annotate data/models.R @ 20:ce94e7a141bb draft default tip

" master branch Updating"
author lain
date Tue, 06 Dec 2022 10:18:10 +0000
parents 2937e72e5891
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
1
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
2 tryCatch({
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
3 DBModelR::ModelDefinition(table = "yui", fields = list(yui = "INTEGER"))
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
4 }, error = function(e) {
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
5 stop("Please, install DBModelR before you source this file.")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
6 })
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
7
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
8 list(
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
9 adduct = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
10 table = "adduct",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
11 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
12 name = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
13 mass = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
14 charge = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
15 multi = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
16 formula_add = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
17 formula_ded = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
18 sign = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
19 oidscore = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
20 quasi = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
21 ips = "FLOAT"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
22 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
23 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
24 cluster = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
25 table = "cluster",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
26 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
27 clusterID = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
28 formula = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
29 annotation = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
30 coeff = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
31 r_squared = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
32 charge = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
33 mean_rt = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
34 score = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
35 deviation = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
36 status = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
37 # adduct = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
38 curent_group = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
39 pc_group = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
40 align_group = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
41 xcms_group = "INTEGER"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
42 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
43 one = list("compound", "adduct"),
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
44 many = list("sample")
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
45 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
46 compound = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
47 table = "compound",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
48 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
49 name = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
50 common_name = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
51 formula = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
52 charge = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
53 date = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
54 mz = "FLOAT"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
55 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
56 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
57 feature = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
58 table = "feature",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
59 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
60 featureID = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
61 mz = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
62 mz_min = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
63 mz_max = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
64 rt = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
65 rt_min = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
66 rt_max = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
67 int_o = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
68 int_b = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
69 max_o = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
70 iso = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
71 abundance = "FLOAT"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
72 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
73 one = list("cluster"),
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
74 many = list("sample")
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
75 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
76 instrument = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
77 table = "instrument",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
78 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
79 model = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
80 manufacturer = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
81 analyzer = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
82 detector_type = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
83 ion_source = "TEXT"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
84 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
85 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
86 instrument_config = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
87 table = "instrument_config",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
88 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
89 resolution = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
90 agc_target = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
91 maximum_IT = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
92 number_of_scan_range = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
93 scan_range = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
94 version = "TEXT"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
95 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
96 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
97 project = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
98 table = "project",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
99 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
100 name = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
101 comment = "TEXT"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
102 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
103 one = list("sample")
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
104 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
105 sample = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
106 table = "sample",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
107 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
108 name = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
109 path = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
110 polarity = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
111 kind = "TEXT", ## rdata or mxml or enriched_rdata
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
112 raw = "BLOB"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
113 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
114 one = list(
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
115 "peak_picking_parameters",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
116 "pairing_parameters",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
117 "alignmenmt_parameters",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
118 "camera_parameters",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
119 "instrument",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
120 "instrument_config",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
121 "software",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
122 "smol_xcms_set"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
123 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
124 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
125 smol_xcms_set = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
126 table = "smol_xcms_set",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
127 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
128 raw = "BLOB"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
129 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
130 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
131 software = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
132 table = "software",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
133 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
134 name = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
135 version = "TEXT"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
136 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
137 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
138 peak_picking_parameters = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
139 table = "peak_picking_parameters",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
140 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
141 ppm = "FLOAT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
142 peakwidth = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
143 snthresh = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
144 prefilterStep = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
145 prefilterLevel = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
146 mzdiff = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
147 fitgauss = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
148 noise = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
149 mzCenterFun = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
150 integrate = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
151 firstBaselineCheck = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
152 snthreshIsoROIs = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
153 maxCharge = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
154 maxIso = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
155 mzIntervalExtension = "TEXT"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
156 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
157 ),
19
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
158 alignmenmt_parameters = DBModelR::ModelDefinition(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
159 table = "alignmenmt_parameters",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
160 fields = list(
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
161 binSize = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
162 centerSample = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
163 response = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
164 distFun = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
165 gapInit = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
166 gapExtend = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
167 factorDiag = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
168 factorGap = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
169 localAlignment = "INTEGER",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
170 initPenalty = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
171 bw = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
172 minFraction = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
173 minSamples = "TEXT",
2937e72e5891 " master branch Updating"
lain
parents: 17
diff changeset
174 maxFeatures = "TEXT"
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
175 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
176 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
177 )