jon48 /
webtrees-lib
| Total Complexity | 82 |
| Total Lines | 742 |
| Duplicated Lines | 0 % |
| Changes | 2 | ||
| Bugs | 0 | Features | 0 |
Complex classes like SosaProvider often do a lot of different things. To break such a class down, we need to identify a cohesive component within that class. A common approach to find such a component is to look for fields/methods that share the same prefixes, or suffixes.
Once you have determined the fields that belong together, you can apply the Extract Class refactoring. If the component makes sense as a sub-class, Extract Subclass is also a candidate, and is often faster.
While breaking up the class, it is a good idea to analyze how other classes use SosaProvider, and based on these observations, apply Extract Interface, too.
| 1 | <?php |
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| 23 | class SosaProvider { |
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| 24 | |||
| 25 | /** |
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| 26 | * Maximum number of generation the database is able to hold. |
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| 27 | * @var int MAX_DB_GENERATIONS |
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| 28 | */ |
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| 29 | const MAX_DB_GENERATIONS = 64; |
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| 30 | |||
| 31 | /** |
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| 32 | * System's default user (ID -1 in the database |
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| 33 | * @var User $default_user |
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| 34 | */ |
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| 35 | protected static $default_user; |
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| 36 | |||
| 37 | /** |
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| 38 | * Reference user |
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| 39 | * @var User $user |
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| 40 | */ |
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| 41 | protected $user; |
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| 42 | |||
| 43 | /** |
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| 44 | * Reference tree |
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| 45 | * @var Tree $tree |
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| 46 | */ |
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| 47 | protected $tree; |
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| 48 | |||
| 49 | /** |
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| 50 | * Cached list of Sosa Individuals by generation |
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| 51 | * Format: key = generation, value = array ( sosa => Individual ID) |
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| 52 | * @var array $sosa_list_by_gen |
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| 53 | */ |
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| 54 | protected $sosa_list_by_gen; |
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| 55 | |||
| 56 | /** |
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| 57 | * Cached list of Sosa Families by generation |
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| 58 | * Format: key = generation, value = array ( sosa => Family ID) |
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| 59 | * @var unknown $sosa_fam_list_by_gen |
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| 60 | */ |
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| 61 | protected $sosa_fam_list_by_gen; |
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| 62 | |||
| 63 | /** |
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| 64 | * Cached array of statistics by generation |
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| 65 | * Format: key = generation, |
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| 66 | * value = array( |
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| 67 | * sosaCount, sosaTotalCount, diffSosaTotalCount, firstBirth, lastBirth, avgBirth |
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| 68 | * ) |
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| 69 | * @var array $statistics_tab |
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| 70 | */ |
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| 71 | protected $statistics_tab; |
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| 72 | |||
| 73 | /** |
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| 74 | * Has the provider's initialisation completed |
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| 75 | * @var bool $is_setup |
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| 76 | */ |
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| 77 | protected $is_setup; |
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| 78 | |||
| 79 | /** |
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| 80 | * Constructor for Sosa Provider. |
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| 81 | * A provider is defined in relation to a specific tree and reference user. |
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| 82 | * |
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| 83 | * @param Tree $tree |
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| 84 | * @param User $user |
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| 85 | */ |
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| 86 | public function __construct(Tree $tree, User $user = null) { |
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| 87 | if(self::$default_user === null) |
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| 88 | self::$default_user = User::find(-1); |
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| 89 | |||
| 90 | $this->tree = $tree; |
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| 91 | $this->user = $user; |
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| 92 | $this->is_setup = true; |
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| 93 | if($this->user === null) $this->user = Auth::user(); |
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| 94 | if(strlen($this->user->getUserId()) == 0) $this->user = self::$default_user; |
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| 95 | |||
| 96 | // Check if the user, or the default user, has a root already setup; |
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| 97 | if(empty($this->getRootIndiId())) { |
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| 98 | if($this->user == self::$default_user) { // If the default user is not setup |
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| 99 | $this->is_setup = false; |
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| 100 | } |
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| 101 | else { |
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| 102 | $this->user = self::$default_user; |
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| 103 | $this->is_setup = $this->getRootIndiId() === null; |
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| 104 | } |
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| 105 | } |
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| 106 | } |
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| 107 | |||
| 108 | /** |
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| 109 | * Returns is the Provider has been successfully set up |
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| 110 | * @return bool |
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| 111 | */ |
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| 112 | public function isSetup() { |
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| 114 | } |
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| 115 | |||
| 116 | /** |
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| 117 | * Return the reference tree |
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| 118 | * |
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| 119 | * @return Tree Reference tree |
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| 120 | */ |
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| 121 | public function getTree() { |
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| 122 | return $this->tree; |
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| 123 | } |
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| 124 | |||
| 125 | /** |
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| 126 | * Return the reference user |
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| 127 | * |
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| 128 | * @return User |
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| 129 | */ |
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| 130 | public function getUser() { |
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| 131 | return $this->user; |
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| 132 | } |
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| 133 | |||
| 134 | /** |
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| 135 | * Return the root individual ID for the reference tree and user. |
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| 136 | * @return string Individual ID |
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| 137 | */ |
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| 138 | public function getRootIndiId() { |
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| 139 | return $this->tree->getUserPreference($this->user, 'MAJ_SOSA_ROOT_ID'); |
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| 140 | } |
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| 141 | |||
| 142 | /** |
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| 143 | * Return the root individual for the reference tree and user. |
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| 144 | * @return Individual Individual |
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| 145 | */ |
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| 146 | public function getRootIndi() { |
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| 147 | $root_indi_id = $this->getRootIndiId(); |
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| 148 | if(!empty($root_indi_id)) { |
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| 149 | return Individual::getInstance($root_indi_id, $this->tree); |
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| 150 | } |
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| 151 | return null; |
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| 152 | } |
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| 153 | |||
| 154 | /***************** |
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| 155 | * DATA CRUD LAYER |
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| 156 | *****************/ |
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| 157 | |||
| 158 | /** |
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| 159 | * Remove all Sosa entries related to the gedcom file and user |
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| 160 | */ |
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| 161 | public function deleteAll() { |
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| 162 | if(!$this->is_setup) return; |
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| 163 | Database::prepare( |
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| 164 | 'DELETE FROM `##maj_sosa`'. |
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| 165 | ' WHERE majs_gedcom_id= :tree_id and majs_user_id = :user_id ') |
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| 166 | ->execute(array( |
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| 167 | 'tree_id' => $this->tree->getTreeId(), |
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| 168 | 'user_id' => $this->user->getUserId() |
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| 169 | )); |
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| 170 | } |
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| 171 | |||
| 172 | /** |
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| 173 | * Remove all ancestors of a sosa number |
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| 174 | * |
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| 175 | * @param int $sosa |
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| 176 | */ |
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| 177 | public function deleteAncestors($sosa) { |
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| 178 | if(!$this->is_setup) return; |
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| 179 | $gen = Functions::getGeneration($sosa); |
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| 180 | Database::prepare( |
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| 181 | 'DELETE FROM `##maj_sosa`'. |
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| 182 | ' WHERE majs_gedcom_id=:tree_id and majs_user_id = :user_id' . |
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| 183 | ' AND majs_gen >= :gen' . |
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| 184 | ' AND FLOOR(majs_sosa / (POW(2, (majs_gen - :gen)))) = :sosa' |
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| 185 | )->execute(array( |
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| 186 | 'tree_id' => $this->tree->getTreeId(), |
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| 187 | 'user_id' => $this->user->getUserId(), |
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| 188 | 'gen' => $gen, |
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| 189 | 'sosa' => $sosa |
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| 190 | )); |
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| 191 | } |
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| 192 | |||
| 193 | /** |
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| 194 | * Insert (or update if already existing) a list of Sosa individuals |
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| 195 | * @param array $sosa_records |
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| 196 | */ |
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| 197 | public function insertOrUpdate($sosa_records) { |
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| 198 | if(!$this->is_setup) return; |
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| 199 | |||
| 200 | $treeid = $this->tree->getTreeId(); |
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| 201 | $userid = $this->user->getUserId(); |
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| 202 | $questionmarks_table = array(); |
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| 203 | $values_table = array(); |
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| 204 | |||
| 205 | $i = 0; |
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| 206 | foreach ($sosa_records as $row) { |
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| 207 | $gen = Functions::getGeneration($row['sosa']); |
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| 208 | if($gen <= self::MAX_DB_GENERATIONS) { |
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| 209 | $questionmarks_table[] = |
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| 210 | '(:tree_id'.$i.', :user_id'.$i.', :sosa'.$i.', :indi_id'.$i.', :gen'.$i.', :byear'.$i.', :byearest'.$i.', :dyear'.$i.', :dyearest'.$i.')'; |
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| 211 | $values_table = array_merge( |
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| 212 | $values_table, |
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| 213 | array( |
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| 214 | 'tree_id'.$i => $treeid, |
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| 215 | 'user_id'.$i => $userid, |
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| 216 | 'sosa'.$i => $row['sosa'], |
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| 217 | 'indi_id'.$i => $row['indi'], |
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| 218 | 'gen'.$i => Functions::getGeneration($row['sosa']), |
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| 219 | 'byear'.$i => $row['birth_year'], |
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| 220 | 'byearest'.$i => $row['birth_year_est'], |
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| 221 | 'dyear'.$i => $row['death_year'], |
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| 222 | 'dyearest'.$i => $row['death_year_est'] |
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| 223 | ) |
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| 224 | ); |
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| 225 | } |
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| 226 | $i++; |
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| 227 | } |
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| 228 | |||
| 229 | $sql = 'REPLACE INTO `##maj_sosa`' . |
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| 230 | ' (majs_gedcom_id, majs_user_id, majs_sosa, majs_i_id, majs_gen, majs_birth_year, majs_birth_year_est, majs_death_year, majs_death_year_est)' . |
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| 231 | ' VALUES '. implode(',', $questionmarks_table); |
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| 232 | Database::prepare($sql)->execute($values_table); |
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| 233 | } |
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| 234 | |||
| 235 | /**************** |
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| 236 | * SIMPLE QUERIES |
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| 237 | ****************/ |
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| 238 | |||
| 239 | /** |
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| 240 | * Returns the list of Sosa numbers to which an individual is related. |
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| 241 | * Format: key = sosa number, value = generation for the Sosa number |
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| 242 | * |
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| 243 | * @param Individual $indi |
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| 244 | * @return array Array of sosa numbers |
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| 245 | */ |
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| 246 | public function getSosaNumbers(Individual $indi) { |
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| 256 | } |
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| 257 | |||
| 258 | /** |
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| 259 | * Get the last generation of Sosa ancestors |
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| 260 | * |
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| 261 | * @return number Last generation if found, 1 otherwise |
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| 262 | */ |
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| 263 | public function getLastGeneration() { |
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| 264 | if(!$this->is_setup) return; |
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| 265 | return Database::prepare( |
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| 266 | 'SELECT MAX(majs_gen) FROM `##maj_sosa`'. |
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| 267 | ' WHERE majs_gedcom_id=:tree_id AND majs_user_id=:user_id' |
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| 268 | )->execute(array( |
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| 269 | 'tree_id' => $this->tree->getTreeId(), |
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| 270 | 'user_id' => $this->user->getUserId() |
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| 271 | ))->fetchOne() ?: 1; |
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| 272 | } |
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| 273 | |||
| 274 | /************* |
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| 275 | * SOSA LISTS |
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| 276 | *************/ |
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| 277 | |||
| 278 | /** |
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| 279 | * Return the list of all sosas, with the generations it belongs to |
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| 280 | * |
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| 281 | * @return array Associative array of Sosa ancestors, with their generation, comma separated |
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| 282 | */ |
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| 283 | public function getAllSosaWithGenerations(){ |
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| 284 | if(!$this->is_setup) return array(); |
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| 285 | return Database::prepare( |
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| 286 | 'SELECT majs_i_id AS indi,' . |
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| 287 | ' GROUP_CONCAT(DISTINCT majs_gen ORDER BY majs_gen ASC SEPARATOR ",") AS generations' . |
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| 288 | ' FROM `##maj_sosa`' . |
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| 289 | ' WHERE majs_gedcom_id=:tree_id AND majs_user_id=:user_id' . |
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| 290 | ' GROUP BY majs_i_id' |
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| 291 | )->execute(array( |
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| 292 | 'tree_id' => $this->tree->getTreeId(), |
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| 293 | 'user_id' => $this->user->getUserId() |
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| 294 | ))->fetchAssoc(); |
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| 295 | } |
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| 296 | |||
| 297 | /** |
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| 298 | * Get an associative array of Sosa individuals in generation G. Keys are Sosa numbers, values individuals. |
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| 299 | * |
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| 300 | * @param number $gen Generation |
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| 301 | * @return array Array of Sosa individuals |
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| 302 | */ |
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| 303 | public function getSosaListAtGeneration($gen){ |
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| 326 | } |
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| 327 | |||
| 328 | /** |
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| 329 | * Get an associative array of Sosa families in generation G. Keys are Sosa numbers for the husband, values families. |
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| 330 | * |
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| 331 | * @param number $gen Generation |
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| 332 | * @return array Array of Sosa families |
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| 333 | */ |
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| 334 | public function getFamilySosaListAtGeneration($gen){ |
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| 335 | if(!$this->is_setup) return array(); |
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| 336 | if(!$this->sosa_fam_list_by_gen) |
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| 337 | $this->sosa_fam_list_by_gen = array(); |
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| 338 | |||
| 339 | if($gen){ |
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| 340 | if(!isset($this->sosa_fam_list_by_gen[$gen])){ |
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| 341 | $this->sosa_fam_list_by_gen[$gen] = Database::prepare( |
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| 342 | 'SELECT s1.majs_sosa AS sosa, f_id AS fam'. |
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| 343 | ' FROM `##families`'. |
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| 344 | ' INNER JOIN `##maj_sosa` AS s1 ON (`##families`.f_husb = s1.majs_i_id AND `##families`.f_file = s1.majs_gedcom_id)'. |
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| 345 | ' INNER JOIN `##maj_sosa` AS s2 ON (`##families`.f_wife = s2.majs_i_id AND `##families`.f_file = s2.majs_gedcom_id)'. |
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| 346 | ' WHERE s1.majs_sosa + 1 = s2.majs_sosa'. |
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| 347 | ' AND s1.majs_gedcom_id= :tree_id AND s1.majs_user_id=:user_id'. |
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| 348 | ' AND s2.majs_gedcom_id= :tree_id AND s2.majs_user_id=:user_id'. |
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| 349 | ' AND s1.majs_gen = :gen'. |
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| 350 | ' ORDER BY s1.majs_sosa ASC' |
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| 351 | ) |
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| 352 | ->execute(array( |
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| 353 | 'tree_id' => $this->tree->getTreeId(), |
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| 354 | 'user_id' => $this->user->getUserId(), |
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| 355 | 'gen' => $gen |
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| 356 | )) |
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| 357 | ->fetchAssoc(); |
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| 358 | } |
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| 359 | return $this->sosa_fam_list_by_gen[$gen]; |
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| 360 | } |
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| 361 | return array(); |
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| 362 | } |
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| 363 | |||
| 364 | /** |
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| 365 | * Get an associative array of Sosa individuals in generation G who are missing parents. Keys are Sosa numbers, values individuals. |
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| 366 | * |
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| 367 | * @param number $gen Generation |
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| 368 | * @return array Array of Sosa individuals |
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| 369 | */ |
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| 370 | public function getMissingSosaListAtGeneration($gen){ |
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| 371 | if(!$this->is_setup) return array(); |
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| 372 | if($gen){ |
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| 373 | return $this->sosa_list_by_gen[$gen] = Database::prepare( |
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| 374 | 'SELECT schild.majs_sosa sosa, schild.majs_i_id indi, sfat.majs_sosa IS NOT NULL has_father, smot.majs_sosa IS NOT NULL has_mother'. |
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| 375 | ' FROM `##maj_sosa` schild'. |
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| 376 | ' LEFT JOIN `##maj_sosa` sfat ON ((schild.majs_sosa * 2) = sfat.majs_sosa AND schild.majs_gedcom_id = sfat.majs_gedcom_id AND schild.majs_user_id = sfat.majs_user_id)'. |
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| 377 | ' LEFT JOIN `##maj_sosa` smot ON ((schild.majs_sosa * 2 + 1) = smot.majs_sosa AND schild.majs_gedcom_id = smot.majs_gedcom_id AND schild.majs_user_id = smot.majs_user_id)'. |
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| 378 | ' WHERE schild.majs_gedcom_id = :tree_id AND schild.majs_user_id = :user_id'. |
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| 379 | ' AND schild.majs_gen = :gen'. |
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| 380 | ' AND (sfat.majs_sosa IS NULL OR smot.majs_sosa IS NULL)'. |
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| 381 | ' ORDER BY schild.majs_sosa ASC') |
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| 382 | ->execute(array( |
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| 383 | 'tree_id' => $this->tree->getTreeId(), |
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| 384 | 'user_id' => $this->user->getUserId(), |
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| 385 | 'gen' => $gen - 1 |
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| 386 | ))->fetchAll(\PDO::FETCH_ASSOC); |
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| 387 | } |
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| 388 | return array(); |
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| 389 | } |
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| 390 | |||
| 391 | |||
| 392 | |||
| 393 | /************* |
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| 394 | * STATISTICS |
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| 395 | *************/ |
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| 396 | /** |
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| 397 | * Get the statistic array detailed by generation. |
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| 398 | * Statistics for each generation are: |
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| 399 | * - The number of Sosa in generation |
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| 400 | * - The number of Sosa up to generation |
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| 401 | * - The number of distinct Sosa up to generation |
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| 402 | * - The year of the first birth in generation |
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| 403 | * - The year of the first estimated birth in generation |
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| 404 | * - The year of the last birth in generation |
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| 405 | * - The year of the last estimated birth in generation |
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| 406 | * - The average year of birth in generation |
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| 407 | * |
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| 408 | * @return array Statistics array |
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| 409 | */ |
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| 410 | public function getStatisticsByGeneration() { |
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| 411 | if(!$this->is_setup) return array(); |
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| 412 | if(!$this->statistics_tab) { |
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| 413 | $this->statistics_tab = array(); |
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| 414 | if($maxGeneration = $this->getLastGeneration()) { |
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| 415 | for ($gen = 1; $gen <= $maxGeneration; $gen++) { |
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| 416 | $birthStats = $this->getStatsBirthYearInGeneration($gen); |
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| 417 | $this->statistics_tab[$gen] = array( |
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| 418 | 'sosaCount' => $this->getSosaCountAtGeneration($gen), |
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| 419 | 'sosaTotalCount' => $this->getSosaCountUpToGeneration($gen), |
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| 420 | 'diffSosaTotalCount' => $this->getDifferentSosaCountUpToGeneration($gen), |
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| 421 | 'firstBirth' => $birthStats['first'], |
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| 422 | 'firstEstimatedBirth' => $birthStats['first_est'], |
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| 423 | 'lastBirth' => $birthStats['last'], |
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| 424 | 'lastEstimatedBirth' => $birthStats['last_est'], |
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| 425 | 'avgBirth' => $birthStats['avg'] |
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| 426 | ); |
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| 427 | } |
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| 428 | } |
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| 429 | } |
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| 430 | return $this->statistics_tab; |
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| 431 | } |
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| 432 | |||
| 433 | /** |
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| 434 | * How many individuals exist in the tree. |
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| 435 | * |
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| 436 | * @return int |
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| 437 | */ |
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| 438 | public function getTotalIndividuals() { |
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| 439 | if(!$this->is_setup) return 0; |
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| 440 | return Database::prepare( |
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| 441 | 'SELECT COUNT(*) FROM `##individuals`' . |
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| 442 | ' WHERE i_file = :tree_id') |
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| 443 | ->execute(array('tree_id' => $this->tree->getTreeId())) |
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| 444 | ->fetchOne() ?: 0; |
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| 445 | } |
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| 446 | |||
| 447 | /** |
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| 448 | * Get the total Sosa count for all generations |
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| 449 | * |
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| 450 | * @return number Number of Sosas |
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| 451 | */ |
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| 452 | public function getSosaCount(){ |
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| 453 | if(!$this->is_setup) return 0; |
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| 454 | return Database::prepare( |
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| 455 | 'SELECT COUNT(majs_sosa) FROM `##maj_sosa`' . |
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| 456 | ' WHERE majs_gedcom_id=:tree_id AND majs_user_id=:user_id') |
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| 457 | ->execute(array( |
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| 458 | 'tree_id' => $this->tree->getTreeId(), |
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| 459 | 'user_id' => $this->user->getUserId() |
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| 460 | ))->fetchOne() ?: 0; |
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| 461 | } |
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| 462 | |||
| 463 | /** |
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| 464 | * Get the number of Sosa in a specific generation. |
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| 465 | * |
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| 466 | * @param number $gen Generation |
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| 467 | * @return number Number of Sosas in generation |
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| 468 | */ |
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| 469 | public function getSosaCountAtGeneration($gen){ |
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| 470 | if(!$this->is_setup) return 0; |
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| 471 | return Database::prepare( |
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| 472 | 'SELECT COUNT(majs_sosa) FROM `##maj_sosa`' . |
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| 473 | ' WHERE majs_gedcom_id=:tree_id AND majs_user_id=:user_id'. |
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| 474 | ' AND majs_gen= :gen') |
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| 475 | ->execute(array( |
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| 476 | 'tree_id' => $this->tree->getTreeId(), |
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| 477 | 'user_id' => $this->user->getUserId(), |
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| 478 | 'gen' => $gen |
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| 479 | ))->fetchOne() ?: 0; |
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| 480 | } |
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| 481 | |||
| 482 | /** |
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| 483 | * Get the total number of Sosa up to a specific generation. |
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| 484 | * |
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| 485 | * @param number $gen Generation |
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| 486 | * @return number Total number of Sosas up to generation |
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| 487 | */ |
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| 488 | public function getSosaCountUpToGeneration($gen){ |
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| 489 | if(!$this->is_setup) return 0; |
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| 490 | return Database::prepare( |
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| 491 | 'SELECT COUNT(majs_sosa) FROM `##maj_sosa`' . |
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| 492 | ' WHERE majs_gedcom_id=:tree_id AND majs_user_id=:user_id'. |
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| 493 | ' AND majs_gen <= :gen') |
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| 494 | ->execute(array( |
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| 495 | 'tree_id' => $this->tree->getTreeId(), |
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| 496 | 'user_id' => $this->user->getUserId(), |
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| 497 | 'gen' => $gen |
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| 498 | ))->fetchOne() ?: 0; |
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| 499 | } |
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| 500 | |||
| 501 | /** |
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| 502 | * Get the total number of distinct Sosa individual for all generations. |
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| 503 | * |
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| 504 | * @return number Total number of distinct individual |
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| 505 | */ |
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| 506 | public function getDifferentSosaCount(){ |
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| 507 | if(!$this->is_setup) return 0; |
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| 508 | return Database::prepare( |
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| 509 | 'SELECT COUNT(DISTINCT majs_i_id) FROM `##maj_sosa`' . |
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| 510 | ' WHERE majs_gedcom_id=:tree_id AND majs_user_id=:user_id') |
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| 511 | ->execute(array( |
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| 512 | 'tree_id' => $this->tree->getTreeId(), |
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| 513 | 'user_id' => $this->user->getUserId() |
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| 514 | ))->fetchOne() ?: 0; |
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| 515 | } |
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| 516 | |||
| 517 | /** |
||
| 518 | * Get the number of distinct Sosa individual up to a specific generation. |
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| 519 | * |
||
| 520 | * @param number $gen Generation |
||
| 521 | * @return number Number of distinct Sosa individuals up to generation |
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| 522 | */ |
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| 523 | public function getDifferentSosaCountUpToGeneration($gen){ |
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| 534 | } |
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| 535 | |||
| 536 | /** |
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| 537 | * Get an array of birth statistics for a specific generation |
||
| 538 | * Statistics are : |
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| 539 | * - first : First birth year in generation |
||
| 540 | * - first_est: First estimated birth year in generation |
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| 541 | * - last : Last birth year in generation |
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| 542 | * - last_est : Last estimated birth year in generation |
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| 543 | * - avg : Average birth year (based on non-estimated birth date) |
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| 544 | * |
||
| 545 | * @param number $gen Generation |
||
| 546 | * @return array Birth statistics array |
||
| 547 | */ |
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| 548 | public function getStatsBirthYearInGeneration($gen){ |
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| 549 | if(!$this->is_setup) return array('first' => 0, 'first_est' => 0, 'avg' => 0, 'last' => 0, 'last_est' => 0); |
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| 550 | return Database::prepare( |
||
| 551 | 'SELECT'. |
||
| 552 | ' MIN(majs_birth_year) AS first, MIN(majs_birth_year_est) AS first_est,'. |
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| 553 | ' AVG(majs_birth_year) AS avg,'. |
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| 554 | ' MAX(majs_birth_year) AS last, MAX(majs_birth_year_est) AS last_est'. |
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| 555 | ' FROM `##maj_sosa`'. |
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| 556 | ' WHERE majs_gedcom_id=:tree_id AND majs_user_id=:user_id'. |
||
| 557 | ' AND majs_gen=:gen') |
||
| 558 | ->execute(array( |
||
| 559 | 'tree_id' => $this->tree->getTreeId(), |
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| 560 | 'user_id' => $this->user->getUserId(), |
||
| 561 | 'gen' => $gen)) |
||
| 562 | ->fetchOneRow(\PDO::FETCH_ASSOC) ?: array('first' => 0, 'first_est' => 0, 'avg' => 0, 'last' => 0, 'last_est' => 0); |
||
| 563 | } |
||
| 564 | |||
| 565 | /** |
||
| 566 | * Get the mean generation time, based on a linear regression of birth years and generations |
||
| 567 | * |
||
| 568 | * @return number|NULL Mean generation time |
||
| 569 | */ |
||
| 570 | public function getMeanGenerationTime(){ |
||
| 571 | if(!$this->is_setup) return; |
||
| 572 | if(!$this->statistics_tab){ |
||
| 573 | $this->getStatisticsByGeneration(); |
||
| 574 | } |
||
| 575 | //Linear regression on x=generation and y=birthdate |
||
| 576 | $sum_xy = 0; |
||
| 577 | $sum_x=0; |
||
| 578 | $sum_y=0; |
||
| 579 | $sum_x2=0; |
||
| 580 | $n=count($this->statistics_tab); |
||
| 581 | foreach($this->statistics_tab as $gen=>$stats){ |
||
| 582 | $sum_xy+=$gen*$stats['avgBirth']; |
||
| 583 | $sum_x+=$gen; |
||
| 584 | $sum_y+=$stats['avgBirth']; |
||
| 585 | $sum_x2+=$gen*$gen; |
||
| 586 | } |
||
| 587 | $denom=($n*$sum_x2)-($sum_x*$sum_x); |
||
| 588 | if($denom!=0){ |
||
| 589 | return -(($n*$sum_xy)-($sum_x*$sum_y))/($denom); |
||
| 590 | } |
||
| 591 | return null; |
||
| 592 | } |
||
| 593 | |||
| 594 | /** |
||
| 595 | * Return an array of the mean generation depth and standard deviation for all Sosa ancestors at a given generation. |
||
| 596 | * Sosa 1 is of generation 1. |
||
| 597 | * |
||
| 598 | * Mean generation depth and deviation are calculated based on the works of Marie-Héléne Cazes and Pierre Cazes, |
||
| 599 | * published in Population (French Edition), Vol. 51, No. 1 (Jan. - Feb., 1996), pp. 117-140 |
||
| 600 | * http://kintip.net/index.php?option=com_jdownloads&task=download.send&id=9&catid=4&m=0 |
||
| 601 | * |
||
| 602 | * Format: |
||
| 603 | * - key : sosa number of the ancestor |
||
| 604 | * - values: array |
||
| 605 | * - root_ancestor_id : ID of the ancestor |
||
| 606 | * - mean_gen_depth : Mean generation depth |
||
| 607 | * - stddev_gen_depth : Standard deviation of generation depth |
||
| 608 | * |
||
| 609 | * @param number $gen Sosa generation |
||
| 610 | * @return array |
||
| 611 | */ |
||
| 612 | public function getGenerationDepthStatsAtGen($gen) { |
||
| 613 | if(!$this->is_setup) return array(); |
||
| 614 | $gen_depth_stats_raw = Database::prepare( |
||
| 615 | 'SELECT stats_by_gen.root_ancestor AS root_ancestor_sosa,'. |
||
| 616 | ' sosa_list.majs_i_id as root_ancestor_id,'. |
||
| 617 | ' 1 + SUM( (majs_gen_norm) * ( 2 * full_root_count + semi_root_count) / (2 * POWER(2, majs_gen_norm))) AS mean_gen_depth,'. |
||
| 618 | ' SQRT('. |
||
| 619 | ' SUM(POWER(majs_gen_norm, 2) * ( 2 * full_root_count + semi_root_count) / (2 * POWER(2, majs_gen_norm)))'. |
||
| 620 | ' - POWER( SUM( (majs_gen_norm) * ( 2 * full_root_count + semi_root_count) / (2 * POWER(2, majs_gen_norm))), 2)'. |
||
| 621 | ' ) AS stddev_gen_depth'. |
||
| 622 | ' FROM('. |
||
| 623 | ' SELECT'. |
||
| 624 | ' sosa.majs_gedcom_id,'. |
||
| 625 | ' sosa.majs_user_id,'. |
||
| 626 | ' sosa.majs_gen - :gen AS majs_gen_norm,'. |
||
| 627 | ' FLOOR(((sosa.majs_sosa / POW(2, sosa.majs_gen -1 )) - 1) * POWER(2, :gen - 1)) + POWER(2, :gen - 1) AS root_ancestor,'. |
||
| 628 | ' SUM(case when sosa_fat.majs_i_id IS NULL AND sosa_mot.majs_i_id IS NULL THEN 1 ELSE 0 END) AS full_root_count,'. |
||
| 629 | ' SUM(case when sosa_fat.majs_i_id IS NULL AND sosa_mot.majs_i_id IS NULL THEN 0 ELSE 1 END) As semi_root_count'. |
||
| 630 | ' FROM `##maj_sosa` AS sosa'. |
||
| 631 | ' LEFT JOIN `##maj_sosa` AS sosa_fat ON sosa_fat.majs_sosa = 2 * sosa.majs_sosa'. |
||
| 632 | ' AND sosa_fat.majs_gedcom_id = sosa.majs_gedcom_id'. |
||
| 633 | ' AND sosa_fat.majs_user_id = sosa.majs_user_id'. |
||
| 634 | ' LEFT JOIN `##maj_sosa` AS sosa_mot ON sosa_mot.majs_sosa = 2 * sosa.majs_sosa + 1'. |
||
| 635 | ' AND sosa_mot.majs_gedcom_id = sosa.majs_gedcom_id'. |
||
| 636 | ' AND sosa_mot.majs_user_id = sosa.majs_user_id'. |
||
| 637 | ' WHERE sosa.majs_gedcom_id = :tree_id'. |
||
| 638 | ' AND sosa.majs_user_id = :user_id'. |
||
| 639 | ' AND sosa.majs_gen >= :gen'. |
||
| 640 | ' AND (sosa_fat.majs_i_id IS NULL OR sosa_mot.majs_i_id IS NULL)'. |
||
| 641 | ' GROUP BY sosa.majs_gen, root_ancestor'. |
||
| 642 | ' ) AS stats_by_gen'. |
||
| 643 | ' INNER JOIN `##maj_sosa` sosa_list ON sosa_list.majs_gedcom_id = stats_by_gen.majs_gedcom_id'. |
||
| 644 | ' AND sosa_list.majs_user_id = stats_by_gen.majs_user_id'. |
||
| 645 | ' AND sosa_list.majs_sosa = stats_by_gen.root_ancestor'. |
||
| 646 | ' GROUP BY stats_by_gen.root_ancestor, sosa_list.majs_i_id'. |
||
| 647 | ' ORDER BY stats_by_gen.root_ancestor') |
||
| 648 | ->execute(array( |
||
| 649 | 'tree_id' => $this->tree->getTreeId(), |
||
| 650 | 'user_id' => $this->user->getUserId(), |
||
| 651 | 'gen' => $gen |
||
| 652 | ))->fetchAll() ?: array(); |
||
| 653 | |||
| 654 | $gen_depth_stats = array(); |
||
| 655 | foreach ($gen_depth_stats_raw as $gen_depth_stat) { |
||
| 656 | $gen_depth_stats[$gen_depth_stat->root_ancestor_sosa] = array( |
||
| 657 | 'root_ancestor_id' => $gen_depth_stat->root_ancestor_id, |
||
| 658 | 'mean_gen_depth' => $gen_depth_stat->mean_gen_depth, |
||
| 659 | 'stddev_gen_depth' => $gen_depth_stat->stddev_gen_depth |
||
| 660 | ); |
||
| 661 | } |
||
| 662 | return $gen_depth_stats; |
||
| 663 | } |
||
| 664 | |||
| 665 | /** |
||
| 666 | * Return a computed array of statistics about the dispersion of ancestors across the ancestors |
||
| 667 | * at a specified generation. |
||
| 668 | * This statistics cannot be used for generations above 11, as it would cause a out of range in MySQL |
||
| 669 | * |
||
| 670 | * Format: |
||
| 671 | * - key : a base-2 representation of the ancestor at generation G for which exclusive ancestors have been found, |
||
| 672 | * -1 is used for shared ancestors |
||
| 673 | * For instance base2(0100) = base10(4) represent the maternal grand father |
||
| 674 | * - values: number of ancestors exclusively in the ancestors of the ancestor in key |
||
| 675 | * |
||
| 676 | * For instance a result at generation 3 could be : |
||
| 677 | * array ( -1 => 12 -> 12 ancestors are shared by the grand-parents |
||
| 678 | * base10(1) => 32 -> 32 ancestors are exclusive to the paternal grand-father |
||
| 679 | * base10(2) => 25 -> 25 ancestors are exclusive to the paternal grand-mother |
||
| 680 | * base10(4) => 12 -> 12 ancestors are exclusive to the maternal grand-father |
||
| 681 | * base10(8) => 30 -> 30 ancestors are exclusive to the maternal grand-mother |
||
| 682 | * ) |
||
| 683 | * |
||
| 684 | * @param int $gen Reference generation |
||
| 685 | * @return array |
||
| 686 | */ |
||
| 687 | public function getAncestorDispersionForGen($gen) { |
||
| 712 | } |
||
| 713 | |||
| 714 | /** |
||
| 715 | * Return an array of the most duplicated root Sosa ancestors. |
||
| 716 | * The number of ancestors to return is limited by the parameter $limit. |
||
| 717 | * If several individuals are tied when reaching the limit, none of them are returned, |
||
| 718 | * which means that there can be less individuals returned than requested. |
||
| 719 | * |
||
| 720 | * Format: |
||
| 721 | * - key : root Sosa individual |
||
| 722 | * - value: number of duplications of the ancestor (e.g. 3 if it appears 3 times) |
||
| 723 | * |
||
| 724 | * @param number $limit Maximum number of individuals to return |
||
| 725 | * @return array |
||
| 726 | */ |
||
| 727 | public function getTopMultiSosaAncestorsNoTies($limit) { |
||
| 765 | } |
||
| 766 | |||
| 767 | |||
| 768 | } |
||
| 769 |
Loading history...
The issue could also be caused by a filter entry in the build configuration. If the path has been excluded in your configuration, e.g.
excluded_paths: ["lib/*"], you can move it to the dependency path list as follows:For further information see https://scrutinizer-ci.com/docs/tools/php/php-scrutinizer/#list-dependency-paths