MARQ 0.0.1
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- data/LICENSE +20 -0
- data/R/CustomDS.R +80 -0
- data/R/GEO.R +249 -0
- data/R/MA.R +359 -0
- data/README.rdoc +29 -0
- data/bin/marq_config +170 -0
- data/install_scripts/CustomDS/Rakefile +223 -0
- data/install_scripts/GEO/Rakefile +258 -0
- data/install_scripts/GEO/platforms/GPL100.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1002.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1007.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL101.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1010.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1073.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1074.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1090.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1104.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL118.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1205.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1211.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1213.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1219.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1223.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1226.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1229.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1230.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1231.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1232.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1260.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1261.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL127.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL128.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1290.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1292.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1293.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1294.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1295.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL13.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1310.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1313.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1323.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1331.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1352.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1355.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1382.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1387.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1397.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL14.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1412.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1415.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1420.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL144.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1449.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1458.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1523.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1524.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1528.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL153.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1530.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1535.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL155.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL163.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL168.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL169.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1704.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1708.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1739.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1740.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1749.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL177.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1790.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1792.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL181.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1818.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1820.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1823.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1826.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL183.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1831.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1833.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1872.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1911.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1914.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1928.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1942.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1945.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL1964.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL198.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL1981.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL200.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2006.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL201.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2011.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2026.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL205.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL207.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2136.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL220.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL226.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL24.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL246.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL247.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2507.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2529.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2531.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL254.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2569.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL257.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2598.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL260.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2614.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2622.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2623.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2660.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2670.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2677.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2700.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2721.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2727.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL273.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2763.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2824.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL284.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL287.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2872.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL288.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2883.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL289.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2895.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2897.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2902.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL2987.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL2995.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3039.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3050.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3084.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3113.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL317.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL319.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL32.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3222.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3295.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3305.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3306.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3307.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL333.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3341.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3349.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL339.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL340.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3408.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL341.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3415.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3423.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3440.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3457.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3504.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3506.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL355.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3558.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3607.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL368.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL3695.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL371.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL3834.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL4006.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL4055.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL409.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL4191.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL4226.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL4371.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL4567.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL4685.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL483.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL49.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL50.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL500.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL507.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL51.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL513.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL519.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL52.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL529.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL53.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL5356.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL538.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL54.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL543.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL544.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL545.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL546.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL547.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL549.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL550.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL56.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL560.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL564.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL57.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL570.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL571.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL576.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL58.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL5823.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL59.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL5915.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL5947.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL61.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL64.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL6419.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL6424.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL65.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL6574.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL6649.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL67.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL6720.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL7054.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL737.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL738.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL74.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL75.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL76.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL764.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL772.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL782.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL783.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL784.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL80.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL81.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL82.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL83.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL85.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL86.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL87.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL870.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL875.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL884.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL887.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL89.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL890.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL891.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL90.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL91.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL92.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL920.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL922.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL924.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL93.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL96.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL968.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL97.yaml +4 -0
- data/install_scripts/GEO/platforms/GPL98.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL981.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL99.yaml +7 -0
- data/install_scripts/GEO/platforms/GPL999.yaml +7 -0
- data/install_scripts/GEO/series/GSE10018.yaml +61 -0
- data/install_scripts/GEO/series/GSE1002.yaml +135 -0
- data/install_scripts/GEO/series/GSE10066.yaml +31 -0
- data/install_scripts/GEO/series/GSE10073.yaml +19 -0
- data/install_scripts/GEO/series/GSE10091.yaml +15 -0
- data/install_scripts/GEO/series/GSE101.yaml +17 -0
- data/install_scripts/GEO/series/GSE10100.yaml +15 -0
- data/install_scripts/GEO/series/GSE10101.yaml +15 -0
- data/install_scripts/GEO/series/GSE10102.yaml +15 -0
- data/install_scripts/GEO/series/GSE10267.yaml +37 -0
- data/install_scripts/GEO/series/GSE10268.yaml +115 -0
- data/install_scripts/GEO/series/GSE10279.yaml +23 -0
- data/install_scripts/GEO/series/GSE103.yaml +19 -0
- data/install_scripts/GEO/series/GSE104.yaml +19 -0
- data/install_scripts/GEO/series/GSE10514.yaml +27 -0
- data/install_scripts/GEO/series/GSE10521.yaml +56 -0
- data/install_scripts/GEO/series/GSE10554.yaml +19 -0
- data/install_scripts/GEO/series/GSE1073.yaml +127 -0
- data/install_scripts/GEO/series/GSE10860.yaml +25 -0
- data/install_scripts/GEO/series/GSE10930.yaml +15 -0
- data/install_scripts/GEO/series/GSE10933.yaml +15 -0
- data/install_scripts/GEO/series/GSE10944.yaml +21 -0
- data/install_scripts/GEO/series/GSE10947.yaml +21 -0
- data/install_scripts/GEO/series/GSE10948.yaml +21 -0
- data/install_scripts/GEO/series/GSE11061.yaml +19 -0
- data/install_scripts/GEO/series/GSE11071.yaml +67 -0
- data/install_scripts/GEO/series/GSE11111.yaml +25 -0
- data/install_scripts/GEO/series/GSE11236.yaml +25 -0
- data/install_scripts/GEO/series/GSE11282.yaml +19 -0
- data/install_scripts/GEO/series/GSE11377.yaml +19 -0
- data/install_scripts/GEO/series/GSE11380.yaml +13 -0
- data/install_scripts/GEO/series/GSE11397.yaml +55 -0
- data/install_scripts/GEO/series/GSE11412.yaml +11 -0
- data/install_scripts/GEO/series/GSE11452.yaml +354 -0
- data/install_scripts/GEO/series/GSE11620.yaml +33 -0
- data/install_scripts/GEO/series/GSE11621.yaml +31 -0
- data/install_scripts/GEO/series/GSE11651.yaml +94 -0
- data/install_scripts/GEO/series/GSE11754.yaml +29 -0
- data/install_scripts/GEO/series/GSE11799.yaml +59 -0
- data/install_scripts/GEO/series/GSE11856.yaml +11 -0
- data/install_scripts/GEO/series/GSE11878.yaml +19 -0
- data/install_scripts/GEO/series/GSE11983.yaml +15 -0
- data/install_scripts/GEO/series/GSE12004.yaml +41 -0
- data/install_scripts/GEO/series/GSE12055.yaml +109 -0
- data/install_scripts/GEO/series/GSE12061.yaml +13 -0
- data/install_scripts/GEO/series/GSE12104.yaml +10 -0
- data/install_scripts/GEO/series/GSE12138.yaml +13 -0
- data/install_scripts/GEO/series/GSE12150.yaml +32 -0
- data/install_scripts/GEO/series/GSE12684.yaml +47 -0
- data/install_scripts/GEO/series/GSE12685.yaml +34 -0
- data/install_scripts/GEO/series/GSE1365.yaml +14 -0
- data/install_scripts/GEO/series/GSE1404.yaml +596 -0
- data/install_scripts/GEO/series/GSE1492.yaml +15 -0
- data/install_scripts/GEO/series/GSE15222.yaml +731 -0
- data/install_scripts/GEO/series/GSE1553.yaml +23 -0
- data/install_scripts/GEO/series/GSE1617.yaml +39 -0
- data/install_scripts/GEO/series/GSE1688.yaml +36 -0
- data/install_scripts/GEO/series/GSE1693.yaml +60 -0
- data/install_scripts/GEO/series/GSE1752.yaml +32 -0
- data/install_scripts/GEO/series/GSE1753.yaml +16 -0
- data/install_scripts/GEO/series/GSE1754.yaml +19 -0
- data/install_scripts/GEO/series/GSE1758.yaml +15 -0
- data/install_scripts/GEO/series/GSE1759.yaml +18 -0
- data/install_scripts/GEO/series/GSE1760.yaml +18 -0
- data/install_scripts/GEO/series/GSE1763.yaml +19 -0
- data/install_scripts/GEO/series/GSE1915.yaml +39 -0
- data/install_scripts/GEO/series/GSE1927.yaml +14 -0
- data/install_scripts/GEO/series/GSE1941.yaml +23 -0
- data/install_scripts/GEO/series/GSE1942.yaml +31 -0
- data/install_scripts/GEO/series/GSE1944.yaml +58 -0
- data/install_scripts/GEO/series/GSE1975.yaml +65 -0
- data/install_scripts/GEO/series/GSE20.yaml +24 -0
- data/install_scripts/GEO/series/GSE2107.yaml +14 -0
- data/install_scripts/GEO/series/GSE2159.yaml +31 -0
- data/install_scripts/GEO/series/GSE2246.yaml +157 -0
- data/install_scripts/GEO/series/GSE2263.yaml +57 -0
- data/install_scripts/GEO/series/GSE2267.yaml +155 -0
- data/install_scripts/GEO/series/GSE23.yaml +58 -0
- data/install_scripts/GEO/series/GSE2329.yaml +43 -0
- data/install_scripts/GEO/series/GSE2330.yaml +55 -0
- data/install_scripts/GEO/series/GSE2349.yaml +19 -0
- data/install_scripts/GEO/series/GSE2412.yaml +58 -0
- data/install_scripts/GEO/series/GSE2419.yaml +27 -0
- data/install_scripts/GEO/series/GSE2420.yaml +29 -0
- data/install_scripts/GEO/series/GSE2434.yaml +37 -0
- data/install_scripts/GEO/series/GSE2526.yaml +23 -0
- data/install_scripts/GEO/series/GSE2579.yaml +19 -0
- data/install_scripts/GEO/series/GSE2806.yaml +11 -0
- data/install_scripts/GEO/series/GSE2831.yaml +35 -0
- data/install_scripts/GEO/series/GSE2832.yaml +17 -0
- data/install_scripts/GEO/series/GSE29.yaml +16 -0
- data/install_scripts/GEO/series/GSE3006.yaml +35 -0
- data/install_scripts/GEO/series/GSE3043.yaml +18 -0
- data/install_scripts/GEO/series/GSE3122.yaml +12 -0
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- metadata +798 -0
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def AllReferences.[](name)
|
70
|
+
@@refs[name]
|
71
|
+
end
|
72
|
+
|
73
|
+
def AllReferences.keys
|
74
|
+
@@refs.keys
|
75
|
+
end
|
76
|
+
end
|
77
|
+
|
78
|
+
|
79
|
+
##
|
80
|
+
# Subclass of the SM::ToHtml class that supports looking
|
81
|
+
# up words in the AllReferences list. Those that are
|
82
|
+
# found (like AllReferences in this comment) will
|
83
|
+
# be hyperlinked
|
84
|
+
|
85
|
+
class HyperlinkHtml < SM::ToHtml
|
86
|
+
# We need to record the html path of our caller so we can generate
|
87
|
+
# correct relative paths for any hyperlinks that we find
|
88
|
+
def initialize(from_path, context)
|
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|
+
super()
|
90
|
+
@from_path = from_path
|
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|
+
|
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|
+
@parent_name = context.parent_name
|
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|
+
@parent_name += "::" if @parent_name
|
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|
+
@context = context
|
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|
+
end
|
96
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+
|
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|
+
# We're invoked when any text matches the CROSSREF pattern
|
98
|
+
# (defined in MarkUp). If we fine the corresponding reference,
|
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|
+
# generate a hyperlink. If the name we're looking for contains
|
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|
+
# no punctuation, we look for it up the module/class chain. For
|
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|
+
# example, HyperlinkHtml is found, even without the Generators::
|
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|
+
# prefix, because we look for it in module Generators first.
|
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|
+
|
104
|
+
def handle_special_CROSSREF(special)
|
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|
+
name = special.text
|
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|
+
if name[0,1] == '#'
|
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|
+
lookup = name[1..-1]
|
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|
+
name = lookup unless Options.instance.show_hash
|
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|
+
else
|
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|
+
lookup = name
|
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|
+
end
|
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|
+
|
113
|
+
if /([A-Z].*)[.\#](.*)/ =~ lookup
|
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|
+
container = $1
|
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+
method = $2
|
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|
+
ref = @context.find_symbol(container, method)
|
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|
+
else
|
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|
+
ref = @context.find_symbol(lookup)
|
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|
+
end
|
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|
+
|
121
|
+
if ref and ref.document_self
|
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|
+
"<a href=\"index.html?a=#{ref.aref}&name=#{name}\">#{name}</a>"
|
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|
+
else
|
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|
+
name #it does not need to be a link
|
125
|
+
end
|
126
|
+
end
|
127
|
+
|
128
|
+
|
129
|
+
# Generate a hyperlink for url, labeled with text. Handle the
|
130
|
+
# special cases for img: and link: described under handle_special_HYPEDLINK
|
131
|
+
def gen_url(url, text)
|
132
|
+
if url =~ /([A-Za-z]+):(.*)/
|
133
|
+
type = $1
|
134
|
+
path = $2
|
135
|
+
else
|
136
|
+
type = "http"
|
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|
+
path = url
|
138
|
+
url = "http://#{url}"
|
139
|
+
end
|
140
|
+
|
141
|
+
if type == "link"
|
142
|
+
url = path
|
143
|
+
end
|
144
|
+
|
145
|
+
if (type == "http" || type == "link") && url =~ /\.(gif|png|jpg|jpeg|bmp)$/
|
146
|
+
"<img src=\"#{url}\">"
|
147
|
+
elsif (type == "http" || type == "link")
|
148
|
+
"<a href=\"#{url}\" target=\"_blank\">#{text}</a>"
|
149
|
+
else
|
150
|
+
"<a href=\"#\" onclick=\"jsHref('#{url}');\">#{text.sub(%r{^#{type}:/*}, '')}</a>"
|
151
|
+
|
152
|
+
end
|
153
|
+
end
|
154
|
+
|
155
|
+
# And we're invoked with a potential external hyperlink mailto:
|
156
|
+
# just gets inserted. http: links are checked to see if they
|
157
|
+
# reference an image. If so, that image gets inserted using an
|
158
|
+
# <img> tag. Otherwise a conventional <a href> is used. We also
|
159
|
+
# support a special type of hyperlink, link:, which is a reference
|
160
|
+
# to a local file whose path is relative to the --op directory.
|
161
|
+
|
162
|
+
def handle_special_HYPERLINK(special)
|
163
|
+
url = special.text
|
164
|
+
gen_url(url, url)
|
165
|
+
end
|
166
|
+
|
167
|
+
# HEre's a hypedlink where the label is different to the URL
|
168
|
+
# <label>[url]
|
169
|
+
#
|
170
|
+
|
171
|
+
def handle_special_TIDYLINK(special)
|
172
|
+
text = special.text
|
173
|
+
# unless text =~ /(\S+)\[(.*?)\]/
|
174
|
+
unless text =~ /\{(.*?)\}\[(.*?)\]/ or text =~ /(\S+)\[(.*?)\]/
|
175
|
+
return text
|
176
|
+
end
|
177
|
+
label = $1
|
178
|
+
url = $2
|
179
|
+
gen_url(url, label)
|
180
|
+
end
|
181
|
+
|
182
|
+
end
|
183
|
+
|
184
|
+
|
185
|
+
|
186
|
+
#####################################################################
|
187
|
+
#
|
188
|
+
# Handle common markup tasks for the various Html classes
|
189
|
+
#
|
190
|
+
|
191
|
+
module MarkUp
|
192
|
+
|
193
|
+
# Convert a string in markup format into HTML. We keep a cached
|
194
|
+
# SimpleMarkup object lying around after the first time we're
|
195
|
+
# called per object.
|
196
|
+
|
197
|
+
def markup(str, remove_para=false)
|
198
|
+
return '' unless str
|
199
|
+
unless defined? @markup
|
200
|
+
@markup = SM::SimpleMarkup.new
|
201
|
+
|
202
|
+
# class names, variable names, file names, or instance variables
|
203
|
+
@markup.add_special(/(
|
204
|
+
\b([A-Z]\w*(::\w+)*[.\#]\w+) # A::B.meth
|
205
|
+
| \b([A-Z]\w+(::\w+)*) # A::B..
|
206
|
+
| \#\w+[!?=]? # #meth_name
|
207
|
+
| \b\w+([_\/\.]+\w+)+[!?=]? # meth_name
|
208
|
+
)/x, :CROSSREF)
|
209
|
+
|
210
|
+
# external hyperlinks
|
211
|
+
@markup.add_special(/((link:|https?:|mailto:|ftp:|www\.)\S+\w)/, :HYPERLINK)
|
212
|
+
|
213
|
+
# and links of the form <text>[<url>]
|
214
|
+
@markup.add_special(/(((\{.*?\})|\b\S+?)\[\S+?\.\S+?\])/, :TIDYLINK)
|
215
|
+
# @markup.add_special(/\b(\S+?\[\S+?\.\S+?\])/, :TIDYLINK)
|
216
|
+
|
217
|
+
end
|
218
|
+
unless defined? @html_formatter
|
219
|
+
@html_formatter = HyperlinkHtml.new(self.path, self)
|
220
|
+
end
|
221
|
+
|
222
|
+
# Convert leading comment markers to spaces, but only
|
223
|
+
# if all non-blank lines have them
|
224
|
+
|
225
|
+
if str =~ /^(?>\s*)[^\#]/
|
226
|
+
content = str
|
227
|
+
else
|
228
|
+
content = str.gsub(/^\s*(#+)/) { $1.tr('#',' ') }
|
229
|
+
end
|
230
|
+
|
231
|
+
res = @markup.convert(content, @html_formatter)
|
232
|
+
if remove_para
|
233
|
+
res.sub!(/^<p>/, '')
|
234
|
+
res.sub!(/<\/p>$/, '')
|
235
|
+
end
|
236
|
+
res
|
237
|
+
end
|
238
|
+
|
239
|
+
|
240
|
+
def style_url(path, css_name=nil)
|
241
|
+
css_name ||= CSS_NAME
|
242
|
+
end
|
243
|
+
|
244
|
+
# Build a webcvs URL with the given 'url' argument. URLs with a '%s' in them
|
245
|
+
# get the file's path sprintfed into them; otherwise they're just catenated
|
246
|
+
# together.
|
247
|
+
|
248
|
+
def cvs_url(url, full_path)
|
249
|
+
if /%s/ =~ url
|
250
|
+
return sprintf( url, full_path )
|
251
|
+
else
|
252
|
+
return url + full_path
|
253
|
+
end
|
254
|
+
end
|
255
|
+
end
|
256
|
+
|
257
|
+
|
258
|
+
#####################################################################
|
259
|
+
#
|
260
|
+
# A Context is built by the parser to represent a container: contexts
|
261
|
+
# hold classes, modules, methods, require lists and include lists.
|
262
|
+
# ClassModule and TopLevel are the context objects we process here
|
263
|
+
#
|
264
|
+
class ContextUser
|
265
|
+
|
266
|
+
include MarkUp
|
267
|
+
|
268
|
+
attr_reader :context
|
269
|
+
|
270
|
+
def initialize(context, options)
|
271
|
+
@context = context
|
272
|
+
@options = options
|
273
|
+
|
274
|
+
end
|
275
|
+
|
276
|
+
# convenience method to build a hyperlink # Where's the DRY in this?? Put this in the template where it belongs
|
277
|
+
def href(link, cls, name)
|
278
|
+
%{"<a href=\"#\" onclick=\"jsHref('#{link}');\" class=\"#{cls}\">#{name}</a>"}
|
279
|
+
end
|
280
|
+
|
281
|
+
# Create a list of HtmlMethod objects for each method
|
282
|
+
# in the corresponding context object. If the @options.show_all
|
283
|
+
# variable is set (corresponding to the <tt>--all</tt> option,
|
284
|
+
# we include all methods, otherwise just the public ones.
|
285
|
+
|
286
|
+
def collect_methods
|
287
|
+
list = @context.method_list
|
288
|
+
unless @options.show_all
|
289
|
+
list = list.find_all {|m| m.visibility == :public || m.visibility == :protected || m.force_documentation }
|
290
|
+
end
|
291
|
+
@methods = list.collect {|m| HtmlMethod.new(m, self, @options) }
|
292
|
+
end
|
293
|
+
|
294
|
+
# Build a summary list of all the methods in this context
|
295
|
+
def build_method_summary_list(path_prefix="")
|
296
|
+
collect_methods unless @methods
|
297
|
+
meths = @methods.sort
|
298
|
+
res = []
|
299
|
+
meths.each do |meth|
|
300
|
+
res << {
|
301
|
+
"name" => CGI.escapeHTML(meth.name),
|
302
|
+
"aref" => meth.aref,
|
303
|
+
"href" => meth.path
|
304
|
+
}
|
305
|
+
end
|
306
|
+
res
|
307
|
+
end
|
308
|
+
|
309
|
+
|
310
|
+
# Build a list of aliases for which we couldn't find a
|
311
|
+
# corresponding method
|
312
|
+
def build_alias_summary_list(section)
|
313
|
+
values = []
|
314
|
+
@context.aliases.each do |al|
|
315
|
+
next unless al.section == section
|
316
|
+
res = {
|
317
|
+
'old_name' => al.old_name,
|
318
|
+
'new_name' => al.new_name,
|
319
|
+
}
|
320
|
+
if al.comment && !al.comment.empty?
|
321
|
+
res['desc'] = markup(al.comment, true)
|
322
|
+
end
|
323
|
+
values << res
|
324
|
+
end
|
325
|
+
values
|
326
|
+
end
|
327
|
+
|
328
|
+
# Build a list of constants
|
329
|
+
def build_constants_summary_list(section)
|
330
|
+
values = []
|
331
|
+
@context.constants.each do |co|
|
332
|
+
next unless co.section == section
|
333
|
+
res = {
|
334
|
+
'name' => co.name,
|
335
|
+
'value' => CGI.escapeHTML(co.value)
|
336
|
+
}
|
337
|
+
res['desc'] = markup(co.comment, true) if co.comment && !co.comment.empty?
|
338
|
+
values << res
|
339
|
+
end
|
340
|
+
values
|
341
|
+
end
|
342
|
+
|
343
|
+
def build_requires_list(context)
|
344
|
+
potentially_referenced_list(context.requires) {|fn| [fn + ".rb"] }
|
345
|
+
end
|
346
|
+
|
347
|
+
def build_include_list(context)
|
348
|
+
potentially_referenced_list(context.includes)
|
349
|
+
end
|
350
|
+
|
351
|
+
# Build a list from an array of <i>Htmlxxx</i> items. Look up each
|
352
|
+
# in the AllReferences hash: if we find a corresponding entry,
|
353
|
+
# we generate a hyperlink to it, otherwise just output the name.
|
354
|
+
# However, some names potentially need massaging. For example,
|
355
|
+
# you may require a Ruby file without the .rb extension,
|
356
|
+
# but the file names we know about may have it. To deal with
|
357
|
+
# this, we pass in a block which performs the massaging,
|
358
|
+
# returning an array of alternative names to match
|
359
|
+
|
360
|
+
def potentially_referenced_list(array)
|
361
|
+
res = []
|
362
|
+
array.each do |i|
|
363
|
+
ref = AllReferences[i.name]
|
364
|
+
# if !ref
|
365
|
+
# container = @context.parent
|
366
|
+
# while !ref && container
|
367
|
+
# name = container.name + "::" + i.name
|
368
|
+
# ref = AllReferences[name]
|
369
|
+
# container = container.parent
|
370
|
+
# end
|
371
|
+
# end
|
372
|
+
|
373
|
+
ref = @context.find_symbol(i.name)
|
374
|
+
ref = ref.viewer if ref
|
375
|
+
|
376
|
+
if !ref && block_given?
|
377
|
+
possibles = yield(i.name)
|
378
|
+
while !ref and !possibles.empty?
|
379
|
+
ref = AllReferences[possibles.shift]
|
380
|
+
end
|
381
|
+
end
|
382
|
+
h_name = CGI.escapeHTML(i.name)
|
383
|
+
if ref and ref.document_self
|
384
|
+
path = ref.path
|
385
|
+
res << { "name" => h_name, "href" => path }
|
386
|
+
else
|
387
|
+
res << { "name" => h_name, "href" => "" }
|
388
|
+
end
|
389
|
+
end
|
390
|
+
res
|
391
|
+
end
|
392
|
+
|
393
|
+
# Build an array of arrays of method details. The outer array has up
|
394
|
+
# to six entries, public, private, and protected for both class
|
395
|
+
# methods, the other for instance methods. The inner arrays contain
|
396
|
+
# a hash for each method
|
397
|
+
|
398
|
+
def build_method_detail_list(section)
|
399
|
+
outer = []
|
400
|
+
|
401
|
+
methods = @methods.sort
|
402
|
+
for singleton in [true, false]
|
403
|
+
for vis in [ :public, :protected, :private ]
|
404
|
+
res = []
|
405
|
+
methods.each do |m|
|
406
|
+
if m.section == section and
|
407
|
+
m.document_self and
|
408
|
+
m.visibility == vis and
|
409
|
+
m.singleton == singleton
|
410
|
+
row = {}
|
411
|
+
if m.call_seq
|
412
|
+
row["callseq"] = m.call_seq.gsub(/->/, '→')
|
413
|
+
else
|
414
|
+
row["name"] = CGI.escapeHTML(m.name)
|
415
|
+
row["params"] = m.params
|
416
|
+
end
|
417
|
+
desc = m.description.strip
|
418
|
+
row["m_desc"] = desc unless desc.empty?
|
419
|
+
row["aref"] = m.aref
|
420
|
+
row["href"] = m.path
|
421
|
+
row["m_seq"] = m.seq
|
422
|
+
row["visibility"] = m.visibility.to_s
|
423
|
+
|
424
|
+
alias_names = []
|
425
|
+
m.aliases.each do |other|
|
426
|
+
if other.viewer # won't be if the alias is private
|
427
|
+
alias_names << {
|
428
|
+
'name' => other.name,
|
429
|
+
'href' => other.viewer.path,
|
430
|
+
'aref' => other.viewer.aref
|
431
|
+
}
|
432
|
+
end
|
433
|
+
end
|
434
|
+
unless alias_names.empty?
|
435
|
+
row["aka"] = alias_names
|
436
|
+
end
|
437
|
+
|
438
|
+
#if @options.inline_source
|
439
|
+
code = m.source_code
|
440
|
+
row["sourcecode"] = code if code
|
441
|
+
#else
|
442
|
+
# code = m.src_url
|
443
|
+
#if code
|
444
|
+
# row["codeurl"] = code
|
445
|
+
# row["imgurl"] = m.img_url
|
446
|
+
#end
|
447
|
+
#end
|
448
|
+
res << row
|
449
|
+
end
|
450
|
+
end
|
451
|
+
if res.size > 0
|
452
|
+
outer << {
|
453
|
+
"type" => vis.to_s.capitalize,
|
454
|
+
"category" => singleton ? "Class" : "Instance",
|
455
|
+
"methods" => res
|
456
|
+
}
|
457
|
+
end
|
458
|
+
end
|
459
|
+
end
|
460
|
+
outer
|
461
|
+
end
|
462
|
+
|
463
|
+
# Build the structured list of classes and modules contained
|
464
|
+
# in this context.
|
465
|
+
|
466
|
+
def build_class_list(level, from, section, infile=nil)
|
467
|
+
res = ""
|
468
|
+
prefix = " ::" * level;
|
469
|
+
|
470
|
+
from.modules.sort.each do |mod|
|
471
|
+
next unless mod.section == section
|
472
|
+
next if infile && !mod.defined_in?(infile)
|
473
|
+
if mod.document_self
|
474
|
+
res <<
|
475
|
+
prefix <<
|
476
|
+
"Module " <<
|
477
|
+
href(mod.viewer.path, "link", mod.full_name) <<
|
478
|
+
"<br />\n" <<
|
479
|
+
build_class_list(level + 1, mod, section, infile)
|
480
|
+
end
|
481
|
+
end
|
482
|
+
|
483
|
+
from.classes.sort.each do |cls|
|
484
|
+
next unless cls.section == section
|
485
|
+
next if infile && !cls.defined_in?(infile)
|
486
|
+
if cls.document_self
|
487
|
+
res <<
|
488
|
+
prefix <<
|
489
|
+
"Class " <<
|
490
|
+
href(cls.viewer.path, "link", cls.full_name) <<
|
491
|
+
"<br />\n" <<
|
492
|
+
build_class_list(level + 1, cls, section, infile)
|
493
|
+
end
|
494
|
+
end
|
495
|
+
|
496
|
+
res
|
497
|
+
end
|
498
|
+
|
499
|
+
def document_self
|
500
|
+
@context.document_self
|
501
|
+
end
|
502
|
+
|
503
|
+
def diagram_reference(diagram)
|
504
|
+
res = diagram.gsub(/((?:src|href)=")(.*?)"/) {
|
505
|
+
$1 + $2 + '"'
|
506
|
+
}
|
507
|
+
res
|
508
|
+
end
|
509
|
+
|
510
|
+
|
511
|
+
# Find a symbol in ourselves or our parent
|
512
|
+
def find_symbol(symbol, method=nil)
|
513
|
+
res = @context.find_symbol(symbol, method)
|
514
|
+
if res
|
515
|
+
res = res.viewer
|
516
|
+
end
|
517
|
+
res
|
518
|
+
end
|
519
|
+
|
520
|
+
# create table of contents if we contain sections
|
521
|
+
|
522
|
+
def add_table_of_sections
|
523
|
+
toc = []
|
524
|
+
@context.sections.each do |section|
|
525
|
+
if section.title
|
526
|
+
toc << {
|
527
|
+
'secname' => section.title,
|
528
|
+
'href' => section.sequence
|
529
|
+
}
|
530
|
+
end
|
531
|
+
end
|
532
|
+
|
533
|
+
@values['toc'] = toc unless toc.empty?
|
534
|
+
end
|
535
|
+
|
536
|
+
|
537
|
+
end
|
538
|
+
|
539
|
+
#####################################################################
|
540
|
+
#
|
541
|
+
# Wrap a ClassModule context
|
542
|
+
|
543
|
+
class HtmlClass < ContextUser
|
544
|
+
|
545
|
+
@@c_seq = "C00000000"
|
546
|
+
|
547
|
+
attr_reader :path
|
548
|
+
|
549
|
+
def initialize(context, html_file, prefix, options)
|
550
|
+
super(context, options)
|
551
|
+
@@c_seq = @@c_seq.succ
|
552
|
+
@c_seq = @@c_seq
|
553
|
+
@html_file = html_file
|
554
|
+
@is_module = context.is_module?
|
555
|
+
@values = {}
|
556
|
+
|
557
|
+
context.viewer = self
|
558
|
+
|
559
|
+
@path = http_url(context.full_name, prefix)
|
560
|
+
|
561
|
+
collect_methods
|
562
|
+
|
563
|
+
AllReferences.add(name, self)
|
564
|
+
end
|
565
|
+
|
566
|
+
# return the relative file name to store this class in,
|
567
|
+
# which is also its url
|
568
|
+
def http_url(full_name, prefix)
|
569
|
+
path = full_name.dup
|
570
|
+
if path['<<']
|
571
|
+
path.gsub!(/<<\s*(\w*)/) { "from-#$1" }
|
572
|
+
end
|
573
|
+
File.join(prefix, path.split("::")) + ".html"
|
574
|
+
end
|
575
|
+
|
576
|
+
def seq
|
577
|
+
@c_seq
|
578
|
+
end
|
579
|
+
|
580
|
+
def aref
|
581
|
+
@c_seq
|
582
|
+
end
|
583
|
+
|
584
|
+
def scope
|
585
|
+
a = @context.full_name.split("::")
|
586
|
+
if a.length > 1
|
587
|
+
a.pop
|
588
|
+
a.join("::")
|
589
|
+
else
|
590
|
+
""
|
591
|
+
end
|
592
|
+
end
|
593
|
+
|
594
|
+
def name
|
595
|
+
@context.full_name.gsub("#{scope}::", '')
|
596
|
+
end
|
597
|
+
|
598
|
+
def full_name
|
599
|
+
@context.full_name
|
600
|
+
end
|
601
|
+
|
602
|
+
def parent_name
|
603
|
+
@context.parent.full_name
|
604
|
+
end
|
605
|
+
|
606
|
+
def write_on(f)
|
607
|
+
value_hash
|
608
|
+
template = TemplatePage.new(RDoc::Page::BODY,
|
609
|
+
RDoc::Page::CLASS_PAGE,
|
610
|
+
RDoc::Page::METHOD_LIST)
|
611
|
+
template.write_html_on(f, @values)
|
612
|
+
end
|
613
|
+
|
614
|
+
def value_hash
|
615
|
+
class_attribute_values
|
616
|
+
add_table_of_sections
|
617
|
+
|
618
|
+
@values["charset"] = @options.charset
|
619
|
+
@values["style_url"] = style_url(path, @options.css)
|
620
|
+
|
621
|
+
# Convert README to html
|
622
|
+
unless File.exist?('files/README.html')
|
623
|
+
File.open('files/README.html', 'w') do |file|
|
624
|
+
file << markup(File.read(File.expand_path(@options.main_page)))
|
625
|
+
end
|
626
|
+
end
|
627
|
+
|
628
|
+
d = markup(@context.comment)
|
629
|
+
@values["description"] = d unless d.empty?
|
630
|
+
|
631
|
+
ml = build_method_summary_list
|
632
|
+
@values["methods"] = ml unless ml.empty?
|
633
|
+
|
634
|
+
il = build_include_list(@context)
|
635
|
+
@values["includes"] = il unless il.empty?
|
636
|
+
|
637
|
+
@values["sections"] = @context.sections.map do |section|
|
638
|
+
|
639
|
+
secdata = {
|
640
|
+
"sectitle" => section.title,
|
641
|
+
"secsequence" => section.sequence,
|
642
|
+
"seccomment" => markup(section.comment)
|
643
|
+
}
|
644
|
+
|
645
|
+
al = build_alias_summary_list(section)
|
646
|
+
secdata["aliases"] = al unless al.empty?
|
647
|
+
|
648
|
+
co = build_constants_summary_list(section)
|
649
|
+
secdata["constants"] = co unless co.empty?
|
650
|
+
|
651
|
+
al = build_attribute_list(section)
|
652
|
+
secdata["attributes"] = al unless al.empty?
|
653
|
+
|
654
|
+
cl = build_class_list(0, @context, section)
|
655
|
+
secdata["classlist"] = cl unless cl.empty?
|
656
|
+
|
657
|
+
mdl = build_method_detail_list(section)
|
658
|
+
secdata["method_list"] = mdl unless mdl.empty?
|
659
|
+
|
660
|
+
secdata
|
661
|
+
end
|
662
|
+
|
663
|
+
@values
|
664
|
+
end
|
665
|
+
|
666
|
+
def build_attribute_list(section)
|
667
|
+
atts = @context.attributes.sort
|
668
|
+
res = []
|
669
|
+
atts.each do |att|
|
670
|
+
next unless att.section == section
|
671
|
+
if att.visibility == :public || att.visibility == :protected || @options.show_all
|
672
|
+
entry = {
|
673
|
+
"name" => CGI.escapeHTML(att.name),
|
674
|
+
"rw" => att.rw,
|
675
|
+
"a_desc" => markup(att.comment, true)
|
676
|
+
}
|
677
|
+
unless att.visibility == :public || att.visibility == :protected
|
678
|
+
entry["rw"] << "-"
|
679
|
+
end
|
680
|
+
res << entry
|
681
|
+
end
|
682
|
+
end
|
683
|
+
res
|
684
|
+
end
|
685
|
+
|
686
|
+
def class_attribute_values
|
687
|
+
h_name = CGI.escapeHTML(name)
|
688
|
+
|
689
|
+
@values["classmod"] = @is_module ? "Module" : "Class"
|
690
|
+
@values["title"] = "#{@values['classmod']}: #{h_name}"
|
691
|
+
|
692
|
+
c = @context
|
693
|
+
c = c.parent while c and !c.diagram
|
694
|
+
if c && c.diagram
|
695
|
+
@values["diagram"] = diagram_reference(c.diagram)
|
696
|
+
end
|
697
|
+
|
698
|
+
@values["full_name"] = h_name
|
699
|
+
@values["class_seq"] = seq
|
700
|
+
parent_class = @context.superclass
|
701
|
+
|
702
|
+
if parent_class
|
703
|
+
@values["parent"] = CGI.escapeHTML(parent_class)
|
704
|
+
|
705
|
+
if parent_name
|
706
|
+
lookup = parent_name + "::" + parent_class
|
707
|
+
else
|
708
|
+
lookup = parent_class
|
709
|
+
end
|
710
|
+
|
711
|
+
parent_url = AllReferences[lookup] || AllReferences[parent_class]
|
712
|
+
|
713
|
+
if parent_url and parent_url.document_self
|
714
|
+
@values["par_url"] = parent_url.path
|
715
|
+
end
|
716
|
+
end
|
717
|
+
|
718
|
+
files = []
|
719
|
+
@context.in_files.each do |f|
|
720
|
+
res = {}
|
721
|
+
full_path = CGI.escapeHTML(f.file_absolute_name)
|
722
|
+
|
723
|
+
res["full_path"] = full_path
|
724
|
+
res["full_path_url"] = f.viewer.path if f.document_self
|
725
|
+
|
726
|
+
if @options.webcvs
|
727
|
+
res["cvsurl"] = cvs_url( @options.webcvs, full_path )
|
728
|
+
end
|
729
|
+
|
730
|
+
files << res
|
731
|
+
end
|
732
|
+
|
733
|
+
@values['infiles'] = files
|
734
|
+
end
|
735
|
+
|
736
|
+
def <=>(other)
|
737
|
+
self.name <=> other.name
|
738
|
+
end
|
739
|
+
|
740
|
+
end
|
741
|
+
|
742
|
+
#####################################################################
|
743
|
+
#
|
744
|
+
# Handles the mapping of a file's information to HTML. In reality,
|
745
|
+
# a file corresponds to a +TopLevel+ object, containing modules,
|
746
|
+
# classes, and top-level methods. In theory it _could_ contain
|
747
|
+
# attributes and aliases, but we ignore these for now.
|
748
|
+
|
749
|
+
class HtmlFile < ContextUser
|
750
|
+
|
751
|
+
@@f_seq = "F00000000"
|
752
|
+
|
753
|
+
attr_reader :path
|
754
|
+
attr_reader :name
|
755
|
+
|
756
|
+
def initialize(context, options, file_dir)
|
757
|
+
super(context, options)
|
758
|
+
@@f_seq = @@f_seq.succ
|
759
|
+
@f_seq = @@f_seq
|
760
|
+
@values = {}
|
761
|
+
|
762
|
+
@path = http_url(file_dir)
|
763
|
+
@source_file_path = File.expand_path(@context.file_relative_name).gsub("\/doc\/", "/")
|
764
|
+
@name = @context.file_relative_name
|
765
|
+
|
766
|
+
collect_methods
|
767
|
+
AllReferences.add(name, self)
|
768
|
+
context.viewer = self
|
769
|
+
end
|
770
|
+
|
771
|
+
def http_url(file_dir)
|
772
|
+
File.join(file_dir, @context.file_relative_name.tr('.', '_')) + ".html"
|
773
|
+
end
|
774
|
+
|
775
|
+
def filename_to_label
|
776
|
+
@context.file_relative_name.gsub(/%|\/|\?|\#/) {|s| '%' + ("%x" % s[0]) }
|
777
|
+
end
|
778
|
+
|
779
|
+
def seq
|
780
|
+
@f_seq
|
781
|
+
end
|
782
|
+
|
783
|
+
def aref
|
784
|
+
@f_seq
|
785
|
+
end
|
786
|
+
|
787
|
+
def name
|
788
|
+
full_path = @context.file_absolute_name
|
789
|
+
short_name = File.basename(full_path)
|
790
|
+
end
|
791
|
+
|
792
|
+
def full_name
|
793
|
+
@context.file_absolute_name
|
794
|
+
end
|
795
|
+
|
796
|
+
def scope
|
797
|
+
@context.file_relative_name.gsub(/\/#{name}$/, '')
|
798
|
+
end
|
799
|
+
|
800
|
+
def parent_name
|
801
|
+
nil
|
802
|
+
end
|
803
|
+
|
804
|
+
def full_file_source
|
805
|
+
ret_str = ""
|
806
|
+
File.open(@source_file_path, 'r') do |f|
|
807
|
+
while(!f.eof?) do
|
808
|
+
ret_str += f.readline()
|
809
|
+
end
|
810
|
+
end
|
811
|
+
ret_str
|
812
|
+
rescue
|
813
|
+
"file not found -#{@source_file_path}-"
|
814
|
+
#@source_file_path
|
815
|
+
end
|
816
|
+
|
817
|
+
def value_hash
|
818
|
+
file_attribute_values
|
819
|
+
add_table_of_sections
|
820
|
+
|
821
|
+
@values["charset"] = @options.charset
|
822
|
+
@values["href"] = path
|
823
|
+
@values["style_url"] = style_url(path, @options.css)
|
824
|
+
@values["file_seq"] = seq
|
825
|
+
|
826
|
+
#pulling in the source for this file
|
827
|
+
#@values["source_code"] = @context.token_stream
|
828
|
+
|
829
|
+
@values["file_source_code"] = CGI.escapeHTML(full_file_source)
|
830
|
+
|
831
|
+
if @context.comment
|
832
|
+
d = markup(@context.comment)
|
833
|
+
@values["description"] = d if d.size > 0
|
834
|
+
end
|
835
|
+
|
836
|
+
ml = build_method_summary_list
|
837
|
+
@values["methods"] = ml unless ml.empty?
|
838
|
+
|
839
|
+
il = build_include_list(@context)
|
840
|
+
@values["includes"] = il unless il.empty?
|
841
|
+
|
842
|
+
rl = build_requires_list(@context)
|
843
|
+
@values["requires"] = rl unless rl.empty?
|
844
|
+
|
845
|
+
|
846
|
+
file_context = @context
|
847
|
+
|
848
|
+
@values["sections"] = @context.sections.map do |section|
|
849
|
+
|
850
|
+
secdata = {
|
851
|
+
"sectitle" => section.title,
|
852
|
+
"secsequence" => section.sequence,
|
853
|
+
"seccomment" => markup(section.comment)
|
854
|
+
}
|
855
|
+
|
856
|
+
cl = build_class_list(0, @context, section, file_context)
|
857
|
+
@values["classlist"] = cl unless cl.empty?
|
858
|
+
|
859
|
+
mdl = build_method_detail_list(section)
|
860
|
+
secdata["method_list"] = mdl unless mdl.empty?
|
861
|
+
|
862
|
+
al = build_alias_summary_list(section)
|
863
|
+
secdata["aliases"] = al unless al.empty?
|
864
|
+
|
865
|
+
co = build_constants_summary_list(section)
|
866
|
+
@values["constants"] = co unless co.empty?
|
867
|
+
|
868
|
+
secdata
|
869
|
+
end
|
870
|
+
|
871
|
+
@values
|
872
|
+
end
|
873
|
+
|
874
|
+
def write_on(f)
|
875
|
+
value_hash
|
876
|
+
template = TemplatePage.new(RDoc::Page::SRC_BODY,RDoc::Page::FILE_PAGE, RDoc::Page::METHOD_LIST)
|
877
|
+
template.write_html_on(f, @values)
|
878
|
+
end
|
879
|
+
|
880
|
+
def file_attribute_values
|
881
|
+
full_path = @context.file_absolute_name
|
882
|
+
short_name = File.basename(full_path)
|
883
|
+
|
884
|
+
@values["title"] = CGI.escapeHTML("File: #{short_name}")
|
885
|
+
|
886
|
+
if @context.diagram
|
887
|
+
@values["diagram"] = diagram_reference(@context.diagram)
|
888
|
+
end
|
889
|
+
|
890
|
+
@values["short_name"] = CGI.escapeHTML(short_name)
|
891
|
+
@values["full_path"] = CGI.escapeHTML(full_path)
|
892
|
+
@values["dtm_modified"] = @context.file_stat.mtime.to_s
|
893
|
+
|
894
|
+
if @options.webcvs
|
895
|
+
@values["cvsurl"] = cvs_url( @options.webcvs, @values["full_path"] )
|
896
|
+
end
|
897
|
+
end
|
898
|
+
|
899
|
+
def <=>(other)
|
900
|
+
self.name <=> other.name
|
901
|
+
end
|
902
|
+
end
|
903
|
+
|
904
|
+
#####################################################################
|
905
|
+
|
906
|
+
class HtmlMethod
|
907
|
+
include MarkUp
|
908
|
+
|
909
|
+
attr_reader :context
|
910
|
+
attr_reader :src_url
|
911
|
+
attr_reader :img_url
|
912
|
+
attr_reader :source_code
|
913
|
+
|
914
|
+
@@m_seq = "M000000"
|
915
|
+
|
916
|
+
@@all_methods = []
|
917
|
+
|
918
|
+
def HtmlMethod::reset
|
919
|
+
@@all_methods = []
|
920
|
+
end
|
921
|
+
|
922
|
+
def initialize(context, html_class, options)
|
923
|
+
@context = context
|
924
|
+
@html_class = html_class
|
925
|
+
@options = options
|
926
|
+
@@m_seq = @@m_seq.succ
|
927
|
+
@m_seq = @@m_seq
|
928
|
+
@@all_methods << self
|
929
|
+
|
930
|
+
context.viewer = self
|
931
|
+
|
932
|
+
if (ts = @context.token_stream)
|
933
|
+
@source_code = markup_code(ts)
|
934
|
+
#unless @options.inline_source
|
935
|
+
# @src_url = create_source_code_file(@source_code)
|
936
|
+
# @img_url = MERBGenerator.gen_url(path, 'source.png')
|
937
|
+
#end
|
938
|
+
end
|
939
|
+
AllReferences.add(name, self)
|
940
|
+
end
|
941
|
+
|
942
|
+
def seq
|
943
|
+
@m_seq
|
944
|
+
end
|
945
|
+
|
946
|
+
def aref
|
947
|
+
@m_seq
|
948
|
+
end
|
949
|
+
|
950
|
+
def scope
|
951
|
+
@html_class.full_name
|
952
|
+
end
|
953
|
+
|
954
|
+
# return a reference to outselves to be used as an href=
|
955
|
+
# the form depends on whether we're all in one file
|
956
|
+
# or in multiple files
|
957
|
+
|
958
|
+
def name
|
959
|
+
@context.name
|
960
|
+
end
|
961
|
+
|
962
|
+
def section
|
963
|
+
@context.section
|
964
|
+
end
|
965
|
+
|
966
|
+
def parent_name
|
967
|
+
if @context.parent.parent
|
968
|
+
@context.parent.parent.full_name
|
969
|
+
else
|
970
|
+
nil
|
971
|
+
end
|
972
|
+
end
|
973
|
+
|
974
|
+
def path
|
975
|
+
@html_class.path
|
976
|
+
end
|
977
|
+
|
978
|
+
def description
|
979
|
+
markup(@context.comment)
|
980
|
+
end
|
981
|
+
|
982
|
+
def visibility
|
983
|
+
@context.visibility
|
984
|
+
end
|
985
|
+
|
986
|
+
def singleton
|
987
|
+
@context.singleton
|
988
|
+
end
|
989
|
+
|
990
|
+
def call_seq
|
991
|
+
cs = @context.call_seq
|
992
|
+
if cs
|
993
|
+
cs.gsub(/\n/, "<br />\n")
|
994
|
+
else
|
995
|
+
nil
|
996
|
+
end
|
997
|
+
end
|
998
|
+
|
999
|
+
def params
|
1000
|
+
# params coming from a call-seq in 'C' will start with the
|
1001
|
+
# method name
|
1002
|
+
p = @context.params
|
1003
|
+
if p !~ /^\w/
|
1004
|
+
p = @context.params.gsub(/\s*\#.*/, '')
|
1005
|
+
p = p.tr("\n", " ").squeeze(" ")
|
1006
|
+
p = "(" + p + ")" unless p[0] == ?(
|
1007
|
+
|
1008
|
+
if (block = @context.block_params)
|
1009
|
+
# If this method has explicit block parameters, remove any
|
1010
|
+
# explicit &block
|
1011
|
+
|
1012
|
+
p.sub!(/,?\s*&\w+/, '')
|
1013
|
+
|
1014
|
+
block.gsub!(/\s*\#.*/, '')
|
1015
|
+
block = block.tr("\n", " ").squeeze(" ")
|
1016
|
+
if block[0] == ?(
|
1017
|
+
block.sub!(/^\(/, '').sub!(/\)/, '')
|
1018
|
+
end
|
1019
|
+
p << " {|#{block.strip}| ...}"
|
1020
|
+
end
|
1021
|
+
end
|
1022
|
+
CGI.escapeHTML(p)
|
1023
|
+
end
|
1024
|
+
|
1025
|
+
def create_source_code_file(code_body)
|
1026
|
+
meth_path = @html_class.path.sub(/\.html$/, '.src')
|
1027
|
+
File.makedirs(meth_path)
|
1028
|
+
file_path = File.join(meth_path, seq) + ".html"
|
1029
|
+
|
1030
|
+
template = TemplatePage.new(RDoc::Page::SRC_PAGE)
|
1031
|
+
File.open(file_path, "w") do |f|
|
1032
|
+
values = {
|
1033
|
+
'title' => CGI.escapeHTML(name),
|
1034
|
+
'code' => code_body,
|
1035
|
+
'style_url' => style_url(file_path, @options.css),
|
1036
|
+
'charset' => @options.charset
|
1037
|
+
}
|
1038
|
+
template.write_html_on(f, values)
|
1039
|
+
end
|
1040
|
+
file_path
|
1041
|
+
end
|
1042
|
+
|
1043
|
+
def HtmlMethod.all_methods
|
1044
|
+
@@all_methods
|
1045
|
+
end
|
1046
|
+
|
1047
|
+
def <=>(other)
|
1048
|
+
@context <=> other.context
|
1049
|
+
end
|
1050
|
+
|
1051
|
+
##
|
1052
|
+
# Given a sequence of source tokens, mark up the source code
|
1053
|
+
# to make it look purty.
|
1054
|
+
|
1055
|
+
|
1056
|
+
def markup_code(tokens)
|
1057
|
+
src = ""
|
1058
|
+
tokens.each do |t|
|
1059
|
+
next unless t
|
1060
|
+
# p t.class
|
1061
|
+
# style = STYLE_MAP[t.class]
|
1062
|
+
style = case t
|
1063
|
+
when RubyToken::TkCONSTANT then "ruby-constant"
|
1064
|
+
when RubyToken::TkKW then "ruby-keyword kw"
|
1065
|
+
when RubyToken::TkIVAR then "ruby-ivar"
|
1066
|
+
when RubyToken::TkOp then "ruby-operator"
|
1067
|
+
when RubyToken::TkId then "ruby-identifier"
|
1068
|
+
when RubyToken::TkNode then "ruby-node"
|
1069
|
+
when RubyToken::TkCOMMENT then "ruby-comment cmt"
|
1070
|
+
when RubyToken::TkREGEXP then "ruby-regexp re"
|
1071
|
+
when RubyToken::TkSTRING then "ruby-value str"
|
1072
|
+
when RubyToken::TkVal then "ruby-value"
|
1073
|
+
else
|
1074
|
+
nil
|
1075
|
+
end
|
1076
|
+
|
1077
|
+
text = CGI.escapeHTML(t.text)
|
1078
|
+
|
1079
|
+
if style
|
1080
|
+
src << "<span class=\"#{style}\">#{text}</span>"
|
1081
|
+
else
|
1082
|
+
src << text
|
1083
|
+
end
|
1084
|
+
end
|
1085
|
+
|
1086
|
+
add_line_numbers(src)
|
1087
|
+
src
|
1088
|
+
end
|
1089
|
+
|
1090
|
+
# we rely on the fact that the first line of a source code
|
1091
|
+
# listing has
|
1092
|
+
# # File xxxxx, line dddd
|
1093
|
+
|
1094
|
+
def add_line_numbers(src)
|
1095
|
+
if src =~ /\A.*, line (\d+)/
|
1096
|
+
first = $1.to_i - 1
|
1097
|
+
last = first + src.count("\n")
|
1098
|
+
size = last.to_s.length
|
1099
|
+
real_fmt = "%#{size}d: "
|
1100
|
+
fmt = " " * (size+2)
|
1101
|
+
src.gsub!(/^/) do
|
1102
|
+
res = sprintf(fmt, first)
|
1103
|
+
first += 1
|
1104
|
+
fmt = real_fmt
|
1105
|
+
res
|
1106
|
+
end
|
1107
|
+
end
|
1108
|
+
end
|
1109
|
+
|
1110
|
+
def document_self
|
1111
|
+
@context.document_self
|
1112
|
+
end
|
1113
|
+
|
1114
|
+
def aliases
|
1115
|
+
@context.aliases
|
1116
|
+
end
|
1117
|
+
|
1118
|
+
def find_symbol(symbol, method=nil)
|
1119
|
+
res = @context.parent.find_symbol(symbol, method)
|
1120
|
+
if res
|
1121
|
+
res = res.viewer
|
1122
|
+
end
|
1123
|
+
res
|
1124
|
+
end
|
1125
|
+
end
|
1126
|
+
|
1127
|
+
#####################################################################
|
1128
|
+
|
1129
|
+
class MERBGenerator
|
1130
|
+
|
1131
|
+
include MarkUp
|
1132
|
+
|
1133
|
+
# Generators may need to return specific subclasses depending
|
1134
|
+
# on the options they are passed. Because of this
|
1135
|
+
# we create them using a factory
|
1136
|
+
|
1137
|
+
def MERBGenerator.for(options)
|
1138
|
+
AllReferences::reset
|
1139
|
+
HtmlMethod::reset
|
1140
|
+
|
1141
|
+
MERBGenerator.new(options)
|
1142
|
+
|
1143
|
+
end
|
1144
|
+
|
1145
|
+
class <<self
|
1146
|
+
protected :new
|
1147
|
+
end
|
1148
|
+
|
1149
|
+
# Set up a new HTML generator. Basically all we do here is load
|
1150
|
+
# up the correct output temlate
|
1151
|
+
|
1152
|
+
def initialize(options) #:not-new:
|
1153
|
+
@options = options
|
1154
|
+
load_html_template
|
1155
|
+
end
|
1156
|
+
|
1157
|
+
|
1158
|
+
##
|
1159
|
+
# Build the initial indices and output objects
|
1160
|
+
# based on an array of TopLevel objects containing
|
1161
|
+
# the extracted information.
|
1162
|
+
|
1163
|
+
def generate(toplevels)
|
1164
|
+
@toplevels = toplevels
|
1165
|
+
@files = []
|
1166
|
+
@classes = []
|
1167
|
+
|
1168
|
+
write_style_sheet
|
1169
|
+
write_javascript
|
1170
|
+
gen_sub_directories()
|
1171
|
+
build_indices
|
1172
|
+
generate_html
|
1173
|
+
end
|
1174
|
+
|
1175
|
+
private
|
1176
|
+
|
1177
|
+
##
|
1178
|
+
# Load up the AJAX HTML template specified in the options.
|
1179
|
+
# If the template name contains a slash, use it literally
|
1180
|
+
#
|
1181
|
+
def load_html_template
|
1182
|
+
template = @options.template
|
1183
|
+
unless template =~ %r{/|\\}
|
1184
|
+
template = File.join("rdoc/generators/template", @options.generator.key, template)
|
1185
|
+
end
|
1186
|
+
require template
|
1187
|
+
extend RDoc::Page
|
1188
|
+
rescue LoadError
|
1189
|
+
$stderr.puts "Could not find AJAX template '#{template}'"
|
1190
|
+
exit 99
|
1191
|
+
end
|
1192
|
+
|
1193
|
+
##
|
1194
|
+
# Write out the style sheet used by the main frames
|
1195
|
+
#
|
1196
|
+
|
1197
|
+
def write_style_sheet
|
1198
|
+
template = TemplatePage.new(RDoc::Page::STYLE)
|
1199
|
+
File.open(CSS_NAME, "w") do |f|
|
1200
|
+
values = { "font" => "helvetica"} #this is not used anywhere but the template function demands a hash of values
|
1201
|
+
template.write_html_on(f, values)
|
1202
|
+
end
|
1203
|
+
end
|
1204
|
+
|
1205
|
+
def write_javascript
|
1206
|
+
#Argh... I couldn't figure out how to copy these from the template dir so they were copied into
|
1207
|
+
# the template file "ajax.rb" and processed similarlly to the style sheets. Not exactly a good thing to do with
|
1208
|
+
# external library code. Not very DRY.
|
1209
|
+
|
1210
|
+
File.open("api_grease.js", "w") do |f|
|
1211
|
+
f << RDoc::Page::API_GREASE_JS
|
1212
|
+
end
|
1213
|
+
|
1214
|
+
File.open("prototype.js", "w") do |f|
|
1215
|
+
f << RDoc::Page::PROTOTYPE_JS
|
1216
|
+
end
|
1217
|
+
|
1218
|
+
rescue LoadError
|
1219
|
+
$stderr.puts "Could not find AJAX template"
|
1220
|
+
exit 99
|
1221
|
+
end
|
1222
|
+
|
1223
|
+
##
|
1224
|
+
# See the comments at the top for a description of the
|
1225
|
+
# directory structure
|
1226
|
+
|
1227
|
+
def gen_sub_directories
|
1228
|
+
File.makedirs(FILE_DIR, CLASS_DIR)
|
1229
|
+
rescue
|
1230
|
+
$stderr.puts $!.message
|
1231
|
+
exit 1
|
1232
|
+
end
|
1233
|
+
|
1234
|
+
##
|
1235
|
+
# Generate:
|
1236
|
+
#
|
1237
|
+
# * a list of HtmlFile objects for each TopLevel object.
|
1238
|
+
# * a list of HtmlClass objects for each first level
|
1239
|
+
# class or module in the TopLevel objects
|
1240
|
+
# * a complete list of all hyperlinkable terms (file,
|
1241
|
+
# class, module, and method names)
|
1242
|
+
|
1243
|
+
def build_indices
|
1244
|
+
|
1245
|
+
@toplevels.each do |toplevel|
|
1246
|
+
@files << HtmlFile.new(toplevel, @options, FILE_DIR)
|
1247
|
+
end
|
1248
|
+
|
1249
|
+
RDoc::TopLevel.all_classes_and_modules.each do |cls|
|
1250
|
+
build_class_list(cls, @files[0], CLASS_DIR)
|
1251
|
+
end
|
1252
|
+
end
|
1253
|
+
|
1254
|
+
def build_class_list(from, html_file, class_dir)
|
1255
|
+
@classes << HtmlClass.new(from, html_file, class_dir, @options)
|
1256
|
+
from.each_classmodule do |mod|
|
1257
|
+
build_class_list(mod, html_file, class_dir)
|
1258
|
+
end
|
1259
|
+
end
|
1260
|
+
|
1261
|
+
##
|
1262
|
+
# Generate all the HTML
|
1263
|
+
#
|
1264
|
+
def generate_html
|
1265
|
+
# the individual descriptions for files and classes
|
1266
|
+
gen_into(@files)
|
1267
|
+
gen_into(@classes)
|
1268
|
+
# and the index files
|
1269
|
+
gen_file_index
|
1270
|
+
gen_class_index
|
1271
|
+
gen_method_index
|
1272
|
+
gen_main_index
|
1273
|
+
|
1274
|
+
# this method is defined in the template file
|
1275
|
+
write_extra_pages if defined? write_extra_pages
|
1276
|
+
end
|
1277
|
+
|
1278
|
+
def gen_into(list)
|
1279
|
+
list.each do |item|
|
1280
|
+
if item.document_self
|
1281
|
+
op_file = item.path
|
1282
|
+
File.makedirs(File.dirname(op_file))
|
1283
|
+
File.open(op_file, "w") { |file| item.write_on(file) }
|
1284
|
+
end
|
1285
|
+
end
|
1286
|
+
|
1287
|
+
end
|
1288
|
+
|
1289
|
+
def gen_file_index
|
1290
|
+
gen_an_index(@files, 'Files',
|
1291
|
+
RDoc::Page::FILE_INDEX,
|
1292
|
+
"fr_file_index.html")
|
1293
|
+
end
|
1294
|
+
|
1295
|
+
def gen_class_index
|
1296
|
+
gen_an_index(@classes, 'Classes',
|
1297
|
+
RDoc::Page::CLASS_INDEX,
|
1298
|
+
"fr_class_index.html")
|
1299
|
+
end
|
1300
|
+
|
1301
|
+
def gen_method_index
|
1302
|
+
gen_an_index(HtmlMethod.all_methods, 'Methods',
|
1303
|
+
RDoc::Page::METHOD_INDEX,
|
1304
|
+
"fr_method_index.html")
|
1305
|
+
end
|
1306
|
+
|
1307
|
+
|
1308
|
+
def gen_an_index(collection, title, template, filename)
|
1309
|
+
template = TemplatePage.new(RDoc::Page::FR_INDEX_BODY, template)
|
1310
|
+
res = []
|
1311
|
+
collection.sort.each do |f|
|
1312
|
+
if f.document_self
|
1313
|
+
res << { "href" => f.path, "name" => f.name, "scope" => f.scope, "seq_id" => f.seq }
|
1314
|
+
end
|
1315
|
+
end
|
1316
|
+
|
1317
|
+
values = {
|
1318
|
+
"entries" => res,
|
1319
|
+
'list_title' => CGI.escapeHTML(title),
|
1320
|
+
'index_url' => main_url,
|
1321
|
+
'charset' => @options.charset,
|
1322
|
+
'style_url' => style_url('', @options.css),
|
1323
|
+
}
|
1324
|
+
|
1325
|
+
File.open(filename, "w") do |f|
|
1326
|
+
template.write_html_on(f, values)
|
1327
|
+
end
|
1328
|
+
end
|
1329
|
+
|
1330
|
+
# The main index page is mostly a template frameset, but includes
|
1331
|
+
# the initial page. If the <tt>--main</tt> option was given,
|
1332
|
+
# we use this as our main page, otherwise we use the
|
1333
|
+
# first file specified on the command line.
|
1334
|
+
|
1335
|
+
def gen_main_index
|
1336
|
+
template = TemplatePage.new(RDoc::Page::INDEX)
|
1337
|
+
File.open("index.html", "w") do |f|
|
1338
|
+
tStr = ""
|
1339
|
+
#File.open(main_url, 'r') do |g|
|
1340
|
+
# tStr = markup(g)
|
1341
|
+
#end
|
1342
|
+
values = {
|
1343
|
+
"initial_page" => tStr,
|
1344
|
+
'title' => CGI.escapeHTML(@options.title),
|
1345
|
+
'charset' => @options.charset,
|
1346
|
+
'content' => File.read('files/README.html')
|
1347
|
+
}
|
1348
|
+
|
1349
|
+
values['inline_source'] = true
|
1350
|
+
template.write_html_on(f, values)
|
1351
|
+
end
|
1352
|
+
end
|
1353
|
+
|
1354
|
+
# return the url of the main page
|
1355
|
+
def main_url
|
1356
|
+
"files/README.html"
|
1357
|
+
end
|
1358
|
+
|
1359
|
+
|
1360
|
+
end
|
1361
|
+
|
1362
|
+
end
|