1: <?php
  2: 
  3: namespace cli_db;
  4: 
  5: require_once ROOT . 'classes/AbstractTable.php';
  6: 
  7: class Biomaterial extends AbstractTable {
  8: 
  9:     /**
 10:      * @inheritdoc
 11:      */
 12:     public static function getKeys() {
 13:         return array(
 14:             'id' => array(
 15:                 'colname' => 'BiomaterialId',
 16:                 'actions' => array(
 17:                     'details' => 'required',
 18:                     'update' => 'required',
 19:                     'delete' => 'required',
 20:                 ),
 21:                 'description' => 'biomaterial id'
 22:             ),
 23:             'name' => array(
 24:                 'colname' => 'Name',
 25:                 'actions' => array(
 26:                     'insert' => 'required',
 27:                     'add_condition' => 'required',
 28:                     'add_condition_sample' => 'required',
 29:                     'update' => 'optional',
 30:                 ),
 31:                 'description' => 'name'
 32:             ),
 33:             'description' => array(
 34:                 'colname' => 'Description',
 35:                 'actions' => array(
 36:                     'insert' => 'optional',
 37:                     'add_condition' => 'optional',
 38:                     'add_condition_sample' => 'optional',
 39:                     'update' => 'optional',
 40:                 ),
 41:                 'description' => 'description'
 42:             ),
 43:             'organism_id' => array(
 44:                 'colname' => 'TaxonId',
 45:                 'actions' => array(
 46:                     'insert' => 'optional',
 47:                     'update' => 'optional',
 48:                 ),
 49:                 'description' => 'organism id'
 50:             ),
 51:             'biosourceprovider_id' => array(
 52:                 'colname' => 'BiosourceproviderId',
 53:                 'actions' => array(
 54:                     'insert' => 'optional',
 55:                     'add_condition' => 'optional',
 56:                     'add_condition_sample' => 'optional',
 57:                     'update' => 'optional',
 58:                 ),
 59:                 'description' => 'contact id'
 60:             ),
 61:             'short' => array(
 62:                 'actions' => array(
 63:                     'insert' => 'optional',
 64:                     'add_condition' => 'optional',
 65:                     'add_condition_sample' => 'optional',
 66:                 ),
 67:                 'description' => 'if set, will just output the ID of newly inserted line on success',
 68:                 'action' => 'StoreTrue'
 69:             ),
 70:             'parent_biomaterial_name' => array(
 71:                 'actions' => array(
 72:                     'add_condition' => 'required',
 73:                 ),
 74:                 'description' => 'parent biomaterial name'
 75:             ),
 76:             'parent_condition_name' => array(
 77:                 'actions' => array(
 78:                     'add_condition_sample' => 'required',
 79:                 ),
 80:                 'description' => 'parent condition name'
 81:             ),
 82:             'type' => array('colname' => 'Type'),
 83:             'parent' => array('colname' => 'Parent')
 84:         );
 85:     }
 86: 
 87:     /**
 88:      * @inheritdoc
 89:      */
 90:     public static function CLI_commandDescription() {
 91:         return 'Manipulate biomaterials, conditions and samples.';
 92:     }
 93: 
 94:     /**
 95:      * @inheritdoc
 96:      */
 97:     public static function CLI_commandName() {
 98:         return 'biomaterial';
 99:     }
100: 
101:     /**
102:      * @inheritdoc
103:      */
104:     public static function CLI_longHelp() {
105:         
106:     }
107: 
108:     /**
109:      * @inheritdoc
110:      */
111:     public static function getSubCommands() {
112:         return array('insert', 'update', 'delete', 'details', 'list', 'add_condition', 'add_condition_sample');
113:     }
114: 
115:     /**
116:      * @inheritdoc
117:      * overwritten to set type to biomaterial
118:      */
119:     protected static function command_insert($options, $keys) {
120:         $biomat = new propel\Biomaterial();
121:         self::setKeys($options, $keys, 'insert', $biomat);
122: 
123:         $lines = $biomat->save();
124:         $biomat->setType('biomaterial');
125:         $lines += $biomat->save();
126: 
127:         if (isset($options['short']) && $options['short'])
128:             print $biomat->getPrimaryKey();
129:         else
130:             printf("%d line(s) inserted.\n", $lines);
131:     }
132: 
133:     /**
134:      * command to add condition. checks for parent biomaterial & parent type, links against parent
135:      * @param Array $options user-specified command line parameters
136:      * @param Array $keys result from self::getKeys()
137:      */
138:     protected static function command_add_condition($options, $keys) {
139:         $parent = propel\BiomaterialQuery::create()->findOneByName($options['parent_biomaterial_name']);
140:         if ($parent == null)
141:             trigger_error('This parent Biomaterial does not exist!', E_USER_ERROR);
142:         if ($parent->getType() != 'biomaterial')
143:             trigger_error('Specified parent is of wrong type!' . $parent->getType(), E_USER_ERROR);
144: 
145: 
146:         $biomat = new propel\Biomaterial();
147:         self::setKeys($options, $keys, 'insert', $biomat);
148: 
149:         $lines = $biomat->save();
150:         $biomat->setType('condition');
151:         $biomat->setParent($parent);
152:         $lines += $biomat->save();
153: 
154:         if (isset($options['short']) && $options['short'])
155:             print $biomat->getPrimaryKey();
156:         else
157:             printf("%d line(s) inserted.\n", $lines);
158:     }
159: 
160:     /**
161:      * command to add sample. checks for parent biomaterial & parent type, links against parent
162:      * @param Array $options user-specified command line parameters
163:      * @param Array $keys result from self::getKeys()
164:      */
165:     protected static function command_add_condition_sample($options, $keys) {
166:         $parent = propel\BiomaterialQuery::create()->findOneByName($options['parent_condition_name']);
167:         if ($parent == null)
168:             trigger_error('This parent Biomaterial does not exist!', E_USER_ERROR);
169:         if ($parent->getType() != 'condition')
170:             trigger_error('Specified parent is of wrong type!', E_USER_ERROR);
171: 
172:         $biomat = new propel\Biomaterial();
173:         self::setKeys($options, $keys, 'insert', $biomat);
174: 
175:         $lines = $biomat->save();
176:         $biomat->setType('condition_sample');
177:         $biomat->setParent($parent);
178:         $lines += $biomat->save();
179: 
180:         if (isset($options['short']) && $options['short'])
181:             print $biomat->getPrimaryKey();
182:         else
183:             printf("%d line(s) inserted.\n", $lines);
184:     }
185: 
186:     /**
187:      * @inheritDoc
188:      * overwritten to display additional information
189:      */
190:     protected static function command_details($options, $keys) {
191:         parent::command_details($options, $keys);
192: 
193:         $references = array();
194: 
195:         $child_relationships = propel\BiomaterialRelationshipQuery::create()->findByObjectId($options['id']);
196:         foreach ($child_relationships as $child_relationship) {
197:             $child = $child_relationship->getBiomaterialRelatedBySubjectId();
198:             $references[] = array($child->getType(), sprintf("Id: %s\nName: %s", $child->getBiomaterialId(), $child->getName()));
199:         }
200: 
201:         if (count($references) > 0) {
202:             print "has relationships:\n";
203:             self::printTable(array('', 'Row'), $references);
204:         }
205:     }
206: 
207:     /**
208:      * @inheritDoc
209:      */
210:     public static function getPropelClass() {
211:         return '\\cli_db\\propel\\Biomaterial';
212:     }
213: 
214: }
215: 
216: ?>
217: