|
0
|
1
|
|
|
2 tryCatch({
|
|
|
3 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
|
|
|
4 }, error=function(e) {
|
|
|
5 stop("Please, install DBModelR before you source this file.")
|
|
|
6 })
|
|
|
7
|
|
|
8 list(
|
|
|
9 adduct=DBModelR::ModelDefinition(
|
|
|
10 table="adduct",
|
|
|
11 fields=list(
|
|
|
12 name="TEXT",
|
|
|
13 mass="FLOAT",
|
|
|
14 charge="INTEGER",
|
|
|
15 multi="INTEGER",
|
|
|
16 formula_add="TEXT",
|
|
|
17 formula_ded="TEXT",
|
|
|
18 sign="TEXT",
|
|
|
19 oidscore="INTEGER",
|
|
|
20 quasi="INTEGER",
|
|
|
21 ips="FLOAT"
|
|
|
22 )
|
|
|
23 ),
|
|
|
24 cluster=DBModelR::ModelDefinition(
|
|
|
25 table="cluster",
|
|
|
26 fields=list(
|
|
|
27 clusterID="INTEGER",
|
|
|
28 formula="TEXT",
|
|
|
29 annotation="TEXT",
|
|
|
30 coeff="FLOAT",
|
|
|
31 r_squared="FLOAT",
|
|
|
32 charge="INTEGER",
|
|
|
33 mean_rt="FLOAT",
|
|
|
34 score="FLOAT",
|
|
|
35 deviation="FLOAT",
|
|
|
36 status="TEXT",
|
|
14
|
37 # adduct="TEXT",
|
|
0
|
38 curent_group="INTEGER",
|
|
|
39 pc_group="INTEGER",
|
|
|
40 align_group="INTEGER",
|
|
|
41 xcms_group="INTEGER"
|
|
|
42 ),
|
|
14
|
43 one=list("compound", "adduct", "sample")
|
|
0
|
44 ),
|
|
|
45 compound=DBModelR::ModelDefinition(
|
|
|
46 table="compound",
|
|
|
47 fields=list(
|
|
|
48 name="TEXT",
|
|
|
49 common_name="TEXT",
|
|
|
50 formula="TEXT",
|
|
|
51 charge="INTEGER",
|
|
|
52 date="TEXT",
|
|
|
53 mz="FLOAT"
|
|
|
54 )
|
|
|
55 ),
|
|
|
56 feature=DBModelR::ModelDefinition(
|
|
|
57 table="feature",
|
|
|
58 fields=list(
|
|
|
59 featureID="INTEGER",
|
|
|
60 mz="FLOAT",
|
|
|
61 mz_min="FLOAT",
|
|
|
62 mz_max="FLOAT",
|
|
|
63 rt="FLOAT",
|
|
|
64 rt_min="FLOAT",
|
|
|
65 rt_max="FLOAT",
|
|
|
66 int_o="FLOAT",
|
|
|
67 int_b="FLOAT",
|
|
|
68 max_o="FLOAT",
|
|
|
69 iso="TEXT",
|
|
|
70 abundance="FLOAT"
|
|
|
71 ),
|
|
14
|
72 one=list("cluster"),
|
|
|
73 many=list("sample")
|
|
0
|
74 ),
|
|
|
75 instrument=DBModelR::ModelDefinition(
|
|
|
76 table="instrument",
|
|
|
77 fields=list(
|
|
|
78 model="TEXT",
|
|
|
79 manufacturer="TEXT",
|
|
|
80 analyzer="TEXT",
|
|
|
81 detector_type="TEXT",
|
|
|
82 ion_source="TEXT"
|
|
|
83 )
|
|
|
84 ),
|
|
|
85 instrument_config=DBModelR::ModelDefinition(
|
|
|
86 table="instrument_config",
|
|
|
87 fields=list(
|
|
|
88 resolution="TEXT",
|
|
|
89 agc_target="TEXT",
|
|
|
90 maximum_IT="TEXT",
|
|
|
91 number_of_scan_range="TEXT",
|
|
|
92 scan_range="TEXT",
|
|
|
93 version="TEXT"
|
|
|
94 )
|
|
|
95 ),
|
|
|
96 project=DBModelR::ModelDefinition(
|
|
|
97 table="project",
|
|
|
98 fields=list(
|
|
|
99 name="TEXT",
|
|
|
100 comment="TEXT"
|
|
|
101 ),
|
|
|
102 one=list("sample")
|
|
|
103 ),
|
|
|
104 sample=DBModelR::ModelDefinition(
|
|
|
105 table="sample",
|
|
|
106 fields=list(
|
|
|
107 name="TEXT",
|
|
|
108 path="TEXT",
|
|
|
109 polarity="TEXT",
|
|
|
110 kind="TEXT", ## rdata or mxml or enriched_rdata
|
|
|
111 raw="BLOB"
|
|
|
112 ),
|
|
|
113 one=list(
|
|
|
114 "peak_picking_parameters",
|
|
|
115 "pairing_parameters",
|
|
|
116 "alignmenmt_parameters",
|
|
|
117 "camera_parameters",
|
|
|
118 "instrument",
|
|
|
119 "instrument_config",
|
|
|
120 "software",
|
|
|
121 "smol_xcms_set"
|
|
|
122 )
|
|
|
123 ),
|
|
|
124 smol_xcms_set=DBModelR::ModelDefinition(
|
|
|
125 table="smol_xcms_set",
|
|
|
126 fields=list(
|
|
|
127 raw="BLOB"
|
|
|
128 )
|
|
|
129 ),
|
|
|
130 software=DBModelR::ModelDefinition(
|
|
|
131 table="software",
|
|
|
132 fields=list(
|
|
|
133 name="TEXT",
|
|
|
134 version="TEXT"
|
|
|
135 )
|
|
|
136 ),
|
|
|
137 # camera_parameters=DBModelR::ModelDefinition(
|
|
|
138 # table="camera_parameters",
|
|
|
139 # fields=list()
|
|
|
140 # ),
|
|
|
141 # pairing_parameters=DBModelR::ModelDefinition(
|
|
|
142 # table="pairing_parameters",
|
|
|
143 # fields=list()
|
|
|
144 # ),
|
|
|
145 peak_picking_parameters=DBModelR::ModelDefinition(
|
|
|
146 table="peak_picking_parameters",
|
|
|
147 fields=list(
|
|
|
148 ppm="FLOAT",
|
|
|
149 peakwidth="TEXT",
|
|
|
150 snthresh="TEXT",
|
|
|
151 prefilterStep="TEXT",
|
|
|
152 prefilterLevel="TEXT",
|
|
|
153 mzdiff="TEXT",
|
|
|
154 fitgauss="TEXT",
|
|
|
155 noise="TEXT",
|
|
|
156 mzCenterFun="TEXT",
|
|
|
157 integrate="INTEGER",
|
|
|
158 firstBaselineCheck="TEXT",
|
|
|
159 snthreshIsoROIs="TEXT",
|
|
|
160 maxCharge="INTEGER",
|
|
|
161 maxIso="INTEGER",
|
|
|
162 mzIntervalExtension="TEXT"
|
|
|
163 )
|
|
|
164 ),
|
|
|
165 alignmenmt_parameters=DBModelR::ModelDefinition(
|
|
|
166 table="alignmenmt_parameters",
|
|
|
167 fields=list(
|
|
|
168 binSize="TEXT",
|
|
|
169 centerSample="TEXT",
|
|
|
170 response="TEXT",
|
|
|
171 distFun="TEXT",
|
|
|
172 gapInit="TEXT",
|
|
|
173 gapExtend="TEXT",
|
|
|
174 factorDiag="TEXT",
|
|
|
175 factorGap="TEXT",
|
|
|
176 localAlignment="INTEGER",
|
|
|
177 initPenalty="TEXT",
|
|
|
178 bw="TEXT",
|
|
|
179 minFraction="TEXT",
|
|
|
180 minSamples="TEXT",
|
|
|
181 maxFeatures="TEXT"
|
|
|
182 )
|
|
|
183 )
|
|
|
184 )
|
