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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/spotname.vschema @ 3:38ad1130d077 draft

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author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 /*===========================================================================
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2 *
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3 * PUBLIC DOMAIN NOTICE
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4 * National Center for Biotechnology Information
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5 *
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6 * This software/database is a "United States Government Work" under the
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7 * terms of the United States Copyright Act. It was written as part of
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8 * the author's official duties as a United States Government employee and
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9 * thus cannot be copyrighted. This software/database is freely available
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10 * to the public for use. The National Library of Medicine and the U.S.
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11 * Government have not placed any restriction on its use or reproduction.
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12 *
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13 * Although all reasonable efforts have been taken to ensure the accuracy
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14 * and reliability of the software and data, the NLM and the U.S.
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15 * Government do not and cannot warrant the performance or results that
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16 * may be obtained by using this software or data. The NLM and the U.S.
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17 * Government disclaim all warranties, express or implied, including
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18 * warranties of performance, merchantability or fitness for any particular
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19 * purpose.
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20 *
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21 * Please cite the author in any work or product based on this material.
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22 *
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23 * ===========================================================================
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24 *
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25 */
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26
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27 /*==========================================================================
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28 * NCBI Sequence Read Archive schema
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29 */
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30 version 1;
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31
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32 include 'vdb/vdb.vschema';
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33 include 'insdc/sra.vschema';
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34
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35
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36 /*--------------------------------------------------------------------------
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37 * types
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38 */
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39
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40 /* spot_name_token
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41 * a vector describing tokens recognized within a spot name
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42 *
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43 * COMPONENTS:
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44 * 0 - token id
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45 * 1 - token starting coordinate
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46 * 2 - token length
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47 */
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48 alias text:token NCBI:SRA:spot_name_token;
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49
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50
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51 /* token values
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52 *
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53 * tokens are produced by a schema-specific tokenizer function
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54 * this function is purposely abstract because it may rely upon
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55 * whatever information it needs to perform its task. the only
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56 * requirement is that it produce these tokens as its output.
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57 *
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58 * an empty name input must produce no tokens. in this case,
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59 * there is no name to tokenize or data to produce.
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60 *
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61 * a non-empty name must produce 1 or more tokens of output.
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62 * all tokens must be ordered by starting character position.
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63 *
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64 * if a name does not conform to any pattern recognized by the
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65 * tokenizer, then the tokenizer emits a single token of "unrecognized"
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66 *
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67 * if a name conforms to some pattern but does not have any
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68 * substitution tokens, the tokenizer emits a single token of "recognized"
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69 *
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70 * if a name may be tokenized, then the resulting tokens should
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71 * describe only the portions of the string that should be removed
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72 * from the name, e.g. "X" or "Y".
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73 *
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74 * the standard coordinates "X".."L" are given in unsigned decimal.
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75 * alternate representations are contained within their respective
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76 * namespaces: "signed", "hex" and "octal".
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77 *
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78 * the special coordinate "Q" represents the 454-specific encoding
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79 * of X and Y into base-36, where the formula for Q is:
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80 * Q = 4096 * X + Y
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81 * and ASCII encoding:
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82 * 0..25 => "A-Z", 26..35 => "0-9"
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83 */
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84 const U16 NCBI:SRA:name_token:unrecognized = 1;
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85 const U16 NCBI:SRA:name_token:recognized = 2;
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86 const U16 NCBI:SRA:name_token:Q = 3;
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87 const U16 NCBI:SRA:name_token:X = 4;
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88 const U16 NCBI:SRA:name_token:Y = 5;
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89 const U16 NCBI:SRA:name_token:T = 6;
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90 const U16 NCBI:SRA:name_token:L = 7;
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91 const U16 NCBI:SRA:name_token:signed:X = 8;
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92 const U16 NCBI:SRA:name_token:signed:Y = 9;
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93 const U16 NCBI:SRA:name_token:signed:T = 10;
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94 const U16 NCBI:SRA:name_token:signed:L = 11;
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95 const U16 NCBI:SRA:name_token:octal:X = 12;
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96 const U16 NCBI:SRA:name_token:octal:Y = 13;
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97 const U16 NCBI:SRA:name_token:octal:T = 14;
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98 const U16 NCBI:SRA:name_token:octal:L = 15;
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99 const U16 NCBI:SRA:name_token:hex:upper:X = 16;
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100 const U16 NCBI:SRA:name_token:hex:upper:Y = 17;
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101 const U16 NCBI:SRA:name_token:hex:upper:T = 18;
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102 const U16 NCBI:SRA:name_token:hex:upper:L = 19;
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103 const U16 NCBI:SRA:name_token:hex:lower:X = 20;
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104 const U16 NCBI:SRA:name_token:hex:lower:Y = 21;
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105 const U16 NCBI:SRA:name_token:hex:lower:T = 22;
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106 const U16 NCBI:SRA:name_token:hex:lower:L = 23;
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107
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108
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109 /* token symbols
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110 * when a name matches some pattern and tokens are recognized,
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111 * the tokens are extracted from the name and sent to individual
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112 * columns, and replaced with the symbols below to create a
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113 * formatted name.
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114 */
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115 const ascii NCBI:SRA:name_symbol:Q = '$Q';
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116 const ascii NCBI:SRA:name_symbol:X = '$X';
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117 const ascii NCBI:SRA:name_symbol:Y = '$Y';
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118 const ascii NCBI:SRA:name_symbol:T = '$T';
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119 const ascii NCBI:SRA:name_symbol:L = '$L';
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120 const ascii NCBI:SRA:name_symbol:octal:X = '$a';
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121 const ascii NCBI:SRA:name_symbol:octal:Y = '$b';
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122 const ascii NCBI:SRA:name_symbol:octal:T = '$c';
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123 const ascii NCBI:SRA:name_symbol:octal:L = '$d';
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124 const ascii NCBI:SRA:name_symbol:hex:upper:X = '$e';
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125 const ascii NCBI:SRA:name_symbol:hex:upper:Y = '$f';
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126 const ascii NCBI:SRA:name_symbol:hex:upper:T = '$g';
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127 const ascii NCBI:SRA:name_symbol:hex:upper:L = '$h';
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128 const ascii NCBI:SRA:name_symbol:hex:lower:X = '$x';
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129 const ascii NCBI:SRA:name_symbol:hex:lower:Y = '$y';
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130 const ascii NCBI:SRA:name_symbol:hex:lower:T = '$t';
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131 const ascii NCBI:SRA:name_symbol:hex:lower:L = '$l';
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132
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133
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134 /*--------------------------------------------------------------------------
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135 * functions
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136 */
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137
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138 /* extract_spot_name
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139 * generates input to .SPOT_NAME column
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140 *
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141 * on NCBI:SRA:name_token:unrecognized, produces the entire spot name row
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142 * otherwise, produces an empty row
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143 *
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144 * "name" [ DATA ] - raw spot names from NAME column
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145 *
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146 * "tok" [ DATA ] - delimiting tokens produced by sub-table
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147 */
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148 function ascii
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149 NCBI:SRA:extract_spot_name #1 ( ascii name, NCBI:SRA:spot_name_token tok );
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150
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151
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152 /* extract_name_fmt
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153 * generates input to .NAME_FMT column and/or updates skey index
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154 *
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155 * on NCBI:SRA:name_token:unrecognized, produces an empty row
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156 * otherwise, it creates a temporary "name_fmt" string from name row
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157 *
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158 * an attempt is made to insert name_fmt into indicated text index
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159 * ( normally 'skey' ). if the insert succeeds, i.e. associates "name_fmt"
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160 * with a row_id, then the output for the row is empty.
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161 *
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162 * if the insert fails due to key duplication, an attempt is made to
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163 * extend the id range of associated rows. depending upon the type of index,
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164 * this may succeed or fail, e.g. if the existing row range for "name_fmt" is
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165 * n..m where m = row_id - 1, the range can be extended to n..row_id and
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166 * the update succeeds. if the index supports discontiguous id ranges, the
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167 * update will also succeed. upon any success updating the index, the output
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168 * row will be empty.
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169 *
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170 * finally, if the temporary "name_fmt" cannot be inserted into the index
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171 * nor the existing id range updated, the output for the row will be "name_fmt".
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172 *
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173 * "name" [ DATA ] - raw spot names from NAME column
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174 *
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175 * "tok" [ DATA ] - delimiting tokens produced by sub-table
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176 */
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177 function ascii
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178 NCBI:SRA:extract_name_fmt #1 < ascii idx > ( ascii name, NCBI:SRA:spot_name_token tok );
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179
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180
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181 /* extract_name_coord
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182 * generates inputs to .X and .Y and possibly other columns
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183 *
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184 * if no tokens match "coord"constant, produces an empty row
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185 * otherwise, produces binary coordinate value
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186 * if multiple tokens match criteria, all values must be equivalent
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187 * because only a single value will be output per row
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188 *
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189 * "coord" [ CONST ] - either NCBI:SRA:name_token:X or NCBI:SRA:name_token:Y
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190 * both of these values also match the token NCBI:SRA:name_token:Q and extract
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191 * contents appropriately.
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192 *
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193 * "name" [ DATA ] - raw spot names from NAME column
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194 *
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195 * "tok" [ DATA ] - delimiting tokens produced by sub-table
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196 */
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197 function INSDC:coord:val
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198 NCBI:SRA:extract_name_coord #1 < U16 coord > ( ascii name, NCBI:SRA:spot_name_token tok );
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199
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200
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201 /* lookup
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202 */
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203 function INSDC:SRA:spot_ids_found NCBI:SRA:lookup #1.0
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204 < ascii index_name, ascii query_by_name, U8 name_fmt_version > ( * ascii name_prefix );
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205
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206
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207 /*--------------------------------------------------------------------------
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208 * spotcoord
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209 * spot coordinate table implementation
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210 */
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211 table NCBI:SRA:tbl:spotcoord #1 = INSDC:SRA:tbl:spotcoord #1
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212 {
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213 // X and Y stored as I32
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214 INSDC:coord:val out_x_coord = .X;
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215 INSDC:coord:val out_y_coord = .Y;
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216
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217 // T and L are usually present but optional
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218 INSDC:coord:val out_t_coord = .T;
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219 INSDC:coord:val out_l_coord = .L;
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220
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221 // .X, .Y, .T and .L get either empty coordinate or proper coordinate
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222 physical column < INSDC:coord:val > izip_encoding .X
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223 = in_x_coord
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224 | in_name_x_coord;
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225 physical column < INSDC:coord:val > izip_encoding .Y
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226 = in_y_coord
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227 | in_name_y_coord;
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228 physical column < INSDC:coord:val > izip_encoding .T
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229 = in_t_coord
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230 | in_name_t_coord;
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231 physical column < INSDC:coord:val > izip_encoding .L
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232 = in_l_coord
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233 | in_name_l_coord;
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234 };
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235
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236
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237 /*--------------------------------------------------------------------------
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238 * skeyname
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239 * spot name table implementation built upon prefix-tree skey index
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240 *
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241 * v1 - maintains a 1->1 key=>spot_id relationship
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242 * with unique constraint on key. it does NOT
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243 * implement name_fmt or x_coord or y_coord.
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244 *
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245 * v2 - maintains a 1->1 key=>spot_id-range relationship
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246 * with unique constraint on key. it does NOT
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247 * implement spot_name. X and Y are stored using
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248 * 16-bit unsigned quantities.
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249 *
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250 * v3 - maintains a flexible naming approach
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251 * retrieves name directly from column if so stored
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252 * synthesizes name from name_fmt, X and Y otherwise
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253 * name_fmt is either retrieved directly from column
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254 * or from skey index. X and Y are stored as 32-bit
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255 * signed quantities.
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256 *
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257 * history:
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258 * 1.0.1 - explicitly account for spotname #1.0.1 ancestry
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259 * 2.0.1 - " "
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260 * 3.0.1 - moved .X and .Y to spotcoord table
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261 */
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262 table NCBI:SRA:tbl:skeyname #1.0.1 = INSDC:SRA:tbl:spotname #1.0.1
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263 {
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264 // read the skey entry
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265 ascii out_skey = ( ascii ) idx:text:project #1.0 < 'skey' > ();
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266
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267 // spot_name
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268 ascii out_spot_name
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269 = rewritten_spot_name
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270 | out_skey;
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271
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272 // search skey entry
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273 INSDC:SRA:spot_ids_found spot_ids_found
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274 = ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 1 > ( out_slx_prefix )
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275 | ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 0 > ();
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276
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277
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278 /* INSDC:SRA:tbl:spotname inherited productions
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279 * out_x_coord
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280 * out_y_coord
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281 * out_name_fmt
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282 */
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283
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284 /* NCBI:SRA:tbl:skeyname productions
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285 * out_slx_prefix
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286 * rewritten_spot_name
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287 */
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288 };
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289
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290 table NCBI:SRA:tbl:skeyname_nocol #2.0.1 = INSDC:SRA:tbl:spotname #1.0.1
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291 {
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292 // name_fmt
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293 // perform reverse lookup through index to get key
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294 ascii out_name_fmt = ( ascii ) idx:text:project #1.0 < 'skey' > ();
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295
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296 // search skey entry
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297 INSDC:SRA:spot_ids_found spot_ids_found
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298 = ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 2 > ( out_slx_prefix )
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299 | ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 2 > ();
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300
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301 // X and Y stored as U16
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302 INSDC:coord:val out_x_coord = cast ( .X );
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303 INSDC:coord:val out_y_coord = cast ( .Y );
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304
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305
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306 /* NCBI:SRA:tbl:skeyname_nocol virtual productions
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307 * out_slx_prefix
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308 */
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309 };
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310
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311 table NCBI:SRA:tbl:skeyname #2.0.1 = NCBI:SRA:tbl:skeyname_nocol #2.0.1
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312 {
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313 // spot_name_tok comes from a platform-specific tokenizer
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314 // and must be of type 'NCBI:SRA:spot_name_token'
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315 physical column < INSDC:coord:val > izip_encoding #1 .X
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316 = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:X > ( NAME, in_spot_name_tok );
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317 physical column < INSDC:coord:val > izip_encoding .Y
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318 = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:Y > ( NAME, in_spot_name_tok );
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319
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320 /* NCBI:SRA:tbl:skeyname_nocol inherited virtual productions
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321 * out_slx_prefix
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322 */
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323
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324 /* NCBI:SRA:tbl:skeyname virtual productions
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325 * in_spot_name_tok
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326 */
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327 };
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328
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329 table NCBI:SRA:tbl:skeyname #3.0.1 = INSDC:SRA:tbl:spotname #1.0.1, NCBI:SRA:tbl:spotcoord #1
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330 {
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331 // spot_name
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332 // retrieve from hard column
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333 ascii out_spot_name = .SPOT_NAME;
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334
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335 // name_fmt
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336 // retrieve from hard column or reverse lookup through index
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337 ascii out_name_fmt = ( ascii ) idx:text:project #1.0 < 'skey' > ( .NAME_FMT );
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338
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339 INSDC:SRA:spot_ids_found spot_ids_found
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340 = ( INSDC:SRA:spot_ids_found ) NCBI:SRA:lookup #1 < 'skey' , 'QUERY_BY_NAME', 2 > ();
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341
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342
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343 /* encoding rules
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344 * the sub-table will provide a platform-specific parser that
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345 * produces as its output a series of NCBI:SRA:spot_name_token
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346 * for each input row in the virtual production "spot_name_tok"
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347 *
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348 * the tokenizer will look for X, Y or Q (combined) coordinates
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349 * within the spot name and issue tokens when found, or in the
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350 * case that none are found, an "unrecognized" token is issued.
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351 *
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352 * the tokens are then processed here by common rules
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353 */
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354
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355 // .SPOT_NAME gets either empty strings or unrecognized strings
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356 physical column < ascii > zip_encoding .SPOT_NAME
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357 = NCBI:SRA:extract_spot_name ( NAME, in_spot_name_tok );
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358
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359 // .NAME_FMT gets either empty strings or unindexed but recognized strings
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360 physical column < ascii > zip_encoding .NAME_FMT
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361 = NCBI:SRA:extract_name_fmt < 'skey' > ( NAME, in_spot_name_tok );
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362
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363 // .X, .Y, .T and .L get either empty coordinate or proper coordinate
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364 INSDC:coord:val in_name_x_coord
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365 = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:X > ( NAME, in_spot_name_tok );
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366 INSDC:coord:val in_name_y_coord
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367 = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:Y > ( NAME, in_spot_name_tok );
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368 INSDC:coord:val in_name_t_coord
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369 = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:T > ( NAME, in_spot_name_tok );
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370 INSDC:coord:val in_name_l_coord
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371 = NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:L > ( NAME, in_spot_name_tok );
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372
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373
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374 /* NCBI:SRA:tbl:skeyname virtual productions
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375 * in_spot_name_tok
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376 */
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377 };