OpenTreeOfLife/treemachine — pull request #120 by josephwb (2014-09-15 21:46:10+00:00)
Title: Pluginsv2

Change format of returned source tree list from a string array to the following (suggested by @mtholder):
```json
{
"root_node_id" : 132,
"study_list" : [ {
"study_id" : "pg_2827",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6577"
}, {
"study_id" : "pg_761",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1415"
}, {
"study_id" : "pg_77",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5878"
}, {
"study_id" : "pg_754",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1392"
}, {
"study_id" : "pg_330",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "325"
}, {
"study_id" : "pg_1131",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2265"
}, {
"study_id" : "pg_2608",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6288"
}, {
"study_id" : "pg_2539",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6294"
}, {
"study_id" : "pg_2645",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6165"
}, {
"study_id" : "pg_2644",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6164"
}, {
"study_id" : "pg_2642",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6161"
}, {
"study_id" : "pg_2626",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6142"
}, {
"study_id" : "pg_332",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "333"
}, {
"study_id" : "pg_2832",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6586"
}, {
"study_id" : "pg_1866",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3765"
}, {
"study_id" : "pg_59",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5731"
}, {
"study_id" : "pg_704",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1266"
}, {
"study_id" : "pg_2638",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6157"
}, {
"study_id" : "pg_1974",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4038"
}, {
"study_id" : "pg_1974",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4039"
}, {
"study_id" : "pg_2901",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6721"
}, {
"study_id" : "pg_2906",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6730"
}, {
"study_id" : "pg_1524",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3046"
}, {
"study_id" : "pg_1414",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2837"
}, {
"study_id" : "pg_1411",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5110"
}, {
"study_id" : "pg_1409",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2822"
}, {
"study_id" : "pg_1408",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2821"
}, {
"study_id" : "pg_1407",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2818"
}, {
"study_id" : "pg_1401",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2812"
}, {
"study_id" : "pg_1391",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2795"
}, {
"study_id" : "pg_1434",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2876"
}, {
"study_id" : "pg_2633",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6153"
}, {
"study_id" : "pg_1539",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3088"
}, {
"study_id" : "pg_2634",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6154"
}, {
"study_id" : "pg_1022",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1967"
}, {
"study_id" : "pg_562",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "817"
}, {
"study_id" : "pg_588",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "878"
}, {
"study_id" : "pg_2048",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4220"
}, {
"study_id" : "pg_1137",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2295"
}, {
"study_id" : "pg_62",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2878"
}, {
"study_id" : "pg_2841",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6597"
}, {
"study_id" : "pg_2085",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4317"
}, {
"study_id" : "pg_180",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "794"
}, {
"study_id" : "pg_576",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "849"
}, {
"study_id" : "pg_581",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "859"
}, {
"study_id" : "pg_582",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "862"
}, {
"study_id" : "pg_598",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "926"
}, {
"study_id" : "pg_599",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "927"
}, {
"study_id" : "pg_603",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "940"
}, {
"study_id" : "pg_721",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1298"
}, {
"study_id" : "pg_723",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1300"
}, {
"study_id" : "pg_921",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4103"
}, {
"study_id" : "pg_61",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "816"
}, {
"study_id" : "pg_573",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "839"
}, {
"study_id" : "pg_566",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "832"
}, {
"study_id" : "pg_1522",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3044"
}, {
"study_id" : "pg_1570",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3142"
}, {
"study_id" : "pg_1583",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3194"
}, {
"study_id" : "pg_1572",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3145"
}, {
"study_id" : "pg_2909",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6735"
}, {
"study_id" : "pg_43",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3862"
}, {
"study_id" : "pg_38",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1750"
}, {
"study_id" : "pg_2878",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6673"
}, {
"study_id" : "pg_2624",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6139"
}, {
"study_id" : "pg_2128",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4437"
}, {
"study_id" : "pg_1102",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2177"
}, {
"study_id" : "pg_1129",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2251"
}, {
"study_id" : "pg_1109",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2201"
}, {
"study_id" : "pg_2004",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4118"
}, {
"study_id" : "pg_53",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1280"
}, {
"study_id" : "pg_1118",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2226"
}, {
"study_id" : "pg_2669",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6213"
}, {
"study_id" : "pg_2032",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5922"
}, {
"study_id" : "pg_1901",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3877"
}, {
"study_id" : "pg_713",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1287"
}, {
"study_id" : "pg_2912",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6740"
}, {
"study_id" : "pg_259",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "142"
}, {
"study_id" : "pg_264",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "150"
}, {
"study_id" : "pg_267",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "161"
}, {
"study_id" : "pg_2077",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4291"
}, {
"study_id" : "pg_293",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "201"
}, {
"study_id" : "pg_197",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "784"
}, {
"study_id" : "pg_595",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "896"
}, {
"study_id" : "pg_131",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6236"
}, {
"study_id" : "pg_2689",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6241"
}, {
"study_id" : "pg_597",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "906"
}, {
"study_id" : "pg_2001",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4100"
}, {
"study_id" : "pg_606",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5290"
}, {
"study_id" : "pg_270",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "159"
}, {
"study_id" : "pg_596",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "901"
}, {
"study_id" : "pg_294",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "202"
}, {
"study_id" : "pg_292",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "199"
}, {
"study_id" : "pg_58",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "775"
}, {
"study_id" : "pg_548",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "798"
}, {
"study_id" : "pg_2055",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4234"
}, {
"study_id" : "pg_2057",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4240"
}, {
"study_id" : "pg_2127",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4426"
}, {
"study_id" : "pg_594",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "890"
}, {
"study_id" : "pg_261",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "145"
}, {
"study_id" : "pg_57",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "777"
}, {
"study_id" : "pg_1087",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2114"
}, {
"study_id" : "pg_1087",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2115"
}, {
"study_id" : "pg_2690",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6243"
}, {
"study_id" : "pg_2045",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4213"
}, {
"study_id" : "pg_605",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "947"
}, {
"study_id" : "pg_271",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5017"
}, {
"study_id" : "pg_2661",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6198"
}, {
"study_id" : "pg_2052",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4228"
}, {
"study_id" : "pg_1103",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2178"
}, {
"study_id" : "pg_14",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "12"
}, {
"study_id" : "pg_2598",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6020"
}, {
"study_id" : "pg_2000",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4098"
}, {
"study_id" : "pg_20",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2162"
}, {
"study_id" : "pg_1101",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2172"
}, {
"study_id" : "pg_2565",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5708"
}, {
"study_id" : "pg_1094",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2138"
}, {
"study_id" : "pg_2641",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6160"
}, {
"study_id" : "pg_99",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5885"
}, {
"study_id" : "pg_93",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1411"
}, {
"study_id" : "pg_898",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1732"
}, {
"study_id" : "pg_216",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5865"
}, {
"study_id" : "pg_901",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1740"
}, {
"study_id" : "pg_2830",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6583"
}, {
"study_id" : "pg_2831",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6584"
}, {
"study_id" : "pg_719",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1296"
}, {
"study_id" : "pg_1975",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4041"
}, {
"study_id" : "pg_1821",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3678"
}, {
"study_id" : "pg_1581",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3188"
}, {
"study_id" : "pg_1575",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3164"
}, {
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}, {
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}, {
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}, {
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}, {
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}, {
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}, {
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}, {
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}, {
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}, {
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}, {
"study_id" : "pg_2822",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6569"
}, {
"study_id" : "taxonomy",
"git_sha" : "",
"tree_id" : ""
} ],
"root_taxon_name" : "cellular organisms",
"num_source_studies" : 484,
"taxonomy_version" : "2.8_5",
"root_ott_id" : 93302,
"num_tips" : 2339460,
"date" : "Sun Sep 14 01:27:06 EDT 2014",
"tree_id" : "otol.draft.22"
}
```
There is an optional argument ```list_sources``` which defaults to ```true```.

I've talked to @jar398 about maybe making this a separate service in the future, but at the moment it is just a better version of the existing service.

Would you like to merge @mtholder?