
      array (
        'format' => 'plain',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  17 =>
  array (
    'label' => 'Antisense sequence',
    'field_name' => 'field_as',
    'type' => 'text',
    'widget_type' => 'text_textarea',
    'change' => 'Change basic information',
    'weight' => '40',
    'rows' => 5,
    'size' => '60',
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_as][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'text_processing' => '0',
    'max_length' => '',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'text',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '40',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 1,
      ),
      'full' =>
      array (
        'format' => 'plain',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  18 =>
  array (
    'label' => 'Fragment ID',
    'field_name' => 'field_fragment_id',
    'type' => 'nodereference',
    'widget_type' => 'nodereference_autocomplete',
    'change' => 'Change basic information',
    'weight' => '41',
    'autocomplete_match' => 'contains',
    'size' => '60',
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'nid' => NULL,
        '_error_element' => 'default_value_widget][field_fragment_id][0][nid][nid',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'referenceable_types' =>
    array (
      'chado_feature' => 'chado_feature',
      'chado_analysis' => 0,
      'chado_analysis_blast' => 0,
      'chado_analysis_interpro' => 0,
      'chado_analysis_kegg' => 0,
      'blog' => 0,
      'book' => 0,
      'tripal_bulk_loader' => 0,
      'forum' => 0,
      'chado_organism' => 0,
      'page' => 0,
      'poll' => 0,
      'chado_project' => 0,
      'rnai_experiment' => 0,
      'story' => 0,
      'chado_analysis_unigene' => false,
      'gallery' => false,
      'gallery_image' => false,
      'in_situ' => false,
      'test_type' => false,
    ),
    'advanced_view' => '--',
    'advanced_view_args' => '',
    'op' => 'Save field settings',
    'module' => 'nodereference',
    'widget_module' => 'nodereference',
    'columns' =>
    array (
      'nid' =>
      array (
        'type' => 'int',
        'unsigned' => true,
        'not null' => false,
        'index' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '41',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  19 =>
  array (
    'label' => 'Fragment Batch ID',
    'field_name' => 'field_fragment_batch_id',
    'type' => 'text',
    'widget_type' => 'autocomplete_widgets_flddata',
    'change' => 'Change basic information',
    'weight' => '42',
    'size' => '60',
    'autocomplete_match' => 'contains',
    'autocomplete_case' => '0',
    'autocomplete_xss' => '0',
    'i18n_flddata' => 0,
    'description' => 'Enter a Batch ID for the fragment assigned by the producer.',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_fragment_batch_id][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'text_processing' => 0,
    'max_length' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'autocomplete_widgets',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '42',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  20 =>
  array (
    'label' => 'Fragment Label ID',
    'field_name' => 'field_fragment_label_id',
    'type' => 'text',
    'widget_type' => 'autocomplete_widgets_allowvals',
    'change' => 'Change basic information',
    'weight' => '43',
    'size' => '60',
    'autocomplete_match' => 'contains',
    'autocomplete_case' => '1',
    'autocomplete_xss' => '0',
    'i18n_flddata' => 0,
    'description' => 'The Label ID which is written on the vessel, containing the fragment.',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_fragment_label_id][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 1,
    'multiple' => '0',
    'text_processing' => 0,
    'max_length' => '',
    'allowed_values' => '',
    'allowed_values_php' => '$a = array();
foreach(range(0,9999) as $e) $a[$e] = "F".$e;
return ($a);',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'autocomplete_widgets',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '43',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  21 =>
  array (
    'label' => 'Fragment Mixture Formula',
    'field_name' => 'field_fragment_mixture',
    'type' => 'text',
    'widget_type' => 'text_textfield',
    'change' => 'Change basic information',
    'weight' => '44',
    'rows' => 5,
    'size' => '60',
    'description' => 'If this solution is a mixture of other fragments, please enter the mixture formula here, e.g.:
F1+F22+F2344',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_fragment_mixture][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'text_processing' => '0',
    'max_length' => '',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'text',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '44',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  22 =>
  array (
    'label' => 'Primer Group',
    'field_name' => 'field_primer_group',
    'type' => 'matrix',
    'widget_type' => 'matrix',
    'change' => 'Change basic information',
    'weight' => '46',
    'description' => '',
    'default_value' =>
    array (
      0 => NULL,
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'size' => '20',
    'rows' => '1
2
3
4',
    'cols' => 'Primer Name
Primer Sequence',
    'op' => 'Save field settings',
    'module' => 'matrix',
    'widget_module' => 'matrix',
    'columns' =>
    array (
    ),
    'display_settings' =>
    array (
      'label' =>
      array (
        'format' => 'above',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'token' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  23 =>
  array (
    'label' => 'Fragment Producer',
    'field_name' => 'field_fragment_producer',
    'type' => 'text',
    'widget_type' => 'autocomplete_widgets_flddata',
    'change' => 'Change basic information',
    'weight' => '47',
    'size' => '60',
    'autocomplete_match' => 'contains',
    'autocomplete_case' => '1',
    'autocomplete_xss' => '0',
    'i18n_flddata' => 0,
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_fragment_producer][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'text_processing' => 0,
    'max_length' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'autocomplete_widgets',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '46',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  24 =>
  array (
    'label' => 'Fragment Producer Contact',
    'field_name' => 'field_fragment_producer_contact',
    'type' => 'userreference',
    'widget_type' => 'userreference_autocomplete',
    'change' => 'Change basic information',
    'weight' => '48',
    'autocomplete_match' => 'contains',
    'size' => '60',
    'reverse_link' => 1,
    'description' => 'Database User who produced these fragments',
    'default_value' =>
    array (
      0 =>
      array (
        'uid' => NULL,
        '_error_element' => 'default_value_widget][field_fragment_producer_contact][0][uid][uid',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_fragment',
    'required' => 0,
    'multiple' => '0',
    'referenceable_roles' =>
    array (
      2 => 2,
      3 => 0,
      4 => 0,
    ),
    'referenceable_status' => '',
    'op' => 'Save field settings',
    'module' => 'userreference',
    'widget_module' => 'userreference',
    'columns' =>
    array (
      'uid' =>
      array (
        'type' => 'int',
        'unsigned' => true,
        'not null' => false,
        'index' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '47',
      'parent' => 'group_fragment',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  25 =>
  array (
    'label' => 'Efficacy of Knock Down',
    'field_name' => 'field_efficacy',
    'type' => 'number_decimal',
    'widget_type' => 'number',
    'change' => 'Change basic information',
    'weight' => '35',
    'description' => 'The minimal knockdown efficacy level in percent. (e.g. F>50, over 50% Knock down when compared to control)',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_efficacy][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_validation',
    'required' => 0,
    'multiple' => '0',
    'min' => '0',
    'max' => '100',
    'precision' => '10',
    'scale' => '2',
    'decimal' => '.',
    'prefix' => 'F>',
    'suffix' => '%',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'number',
    'widget_module' => 'number',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'numeric',
        'precision' => '10',
        'scale' => '2',
        'not null' => false,
        'sortable' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '35',
      'parent' => 'group_validation',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  26 =>
  array (
    'label' => 'Validation protocol',
    'field_name' => 'field_validation_protocol',
    'type' => 'nodereference',
    'widget_type' => 'nodereference_autocomplete',
    'change' => 'Change basic information',
    'weight' => '36',
    'autocomplete_match' => 'contains',
    'size' => '60',
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'nid' => NULL,
        '_error_element' => 'default_value_widget][field_validation_protocol][0][nid][nid',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_validation',
    'required' => 0,
    'multiple' => '0',
    'referenceable_types' =>
    array (
      'page' => 'page',
      'chado_analysis' => 0,
      'chado_analysis_blast' => 0,
      'chado_analysis_interpro' => 0,
      'chado_analysis_kegg' => 0,
      'blog' => 0,
      'book' => 0,
      'tripal_bulk_loader' => 0,
      'chado_feature' => 0,
      'forum' => 0,
      'chado_organism' => 0,
      'poll' => 0,
      'chado_project' => 0,
      'rnai_experiment' => 0,
      'story' => 0,
      'chado_analysis_unigene' => false,
      'gallery' => false,
      'gallery_image' => false,
      'in_situ' => false,
      'test_type' => false,
    ),
    'advanced_view' => '--',
    'advanced_view_args' => '',
    'op' => 'Save field settings',
    'module' => 'nodereference',
    'widget_module' => 'nodereference',
    'columns' =>
    array (
      'nid' =>
      array (
        'type' => 'int',
        'unsigned' => true,
        'not null' => false,
        'index' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '36',
      'parent' => 'group_validation',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  27 =>
  array (
    'label' => 'Number of Individuals (End)',
    'field_name' => 'field_n_individuals_end',
    'type' => 'number_integer',
    'widget_type' => 'number',
    'change' => 'Change basic information',
    'weight' => '48',
    'description' => 'Number of surviving individuals harvested at the end of the experiment.',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_n_individuals_end][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_phenotype',
    'required' => 0,
    'multiple' => '0',
    'min' => '0',
    'max' => '',
    'prefix' => '',
    'suffix' => '',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'number',
    'widget_module' => 'number',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'int',
        'not null' => false,
        'sortable' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '48',
      'parent' => 'group_phenotype',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  28 =>
  array (
    'label' => 'Phenotype',
    'field_name' => 'field_phenotype',
    'type' => 'text',
    'widget_type' => 'text_textfield',
    'change' => 'Change basic information',
    'weight' => '49',
    'rows' => 5,
    'size' => '60',
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'value' => '',
        '_error_element' => 'default_value_widget][field_phenotype][0][value',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_phenotype',
    'required' => 0,
    'multiple' => '0',
    'text_processing' => '0',
    'max_length' => '',
    'allowed_values' => '',
    'allowed_values_php' => '',
    'op' => 'Save field settings',
    'module' => 'text',
    'widget_module' => 'text',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
        'size' => 'big',
        'not null' => false,
        'sortable' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '49',
      'parent' => 'group_phenotype',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  29 =>
  array (
    'label' => 'Quantitative Phenotype',
    'field_name' => 'field_quantitative_phenotype',
    'type' => 'tablefield',
    'widget_type' => 'tablefield',
    'change' => 'Change basic information',
    'weight' => '50',
    'description' => '',
    'default_value' =>
    array (
      0 =>
      array (
        'tablefield' =>
        array (
          'count_cols' => '5',
          'count_rows' => '2',
          'cell_0_0' => '',
          'cell_0_1' => '',
          'cell_0_2' => '',
          'cell_0_3' => '',
          'cell_0_4' => '',
          'cell_1_0' => '',
          'cell_1_1' => '',
          'cell_1_2' => '',
          'cell_1_3' => '',
          'cell_1_4' => '',
          'rebuild' => 'Rebuild Table',
        ),
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'tablefield_csv_field_quantitative_phenotype_0' => '',
    'rebuild_field_quantitative_phenotype_0' => 'Import File to: field_quantitative_phenotype-0',
    'group' => 'group_phenotype',
    'required' => 0,
    'multiple' => '0',
    'cell_processing' => '0',
    'op' => 'Save field settings',
    'module' => 'tablefield',
    'widget_module' => 'tablefield',
    'columns' =>
    array (
      'value' =>
      array (
        'type' => 'text',
      ),
    ),
    'display_settings' =>
    array (
      'label' =>
      array (
        'format' => 'above',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'token' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  30 =>
  array (
    'label' => 'Image file',
    'field_name' => 'field_image1',
    'type' => 'filefield',
    'widget_type' => 'filefield_widget',
    'change' => 'Change basic information',
    'weight' => '6',
    'file_extensions' => 'tif tiff TIF TIFF jpg jpeg JPG JPEG png PNG',
    'progress_indicator' => 'bar',
    'file_path' => '',
    'max_filesize_per_file' => '50M',
    'max_filesize_per_node' => '50M',
    'description' => 'Upload the original tiff, jpg, or png images here.',
    'group' => 'group_upload',
    'required' => 0,
    'multiple' => '1',
    'list_field' => '1',
    'list_default' => 1,
    'description_field' => '1',
    'op' => 'Save field settings',
    'module' => 'filefield',
    'widget_module' => 'filefield',
    'columns' =>
    array (
      'fid' =>
      array (
        'type' => 'int',
        'not null' => false,
        'views' => true,
      ),
      'list' =>
      array (
        'type' => 'int',
        'size' => 'tiny',
        'not null' => false,
        'views' => true,
      ),
      'data' =>
      array (
        'type' => 'text',
        'serialize' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '6',
      'parent' => 'group_upload',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
  31 =>
  array (
    'label' => 'Gallery Image',
    'field_name' => 'field_image',
    'type' => 'filefield',
    'widget_type' => 'imagefield_widget',
    'change' => 'Change basic information',
    'weight' => '7',
    'file_extensions' => 'png gif jpg jpeg',
    'progress_indicator' => 'bar',
    'file_path' => '',
    'max_filesize_per_file' => '',
    'max_filesize_per_node' => '',
    'max_resolution' => '640x480',
    'min_resolution' => 0,
    'custom_alt' => 0,
    'alt' => '',
    'custom_title' => 0,
    'title_type' => 'textfield',
    'title' => '',
    'use_default_image' => 0,
    'default_image_upload' => '',
    'default_image' => NULL,
    'description' => 'Add a small web-version of the image for the gallery, <em>image will be rescaled and EXIF data removed!</em> The original image should be added as a tiff file above. Even if you have uploaded multiple images above, you have to chose a single representative image for the gallery.',
    'group' => 'group_upload',
    'required' => 0,
    'multiple' => '0',
    'list_field' => '1',
    'list_default' => 1,
    'description_field' => '1',
    'op' => 'Save field settings',
    'module' => 'filefield',
    'widget_module' => 'imagefield',
    'columns' =>
    array (
      'fid' =>
      array (
        'type' => 'int',
        'not null' => false,
        'views' => true,
      ),
      'list' =>
      array (
        'type' => 'int',
        'size' => 'tiny',
        'not null' => false,
        'views' => true,
      ),
      'data' =>
      array (
        'type' => 'text',
        'serialize' => true,
        'views' => true,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '7',
      'parent' => 'group_upload',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'image_plain',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'image_plain',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'image_plain',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'image_plain',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'image_plain',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'image_plain',
        'exclude' => 0,
      ),
    ),
  ),
  32 =>
  array (
    'label' => 'Image Quality',
    'field_name' => 'field_rating',
    'type' => 'fivestar',
    'widget_type' => 'stars',
    'change' => 'Change basic information',
    'weight' => '8',
    'allow_clear' => 1,
    'description' => 'Rate the overall image quality. Only the submitter can change this.',
    'default_value' =>
    array (
      0 =>
      array (
        'rating' => '-',
        'target' => NULL,
        'axis' => 'quality',
      ),
    ),
    'default_value_php' => '',
    'default_value_widget' => NULL,
    'group' => 'group_upload',
    'required' => 0,
    'multiple' => 0,
    'stars' => '10',
    'dynamic_target' => '',
    'php_target' => '',
    'axis' => 'image quality',
    'op' => 'Save field settings',
    'module' => 'fivestar',
    'widget_module' => 'fivestar',
    'columns' =>
    array (
      'rating' =>
      array (
        'type' => 'int',
        'unsigned' => true,
        'not null' => false,
        'sortable' => true,
      ),
      'target' =>
      array (
        'type' => 'int',
        'unsigned' => true,
        'not null' => false,
      ),
    ),
    'display_settings' =>
    array (
      'weight' => '8',
      'parent' => 'group_upload',
      'label' =>
      array (
        'format' => 'above',
      ),
      'teaser' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      'full' =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      5 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      4 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      2 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
      3 =>
      array (
        'format' => 'default',
        'exclude' => 0,
      ),
    ),
  ),
);
$content['extra']  = array (
  'title' => '12',
  'body_field' => '21',
  'revision_information' => '23',
  'author' => '24',
  'options' => '25',
  'comment_settings' => '26',
  'menu' => '27',
  'taxonomy' => '19',
  'book' => '22',
  'path' => '28',
);

--- END Datatype ---

---- START VIEW -----
$view = new view;
$view->name = 'rnai_experiments';
$view->description = 'List RNAi experiments';
$view->tag = 'rnai';
$view->base_table = 'node';
$view->core = 6;
$view->api_version = '2';
$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('fields', array(
  'field_image_fid' => array(
    'id' => 'field_image_fid',
    'table' => 'node_data_field_image',
    'field' => 'field_image_fid',
  ),
));
$handler->override_option('arguments', array(
  'field_gene_symbol_value' => array(
    'default_action' => 'ignore',
    'style_plugin' => 'default_summary',
    'style_options' => array(),
    'wildcard' => 'all',
    'wildcard_substitution' => 'All',
    'title' => '',
    'breadcrumb' => '',
    'default_argument_type' => 'fixed',
    'default_argument' => '',
    'validate_type' => 'none',
    'validate_fail' => 'not found',
    'glossary' => 0,
    'ignorecase' => 0,
    'limit' => '0',
    'case' => 'none',
    'path_case' => 'none',
    'transform_dash' => 0,
    'id' => 'field_gene_symbol_value',
    'table' => 'node_data_field_gene_symbol',
    'field' => 'field_gene_symbol_value',
    'validate_user_argument_type' => 'uid',
    'validate_user_roles' => array(
      2 => 0,
    ),
    'relationship' => 'none',
    'default_options_div_prefix' => '',
    'default_taxonomy_tid_term_page' => 0,
    'default_taxonomy_tid_node' => 0,
    'default_taxonomy_tid_limit' => 0,
    'default_taxonomy_tid_vids' => array(
      2 => 0,
      1 => 0,
      7 => 0,
      8 => 0,
      9 => 0,
      10 => 0,
    ),
    'default_argument_user' => 0,
    'default_argument_fixed' => '',
    'default_argument_php' => '',
    'validate_argument_node_type' => array(
      'blog' => 0,
      'chado_analysis' => 0,
      'chado_feature' => 0,
      'chado_library' => 0,
      'chado_organism' => 0,
      'chado_stock' => 0,
      'forum' => 0,
      'panel' => 0,
      'book' => 0,
      'microscope_image' => 0,
      'page' => 0,
      'story' => 0,
    ),
    'validate_argument_node_access' => 0,
    'validate_argument_nid_type' => 'nid',
    'validate_argument_vocabulary' => array(
      2 => 0,
      1 => 0,
      7 => 0,
      8 => 0,
      9 => 0,
      10 => 0,
    ),
    'validate_argument_type' => 'tid',
    'validate_argument_transform' => 0,
    'validate_user_restrict_roles' => 0,
    'validate_argument_php' => '',
  ),
));
$handler->override_option('filters', array(
  'type' => array(
    'operator' => 'in',
    'value' => array(
      'rnai_experiment' => 'rnai_experiment',
    ),
    'group' => '0',
    'exposed' => FALSE,
    'expose' => array(
      'operator' => FALSE,
      'label' => '',
    ),
    'id' => 'type',
    'table' => 'node',
    'field' => 'type',
    'relationship' => 'none',
  ),
  'field_gene_symbol_value' => array(
    'operator' => 'contains',
    'value' => '',
    'group' => '0',
    'exposed' => TRUE,
    'expose' => array(
      'use_operator' => 1,
      'operator' => 'field_gene_symbol_value_op',
      'identifier' => 'field_gene_symbol_value',
      'label' => 'Content: Gene symbol (field_gene_symbol)',
      'remember' => 1,
    ),
    'case' => 0,
    'id' => 'field_gene_symbol_value',
    'table' => 'node_data_field_gene_symbol',
    'field' => 'field_gene_symbol_value',
    'relationship' => 'none',
  ),
  'field_phenotype_value' => array(
    'operator' => 'word',
    'value' => '',
    'group' => '0',
    'exposed' => TRUE,
    'expose' => array(
      'use_operator' => 1,
      'operator' => 'field_phenotype_value_op',
      'identifier' => 'field_phenotype_value',
      'label' => 'Content: Phenotype (field_phenotype)',
      'remember' => 1,
    ),
    'case' => 0,
    'id' => 'field_phenotype_value',
    'table' => 'node_data_field_phenotype',
    'field' => 'field_phenotype_value',
    'relationship' => 'none',
  ),
  'field_organism_nid' => array(
    'operator' => 'or',
    'value' => array(),
    'group' => '0',
    'exposed' => TRUE,
    'expose' => array(
      'use_operator' => FALSE,
      'operator' => 'field_organism_nid_op',
      'identifier' => 'field_organism_nid',
      'label' => 'Content: Organism (field_organism)',
      'remember' => FALSE,
      'single' => TRUE,
      'optional' => TRUE,
      'reduce' => FALSE,
    ),
    'id' => 'field_organism_nid',
    'table' => 'node_data_field_organism',
    'field' => 'field_organism_nid',
  ),
  'field_gene_id_nid' => array(
    'id' => 'field_gene_id_nid',
    'table' => 'node_data_field_gene_id',
    'field' => 'field_gene_id_nid',
  ),
));
$handler->override_option('access', array(
  'type' => 'role',
  'role' => array(
    2 => 2,
  ),
));
$handler->override_option('cache', array(
  'type' => 'none',
));
$handler->override_option('title', 'Microscope Images');
$handler->override_option('empty', 'Nothing found');
$handler->override_option('empty_format', '1');
$handler->override_option('use_pager', '1');
$handler->override_option('distinct', 0);
$handler->override_option('style_plugin', 'table');
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('fields', array(
  'title' => array(
    'label' => 'Title',
    'alter' => array(
      'alter_text' => 0,
      'text' => '',
      'make_link' => 0,
      'path' => '',
      'absolute' => 0,
      'link_class' => '',
      'alt' => '',
      'rel' => '',
      'prefix' => '',
      'suffix' => '',
      'target' => '',
      'help' => '',
      'trim' => 0,
      'max_length' => '',
      'word_boundary' => 1,
      'ellipsis' => 1,
      'html' => 0,
      'strip_tags' => 0,
    ),
    'empty' => '',
    'hide_empty' => 0,
    'empty_zero' => 0,
    'hide_alter_empty' => 1,
    'link_to_node' => 1,
    'exclude' => 0,
    'id' => 'title',
    'table' => 'node',
    'field' => 'title',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
  'field_image_fid' => array(
    'label' => '',
    'alter' => array(
      'alter_text' => 0,
      'text' => '',
      'make_link' => 0,
      'path' => '',
      'absolute' => 0,
      'link_class' => '',
      'alt' => '',
      'rel' => '',
      'prefix' => '',
      'suffix' => '',
      'target' => '',
      'help' => '',
      'trim' => 0,
      'max_length' => '',
      'word_boundary' => 1,
      'ellipsis' => 1,
      'html' => 0,
      'strip_tags' => 0,
    ),
    'empty' => '',
    'hide_empty' => 0,
    'empty_zero' => 0,
    'hide_alter_empty' => 1,
    'link_to_node' => 0,
    'label_type' => 'none',
    'format' => 'tiny_linked',
    'multiple' => array(
      'group' => TRUE,
      'multiple_number' => '',
      'multiple_from' => '',
      'multiple_reversed' => FALSE,
    ),
    'exclude' => 0,
    'id' => 'field_image_fid',
    'table' => 'node_data_field_image',
    'field' => 'field_image_fid',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
  'field_gene_symbol_value' => array(
    'id' => 'field_gene_symbol_value',
    'table' => 'node_data_field_gene_symbol',
    'field' => 'field_gene_symbol_value',
  ),
  'field_devstage_value' => array(
    'label' => 'Dev Stage',
    'alter' => array(
      'alter_text' => 0,
      'text' => '',
      'make_link' => 0,
      'path' => '',
      'absolute' => 0,
      'link_class' => '',
      'alt' => '',
      'rel' => '',
      'prefix' => '',
      'suffix' => '',
      'target' => '',
      'help' => '',
      'trim' => 0,
      'max_length' => '',
      'word_boundary' => 1,
      'ellipsis' => 1,
      'html' => 0,
      'strip_tags' => 0,
    ),
    'empty' => '',
    'hide_empty' => 0,
    'empty_zero' => 0,
    'hide_alter_empty' => 1,
    'link_to_node' => 0,
    'label_type' => 'custom',
    'format' => 'default',
    'multiple' => array(
      'group' => 1,
      'multiple_number' => '',
      'multiple_from' => '',
      'multiple_reversed' => 0,
    ),
    'exclude' => 0,
    'id' => 'field_devstage_value',
    'table' => 'node_data_field_devstage',
    'field' => 'field_devstage_value',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
  'tid' => array(
    'label' => 'Phenotype CV',
    'alter' => array(
      'alter_text' => 0,
      'text' => '',
      'make_link' => 0,
      'path' => '',
      'absolute' => 0,
      'link_class' => '',
      'alt' => '',
      'rel' => '',
      'prefix' => '',
      'suffix' => '',
      'target' => '',
      'help' => '',
      'trim' => 0,
      'max_length' => '',
      'word_boundary' => 1,
      'ellipsis' => 1,
      'html' => 0,
      'strip_tags' => 0,
    ),
    'empty' => '',
    'hide_empty' => 0,
    'empty_zero' => 0,
    'hide_alter_empty' => 0,
    'type' => 'separator',
    'separator' => ', ',
    'link_to_taxonomy' => 1,
    'limit' => 1,
    'vids' => array(
      14 => 14,
      15 => 0,
      10 => 0,
      11 => 0,
      12 => 0,
      13 => 0,
    ),
    'exclude' => 0,
    'id' => 'tid',
    'table' => 'term_node',
    'field' => 'tid',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
  'field_phenotype_value' => array(
    'id' => 'field_phenotype_value',
    'table' => 'node_data_field_phenotype',
    'field' => 'field_phenotype_value',
  ),
  'field_image_data' => array(
    'label' => 'Image',
    'alter' => array(
      'alter_text' => 0,
      'text' => '',
      'make_link' => 0,
      'path' => '',
      'absolute' => 0,
      'link_class' => '',
      'alt' => '',
      'rel' => '',
      'prefix' => '',
      'suffix' => '',
      'target' => '',
      'help' => '',
      'trim' => 1,
      'max_length' => '30',
      'word_boundary' => 1,
      'ellipsis' => 1,
      'html' => 0,
      'strip_tags' => 1,
    ),
    'empty' => '',
    'hide_empty' => 1,
    'empty_zero' => 0,
    'hide_alter_empty' => 1,
    'link_to_node' => 1,
    'data_key' => 'description',
    'exclude' => 0,
    'id' => 'field_image_data',
    'table' => 'node_data_field_image',
    'field' => 'field_image_data',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
  'field_organism_nid' => array(
    'label' => 'Organism',
    'alter' => array(
      'alter_text' => 0,
      'text' => '',
      'make_link' => 0,
      'path' => '',
      'absolute' => 0,
      'link_class' => '',
      'alt' => '',
      'rel' => '',
      'prefix' => '',
      'suffix' => '',
      'target' => '',
      'help' => '',
      'trim' => 0,
      'max_length' => '',
      'word_boundary' => 1,
      'ellipsis' => 1,
      'html' => 0,
      'strip_tags' => 0,
    ),
    'empty' => '',
    'hide_empty' => 0,
    'empty_zero' => 0,
    'hide_alter_empty' => 1,
    'link_to_node' => 0,
    'label_type' => 'widget',
    'format' => 'default',
    'multiple' => array(
      'group' => TRUE,
      'multiple_number' => '',
      'multiple_from' => '',
      'multiple_reversed' => FALSE,
    ),
    'exclude' => 0,
    'id' => 'field_organism_nid',
    'table' => 'node_data_field_organism',
    'field' => 'field_organism_nid',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
  'created' => array(
    'label' => 'Post date',
    'alter' => array(
      'alter_text' => 0,
      'text' => '',
      'make_link' => 0,
      'path' => '',
      'absolute' => 0,
      'link_class' => '',
      'alt' => '',
      'rel' => '',
      'prefix' => '',
      'suffix' => '',
      'target' => '',
      'help' => '',
      'trim' => 0,
      'max_length' => '',
      'word_boundary' => 1,
      'ellipsis' => 1,
      'html' => 0,
      'strip_tags' => 0,
    ),
    'empty' => '',
    'hide_empty' => 0,
    'empty_zero' => 0,
    'hide_alter_empty' => 1,
    'date_format' => 'small',
    'custom_date_format' => '',
    'exclude' => 0,
    'id' => 'created',
    'table' => 'node',
    'field' => 'created',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
  'name' => array(
    'label' => 'Created by',
    'alter' => array(
      'alter_text' => 0,
      'text' => '',
      'make_link' => 0,
      'path' => '',
      'absolute' => 0,
      'link_class' => '',
      'alt' => '',
      'rel' => '',
      'prefix' => '',
      'suffix' => '',
      'target' => '',
      'help' => '',
      'trim' => 0,
      'max_length' => '',
      'word_boundary' => 1,
      'ellipsis' => 1,
      'html' => 0,
      'strip_tags' => 0,
    ),
    'empty' => 'nobody',
    'hide_empty' => 0,
    'empty_zero' => 0,
    'hide_alter_empty' => 1,
    'link_to_user' => 1,
    'overwrite_anonymous' => 0,
    'anonymous_text' => '',
    'exclude' => 0,
    'id' => 'name',
    'table' => 'users',
    'field' => 'name',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
));
$handler->override_option('filters', array(
  'type' => array(
    'operator' => 'in',
    'value' => array(
      'rnai_experiment' => 'rnai_experiment',
    ),
    'group' => '0',
    'exposed' => FALSE,
    'expose' => array(
      'operator' => FALSE,
      'label' => '',
    ),
    'id' => 'type',
    'table' => 'node',
    'field' => 'type',
    'relationship' => 'none',
    'override' => array(
      'button' => 'Use default',
    ),
  ),
  'field_devstage_value' => array(
    'operator' => 'word',
    'value' => '',
    'group' => '0',
    'exposed' => TRUE,
    'expose' => array(
      'use_operator' => 1,
      'operator' => 'field_devstage_value_op',
      'identifier' => 'field_devstage_value',
      'label' => 'Developmental Stage CV',
      'remember' => 1,
    ),
    'case' => 0,
    'id' => 'field_devstage_value',
    'table' => 'node_data_field_devstage',
    'field' => 'field_devstage_value',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
  'term_node_tid_depth' => array(
    'operator' => 'or',
    'value' => NULL,
    'group' => '0',
    'exposed' => TRUE,
    'expose' => array(
      'use_operator' => 0,
      'operator' => 'term_node_tid_depth_op',
      'identifier' => 'term_node_tid_depth',
      'label' => 'Phenotype CV',
      'optional' => 1,
      'remember' => 1,
    ),
    'type' => 'hierarchical_select',
    'limit' => TRUE,
    'vid' => '14',
    'depth' => '2',
    'id' => 'term_node_tid_depth',
    'table' => 'node',
    'field' => 'term_node_tid_depth',
    'hierarchy' => 0,
    'configure_hs' => '<a href="/?q=admin/build/views/hs_config/rnai_experiments/page_1/term_node_tid_depth">Configure Hierarchical Select</a>',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
  'field_organism_nid' => array(
    'operator' => 'or',
    'value' => array(),
    'group' => '0',
    'exposed' => TRUE,
    'expose' => array(
      'use_operator' => 0,
      'operator' => 'field_organism_nid_op',
      'identifier' => 'field_organism_nid',
      'label' => 'Organism',
      'optional' => 1,
      'single' => 1,
      'remember' => 1,
      'reduce' => 0,
    ),
    'id' => 'field_organism_nid',
    'table' => 'node_data_field_organism',
    'field' => 'field_organism_nid',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
    'reduce_duplicates' => 0,
  ),
  'field_batch_id_value' => array(
    'operator' => 'contains',
    'value' => '',
    'group' => '0',
    'exposed' => TRUE,
    'expose' => array(
      'use_operator' => 0,
      'operator' => 'field_batch_id_value_op',
      'identifier' => 'field_batch_id_value',
      'label' => 'Content: Experiment Batch ID (field_batch_id)',
      'remember' => 1,
    ),
    'case' => 0,
    'id' => 'field_batch_id_value',
    'table' => 'node_data_field_batch_id',
    'field' => 'field_batch_id_value',
    'override' => array(
      'button' => 'Use default',
    ),
    'relationship' => 'none',
  ),
));
$handler->override_option('title', 'RNAi');
$handler->override_option('header', 'Search RNAi experiements');
$handler->override_option('header_format', '1');
$handler->override_option('header_empty', 0);
$handler->override_option('use_ajax', TRUE);
$handler->override_option('style_options', array(
  'grouping' => '',
  'override' => 1,
  'sticky' => 0,
  'order' => 'desc',
  'summary' => 'RNAi experiment overview',
  'columns' => array(
    'field_gene_id_nid' => 'field_gene_id_nid',
    'field_gene_symbol_value' => 'field_gene_symbol_value',
    'field_devstage_value' => 'field_devstage_value',
    'tid' => 'tid',
    'field_phenotype_value' => 'field_phenotype_value',
    'field_image_data' => 'field_image_data',
    'field_organism_nid' => 'field_organism_nid',
    'view_node' => 'view_node',
    'created' => 'created',
    'name' => 'name',
    'field_rating_rating' => 'field_rating_rating',
  ),
  'info' => array(
    'field_gene_id_nid' => array(
      'separator' => '',
    ),
    'field_gene_symbol_value' => array(
      'sortable' => 0,
      'separator' => '',
    ),
    'field_devstage_value' => array(
      'separator' => '',
    ),
    'tid' => array(
      'separator' => '',
    ),
    'field_phenotype_value' => array(
      'sortable' => 0,
      'separator' => '',
    ),
    'field_image_data' => array(
      'separator' => '',
    ),
    'field_organism_nid' => array(
      'separator' => '',
    ),
    'view_node' => array(
      'separator' => '',
    ),
    'created' => array(
      'sortable' => 1,
      'separator' => '',
    ),
    'name' => array(
      'sortable' => 1,
      'separator' => '',
    ),
    'field_rating_rating' => array(
      'sortable' => 1,
      'separator' => '',
    ),
  ),
  'default' => '-1',
));
$handler->override_option('path', 'browse_rnai');
$handler->override_option('menu', array(
  'type' => 'normal',
  'title' => 'RNAi',
  'description' => 'View all RNAi',
  'weight' => '0',
  'name' => 'primary-links',
));
$handler->override_option('tab_options', array(
  'type' => 'none',
  'title' => '',
  'description' => '',
  'weight' => 0,
  'name' => 'navigation',
));


--- END VIEW ----





On Jun 26, 2013, at 11:54 AM, Michael Dondrup wrote:

> Hi again,
>
> I have observed some more rare glitches after updating from devel to 1.1. I must say that these are quite
> seldom use-cases and I am unsure if anyone else has ever used the modules this way, but still it might be useful to
> document.
> The cases involve:
> - creating custom data types and views referencing Feature Node objects
> - having these content types and objects from before the update and trying to use them after.
>
> 1) I have made custom content types (with CCK) containing
> fields referencing Feature Nodes. The filed-widget is set to
> autocomplete widget to select feature nodes as you type.
> Using the Autocomplete widget after the update
> with a feature and saving the content gave an error: "Target ID: Title mismatch. Please check your input."
> Being unable to save the content.
> Solution: changing the *widget_type* to something else temporarily, saving, and changing *widget_type* back to
> autocomplete helped.
>
> 1) I have made a view for said content-type containing an exposed filter for the Feature name to be able to filter
> entries referencing a given Feature. Entering something
> into the filter field, yielded a syntax error: "Syntax error at '.':" (see [1])
> … AND ((.name) LIKE ('%my%') …
> somehow the filter was looking for the field name in an undefined table.
> Assuming, that this might be somehow related to
> the Tripal Views Integration ( admin/tripal/views/integration/list ) and edited the "Chado Feature" Drupal View for table 'feature'. (have never edited something here before)
> I didn't change any setting but simply saved it with priority '0' (I now have three instances of "Chado Feature" with priorities 10,9,and 0). Indeed this solved the missing table name,
> yielding a new error (see [2]):
> ERROR: column chado_feature.organism_id does not exist
> The table chado_feature has these columns:  vid nid feature_id sync_date
>
> I have tried to remove and add the Field and the filter but to no avail. I cannot remove the field from the datatype, because it contains data already.
> It seems like there is something wrong with my views integration now.
>
> What am I missing here?
>
> Michael
>
>
>
>
>
>
>
>
>
> [1] SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.
>
> [2]
> • warning: pg_query(): Query failed: ERROR: column chado_feature.organism_id does not exist at character 383 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>
> • user warning: ERROR: column chado_feature.organism_id does not exist at character 383 query: SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((feature.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.
>
>
>
>
>
>
>
>
> Michael Dondrup
> Postdoctoral fellow
> Sea Lice Research Centre/Department of Informatics
> University of Bergen
> Thormøhlensgate 55, N-5008 Bergen,
> Norway
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Problems with Views after Tripal update

Stephen Ficklin-2
In reply to this post by Michael Dondrup-3
Hi Michael,

Thanks for sending along the the Content Type export and Views export for your content type and view.  That was very helpful.  I was able to get your content type imported (after adding a few modules), but not your view.  I'm getting this error message:

Field handler node_data_field_devstage.field_devstage_value is not available.
Filter handler node_data_field_devstage.field_devstage_value is not available.
Unable to import view.

Does that mean anything to you? I'm not familiar with those handlers.


Thanks,
Stephen

On 6/26/2013 5:54 AM, Michael Dondrup wrote:
Hi again,

I have observed some more rare glitches after updating from devel to 1.1. I must say that these are quite
seldom use-cases and I am unsure if anyone else has ever used the modules this way, but still it might be useful to 
document.
The cases involve:
- creating custom data types and views referencing Feature Node objects
- having these content types and objects from before the update and trying to use them after.

1) I have made custom content types (with CCK) containing 
fields referencing Feature Nodes. The filed-widget is set to 
autocomplete widget to select feature nodes as you type. 
Using the Autocomplete widget after the update
with a feature and saving the content gave an error: "Target ID: Title mismatch. Please check your input."
Being unable to save the content.
Solution: changing the *widget_type* to something else temporarily, saving, and changing *widget_type* back to
autocomplete helped. 

1) I have made a view for said content-type containing an exposed filter for the Feature name to be able to filter
entries referencing a given Feature. Entering something
into the filter field, yielded a syntax error: "Syntax error at '.':" (see [1])
… AND ((.name) LIKE ('%my%') …
somehow the filter was looking for the field name in an undefined table. 
Assuming, that this might be somehow related to
the Tripal Views Integration ( admin/tripal/views/integration/list ) and edited the "Chado Feature" Drupal View for table 'feature'. (have never edited something here before)
I didn't change any setting but simply saved it with priority '0' (I now have three instances of "Chado Feature" with priorities 10,9,and 0). Indeed this solved the missing table name,
yielding a new error (see [2]):
ERROR: column chado_feature.organism_id does not exist
The table chado_feature has these columns:  vid nid feature_id sync_date

I have tried to remove and add the Field and the filter but to no avail. I cannot remove the field from the datatype, because it contains data already.
 It seems like there is something wrong with my views integration now.

What am I missing here?

Michael









[1] SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.

[2]
• warning: pg_query(): Query failed: ERROR: column chado_feature.organism_id does not exist at character 383 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
	
• user warning: ERROR: column chado_feature.organism_id does not exist at character 383 query: SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((feature.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.








Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen, 
Norway


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Re: [Gmod-tripal-devel] Problems with Views after Tripal update

Michael Dondrup-3
Hi Stephen,

the dev_stage field is in fact something I made using this module https://github.com/mdondrup/CVautocomplete,
which is a modified version of the autocomplete module to support chado CV data. Possibly, this module is also required to be able to install
the view. Alternatively, it should be possible to set the widget to plain text in the content type itself. This should be unrelated to the other
problem with the feature table, but who knows. Sorry, for not listing the dependencies with the data type. Could you install the CVautocomplete
module?

Best
Michael



On Jun 27, 2013, at 6:06 AM, Stephen Ficklin wrote:

> Hi Michael,
>
> Thanks for sending along the the Content Type export and Views export for your content type and view.  That was very helpful.  I was able to get your content type imported (after adding a few modules), but not your view.  I'm getting this error message:
>
> Field handler node_data_field_devstage.field_devstage_value is not available.
> Filter handler node_data_field_devstage.field_devstage_value is not available.
> Unable to import view.
>
> Does that mean anything to you? I'm not familiar with those handlers.
>
>
> Thanks,
> Stephen
>
> On 6/26/2013 5:54 AM, Michael Dondrup wrote:
>> Hi again,
>>
>> I have observed some more rare glitches after updating from devel to 1.1. I must say that these are quite
>> seldom use-cases and I am unsure if anyone else has ever used the modules this way, but still it might be useful to
>> document.
>> The cases involve:
>> - creating custom data types and views referencing Feature Node objects
>> - having these content types and objects from before the update and trying to use them after.
>>
>> 1) I have made custom content types (with CCK) containing
>> fields referencing Feature Nodes. The filed-widget is set to
>> autocomplete widget to select feature nodes as you type.
>> Using the Autocomplete widget after the update
>> with a feature and saving the content gave an error: "Target ID: Title mismatch. Please check your input."
>> Being unable to save the content.
>> Solution: changing the *widget_type* to something else temporarily, saving, and changing *widget_type* back to
>> autocomplete helped.
>>
>> 1) I have made a view for said content-type containing an exposed filter for the Feature name to be able to filter
>> entries referencing a given Feature. Entering something
>> into the filter field, yielded a syntax error: "Syntax error at '.':" (see [1])
>> … AND ((.name) LIKE ('%my%') …
>> somehow the filter was looking for the field name in an undefined table.
>> Assuming, that this might be somehow related to
>> the Tripal Views Integration ( admin/tripal/views/integration/list ) and edited the "Chado Feature" Drupal View for table 'feature'. (have never edited something here before)
>> I didn't change any setting but simply saved it with priority '0' (I now have three instances of "Chado Feature" with priorities 10,9,and 0). Indeed this solved the missing table name,
>> yielding a new error (see [2]):
>> ERROR: column chado_feature.organism_id does not exist
>> The table chado_feature has these columns:  vid nid feature_id sync_date
>>
>> I have tried to remove and add the Field and the filter but to no avail. I cannot remove the field from the datatype, because it contains data already.
>>  It seems like there is something wrong with my views integration now.
>>
>> What am I missing here?
>>
>> Michael
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> [1] SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.
>>
>> [2]
>> • warning: pg_query(): Query failed: ERROR: column chado_feature.organism_id does not exist at character 383 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>>
>> • user warning: ERROR: column chado_feature.organism_id does not exist at character 383 query: SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((feature.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.
>>
>>
>>
>>
>>
>>
>>
>>
>> Michael Dondrup
>> Postdoctoral fellow
>> Sea Lice Research Centre/Department of Informatics
>> University of Bergen
>> Thormøhlensgate 55, N-5008 Bergen,
>> Norway
>>
>>
>> ------------------------------------------------------------------------------
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>>
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Re: [Gmod-tripal-devel] Problems with Views after Tripal update

Michael Dondrup-3
Hi,
I have made I little reduced example to make debugging easier and doesn't require installing a lot of modules.
_ATEST01: consists of only
a Chado Feature node reference. Saving and editing the content works fine.
_ATEST_VIEW has a filter for type _ATEST01 and tries to display the Field Chado: Feature name
in a table. The result for me is:

• warning: pg_query(): Query failed: ERROR: column chado_feature.organism_id does not exist at character 248 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
       
• user warning: query: SELECT DISTINCT node.nid AS nid, node.title AS node_title, node.language AS node_language, feature.name AS feature_name FROM node node LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id WHERE node.type in ('test_type01') LIMIT 10 OFFSET 0 in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 810.


You can also see this at: https://lb-test.bccs.uib.no/_ATEST_VIEW
 

The resulting SQL query is:

SELECT node.nid AS nid, node.title AS node_title, node.language AS node_language, feature.name AS feature_name FROM node node
LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid
LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id WHERE node.type in ('test_type01')

However, my table chado_feature doesn't have the column organism_id and hence the error.




On Jun 27, 2013, at 10:00 AM, Michael Dondrup wrote:

> Hi Stephen,
>
> the dev_stage field is in fact something I made using this module https://github.com/mdondrup/CVautocomplete,
> which is a modified version of the autocomplete module to support chado CV data. Possibly, this module is also required to be able to install
> the view. Alternatively, it should be possible to set the widget to plain text in the content type itself. This should be unrelated to the other
> problem with the feature table, but who knows. Sorry, for not listing the dependencies with the data type. Could you install the CVautocomplete
> module?
>
> Best
> Michael
>
>
>
> On Jun 27, 2013, at 6:06 AM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> Thanks for sending along the the Content Type export and Views export for your content type and view.  That was very helpful.  I was able to get your content type imported (after adding a few modules), but not your view.  I'm getting this error message:
>>
>> Field handler node_data_field_devstage.field_devstage_value is not available.
>> Filter handler node_data_field_devstage.field_devstage_value is not available.
>> Unable to import view.
>>
>> Does that mean anything to you? I'm not familiar with those handlers.
>>
>>
>> Thanks,
>> Stephen
>>
>> On 6/26/2013 5:54 AM, Michael Dondrup wrote:
>>> Hi again,
>>>
>>> I have observed some more rare glitches after updating from devel to 1.1. I must say that these are quite
>>> seldom use-cases and I am unsure if anyone else has ever used the modules this way, but still it might be useful to
>>> document.
>>> The cases involve:
>>> - creating custom data types and views referencing Feature Node objects
>>> - having these content types and objects from before the update and trying to use them after.
>>>
>>> 1) I have made custom content types (with CCK) containing
>>> fields referencing Feature Nodes. The filed-widget is set to
>>> autocomplete widget to select feature nodes as you type.
>>> Using the Autocomplete widget after the update
>>> with a feature and saving the content gave an error: "Target ID: Title mismatch. Please check your input."
>>> Being unable to save the content.
>>> Solution: changing the *widget_type* to something else temporarily, saving, and changing *widget_type* back to
>>> autocomplete helped.
>>>
>>> 1) I have made a view for said content-type containing an exposed filter for the Feature name to be able to filter
>>> entries referencing a given Feature. Entering something
>>> into the filter field, yielded a syntax error: "Syntax error at '.':" (see [1])
>>> … AND ((.name) LIKE ('%my%') …
>>> somehow the filter was looking for the field name in an undefined table.
>>> Assuming, that this might be somehow related to
>>> the Tripal Views Integration ( admin/tripal/views/integration/list ) and edited the "Chado Feature" Drupal View for table 'feature'. (have never edited something here before)
>>> I didn't change any setting but simply saved it with priority '0' (I now have three instances of "Chado Feature" with priorities 10,9,and 0). Indeed this solved the missing table name,
>>> yielding a new error (see [2]):
>>> ERROR: column chado_feature.organism_id does not exist
>>> The table chado_feature has these columns:  vid nid feature_id sync_date
>>>
>>> I have tried to remove and add the Field and the filter but to no avail. I cannot remove the field from the datatype, because it contains data already.
>>> It seems like there is something wrong with my views integration now.
>>>
>>> What am I missing here?
>>>
>>> Michael
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> [1] SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.
>>>
>>> [2]
>>> • warning: pg_query(): Query failed: ERROR: column chado_feature.organism_id does not exist at character 383 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>>>
>>> • user warning: ERROR: column chado_feature.organism_id does not exist at character 383 query: SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((feature.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Michael Dondrup
>>> Postdoctoral fellow
>>> Sea Lice Research Centre/Department of Informatics
>>> University of Bergen
>>> Thormøhlensgate 55, N-5008 Bergen,
>>> Norway
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by Windows:
>>>
>>> Build for Windows Store.
>>>
>>>
>>> http://p.sf.net/sfu/windows-dev2dev
>>>
>>> _______________________________________________
>>> Gmod-tripal-devel mailing list
>>>
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>> ------------------------------------------------------------------------------
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>>
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>
>
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Re: [Gmod-tripal-devel] Problems with Views after Tripal update

Michael Dondrup-3
Hi,

I have tried to track down the problem a little bit further, and I think have come closer to a solution.
Somehow, my tripal views integration for feature is broken. Would be interesting to know if that only
happened to me, e.g. by moving from devel branch to 1.1 or doing something else
or if others have this effect as well.

So I went to /admin/tripal/views/integration/  Looking at some of the integrated chado tables, e.g.
admin/tripal/views/integration/edit/1 (Chado Acquisition), I see that in fieldgroup:
- Join Selection, all fields are filled.


Then, when I go to to Chado Feature (/admin/tripal/views/integration/edit/191 in my case) under
Join Selection, none of the fields is filled (I have two such entries "Chado Feature" with priorities 9 and 10, both are the same),
none of selection boxes for "Select Join table", "Select join column", etc. are set.

In conclusion, my view integration got somehow broken, and possibly, repairing the correct values could fix  this issue.
Now, two questions, how could I have possibly have lost these entries, and how can I restore them? Possibly I can enter them
from scratch, or could someone please send me an Export of their Views integration for Chado Feature? Mine looked like
this at the moment.

array ( 'table' => 'feature', 'name' => 'Chado Feature', 'type' => 'chado', 'description' => 'TODO: please describe this table!', 'priority' => '9', 'base_table' => '1', 'fields' => array ( ), )









On Jun 27, 2013, at 10:45 AM, Michael Dondrup wrote:

> Hi,
> I have made I little reduced example to make debugging easier and doesn't require installing a lot of modules.
> _ATEST01: consists of only
> a Chado Feature node reference. Saving and editing the content works fine.
> _ATEST_VIEW has a filter for type _ATEST01 and tries to display the Field Chado: Feature name
> in a table. The result for me is:
>
> • warning: pg_query(): Query failed: ERROR: column chado_feature.organism_id does not exist at character 248 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>
> • user warning: query: SELECT DISTINCT node.nid AS nid, node.title AS node_title, node.language AS node_language, feature.name AS feature_name FROM node node LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id WHERE node.type in ('test_type01') LIMIT 10 OFFSET 0 in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 810.
>
>
> You can also see this at: https://lb-test.bccs.uib.no/_ATEST_VIEW
>
>
> The resulting SQL query is:
>
> SELECT node.nid AS nid, node.title AS node_title, node.language AS node_language, feature.name AS feature_name FROM node node
> LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid
> LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id WHERE node.type in ('test_type01')
>
> However, my table chado_feature doesn't have the column organism_id and hence the error.
>
>
>
>
> On Jun 27, 2013, at 10:00 AM, Michael Dondrup wrote:
>
>> Hi Stephen,
>>
>> the dev_stage field is in fact something I made using this module https://github.com/mdondrup/CVautocomplete,
>> which is a modified version of the autocomplete module to support chado CV data. Possibly, this module is also required to be able to install
>> the view. Alternatively, it should be possible to set the widget to plain text in the content type itself. This should be unrelated to the other
>> problem with the feature table, but who knows. Sorry, for not listing the dependencies with the data type. Could you install the CVautocomplete
>> module?
>>
>> Best
>> Michael
>>
>>
>>
>> On Jun 27, 2013, at 6:06 AM, Stephen Ficklin wrote:
>>
>>> Hi Michael,
>>>
>>> Thanks for sending along the the Content Type export and Views export for your content type and view.  That was very helpful.  I was able to get your content type imported (after adding a few modules), but not your view.  I'm getting this error message:
>>>
>>> Field handler node_data_field_devstage.field_devstage_value is not available.
>>> Filter handler node_data_field_devstage.field_devstage_value is not available.
>>> Unable to import view.
>>>
>>> Does that mean anything to you? I'm not familiar with those handlers.
>>>
>>>
>>> Thanks,
>>> Stephen
>>>
>>> On 6/26/2013 5:54 AM, Michael Dondrup wrote:
>>>> Hi again,
>>>>
>>>> I have observed some more rare glitches after updating from devel to 1.1. I must say that these are quite
>>>> seldom use-cases and I am unsure if anyone else has ever used the modules this way, but still it might be useful to
>>>> document.
>>>> The cases involve:
>>>> - creating custom data types and views referencing Feature Node objects
>>>> - having these content types and objects from before the update and trying to use them after.
>>>>
>>>> 1) I have made custom content types (with CCK) containing
>>>> fields referencing Feature Nodes. The filed-widget is set to
>>>> autocomplete widget to select feature nodes as you type.
>>>> Using the Autocomplete widget after the update
>>>> with a feature and saving the content gave an error: "Target ID: Title mismatch. Please check your input."
>>>> Being unable to save the content.
>>>> Solution: changing the *widget_type* to something else temporarily, saving, and changing *widget_type* back to
>>>> autocomplete helped.
>>>>
>>>> 1) I have made a view for said content-type containing an exposed filter for the Feature name to be able to filter
>>>> entries referencing a given Feature. Entering something
>>>> into the filter field, yielded a syntax error: "Syntax error at '.':" (see [1])
>>>> … AND ((.name) LIKE ('%my%') …
>>>> somehow the filter was looking for the field name in an undefined table.
>>>> Assuming, that this might be somehow related to
>>>> the Tripal Views Integration ( admin/tripal/views/integration/list ) and edited the "Chado Feature" Drupal View for table 'feature'. (have never edited something here before)
>>>> I didn't change any setting but simply saved it with priority '0' (I now have three instances of "Chado Feature" with priorities 10,9,and 0). Indeed this solved the missing table name,
>>>> yielding a new error (see [2]):
>>>> ERROR: column chado_feature.organism_id does not exist
>>>> The table chado_feature has these columns:  vid nid feature_id sync_date
>>>>
>>>> I have tried to remove and add the Field and the filter but to no avail. I cannot remove the field from the datatype, because it contains data already.
>>>> It seems like there is something wrong with my views integration now.
>>>>
>>>> What am I missing here?
>>>>
>>>> Michael
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> [1] SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.
>>>>
>>>> [2]
>>>> • warning: pg_query(): Query failed: ERROR: column chado_feature.organism_id does not exist at character 383 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>>>>
>>>> • user warning: ERROR: column chado_feature.organism_id does not exist at character 383 query: SELECT COUNT(*) FROM (SELECT DISTINCT node.nid AS nid FROM node node LEFT JOIN content_field_devstage node_data_field_devstage ON node.vid = node_data_field_devstage.vid LEFT JOIN content_type_rnai_experiment node_data_field_batch_id ON node.vid = node_data_field_batch_id.vid LEFT JOIN chado_feature chado_feature ON node.nid = chado_feature.nid LEFT JOIN feature feature ON chado_feature.organism_id = feature.organism_id LEFT JOIN content_field_gene_symbol node_data_field_gene_symbol ON node.vid = node_data_field_gene_symbol.vid INNER JOIN users users ON node.uid = users.uid WHERE (node.type in ('rnai_experiment')) AND (UPPER(node_data_field_batch_id.field_batch_id_value) LIKE UPPER('%%')) AND ((feature.name) LIKE ('%my%')) ) count_alias in /export/home/licebase/drupal/sites/all/modules/views/includes/view.inc on line 805.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Michael Dondrup
>>>> Postdoctoral fellow
>>>> Sea Lice Research Centre/Department of Informatics
>>>> University of Bergen
>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>> Norway
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by Windows:
>>>>
>>>> Build for Windows Store.
>>>>
>>>>
>>>> http://p.sf.net/sfu/windows-dev2dev
>>>>
>>>> _______________________________________________
>>>> Gmod-tripal-devel mailing list
>>>>
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>
>>> ------------------------------------------------------------------------------
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