Mercurial > repos > lain > xseekerpreparator

comparison data/models.R @ 19:2937e72e5891 draft

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" master branch Updating"
author lain
date Tue, 18 Oct 2022 12:57:28 +0000
parents d8112d636210
children
comparison
equal deleted inserted replaced
18:2c7e7fd1f740 19:2937e72e5891
1 1
2 tryCatch({ 2 tryCatch({
3 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER")) 3 DBModelR::ModelDefinition(table = "yui", fields = list(yui = "INTEGER"))
4 }, error=function(e) { 4 }, error = function(e) {
5 stop("Please, install DBModelR before you source this file.") 5 stop("Please, install DBModelR before you source this file.")
6 }) 6 })
7 7
8 list( 8 list(
9 adduct=DBModelR::ModelDefinition( 9 adduct = DBModelR::ModelDefinition(
10 table="adduct", 10 table = "adduct",
11 fields=list( 11 fields = list(
12 name="TEXT", 12 name = "TEXT",
13 mass="FLOAT", 13 mass = "FLOAT",
14 charge="INTEGER", 14 charge = "INTEGER",
15 multi="INTEGER", 15 multi = "INTEGER",
16 formula_add="TEXT", 16 formula_add = "TEXT",
17 formula_ded="TEXT", 17 formula_ded = "TEXT",
18 sign="TEXT", 18 sign = "TEXT",
19 oidscore="INTEGER", 19 oidscore = "INTEGER",
20 quasi="INTEGER", 20 quasi = "INTEGER",
21 ips="FLOAT" 21 ips = "FLOAT"
22 ) 22 )
23 ), 23 ),
24 cluster=DBModelR::ModelDefinition( 24 cluster = DBModelR::ModelDefinition(
25 table="cluster", 25 table = "cluster",
26 fields=list( 26 fields = list(
27 clusterID="INTEGER", 27 clusterID = "INTEGER",
28 formula="TEXT", 28 formula = "TEXT",
29 annotation="TEXT", 29 annotation = "TEXT",
30 coeff="FLOAT", 30 coeff = "FLOAT",
31 r_squared="FLOAT", 31 r_squared = "FLOAT",
32 charge="INTEGER", 32 charge = "INTEGER",
33 mean_rt="FLOAT", 33 mean_rt = "FLOAT",
34 score="FLOAT", 34 score = "FLOAT",
35 deviation="FLOAT", 35 deviation = "FLOAT",
36 status="TEXT", 36 status = "TEXT",
37 # adduct="TEXT", 37 # adduct = "TEXT",
38 curent_group="INTEGER", 38 curent_group = "INTEGER",
39 pc_group="INTEGER", 39 pc_group = "INTEGER",
40 align_group="INTEGER", 40 align_group = "INTEGER",
41 xcms_group="INTEGER" 41 xcms_group = "INTEGER"
42 ), 42 ),
43 one=list("compound", "adduct"), 43 one = list("compound", "adduct"),
44 many=list("sample") 44 many = list("sample")
45 ), 45 ),
46 compound=DBModelR::ModelDefinition( 46 compound = DBModelR::ModelDefinition(
47 table="compound", 47 table = "compound",
48 fields=list( 48 fields = list(
49 name="TEXT", 49 name = "TEXT",
50 common_name="TEXT", 50 common_name = "TEXT",
51 formula="TEXT", 51 formula = "TEXT",
52 charge="INTEGER", 52 charge = "INTEGER",
53 date="TEXT", 53 date = "TEXT",
54 mz="FLOAT" 54 mz = "FLOAT"
55 ) 55 )
56 ), 56 ),
57 feature=DBModelR::ModelDefinition( 57 feature = DBModelR::ModelDefinition(
58 table="feature", 58 table = "feature",
59 fields=list( 59 fields = list(
60 featureID="INTEGER", 60 featureID = "INTEGER",
61 mz="FLOAT", 61 mz = "FLOAT",
62 mz_min="FLOAT", 62 mz_min = "FLOAT",
63 mz_max="FLOAT", 63 mz_max = "FLOAT",
64 rt="FLOAT", 64 rt = "FLOAT",
65 rt_min="FLOAT", 65 rt_min = "FLOAT",
66 rt_max="FLOAT", 66 rt_max = "FLOAT",
67 int_o="FLOAT", 67 int_o = "FLOAT",
68 int_b="FLOAT", 68 int_b = "FLOAT",
69 max_o="FLOAT", 69 max_o = "FLOAT",
70 iso="TEXT", 70 iso = "TEXT",
71 abundance="FLOAT" 71 abundance = "FLOAT"
72 ), 72 ),
73 one=list("cluster"), 73 one = list("cluster"),
74 many=list("sample") 74 many = list("sample")
75 ), 75 ),
76 instrument=DBModelR::ModelDefinition( 76 instrument = DBModelR::ModelDefinition(
77 table="instrument", 77 table = "instrument",
78 fields=list( 78 fields = list(
79 model="TEXT", 79 model = "TEXT",
80 manufacturer="TEXT", 80 manufacturer = "TEXT",
81 analyzer="TEXT", 81 analyzer = "TEXT",
82 detector_type="TEXT", 82 detector_type = "TEXT",
83 ion_source="TEXT" 83 ion_source = "TEXT"
84 ) 84 )
85 ), 85 ),
86 instrument_config=DBModelR::ModelDefinition( 86 instrument_config = DBModelR::ModelDefinition(
87 table="instrument_config", 87 table = "instrument_config",
88 fields=list( 88 fields = list(
89 resolution="TEXT", 89 resolution = "TEXT",
90 agc_target="TEXT", 90 agc_target = "TEXT",
91 maximum_IT="TEXT", 91 maximum_IT = "TEXT",
92 number_of_scan_range="TEXT", 92 number_of_scan_range = "TEXT",
93 scan_range="TEXT", 93 scan_range = "TEXT",
94 version="TEXT" 94 version = "TEXT"
95 ) 95 )
96 ), 96 ),
97 project=DBModelR::ModelDefinition( 97 project = DBModelR::ModelDefinition(
98 table="project", 98 table = "project",
99 fields=list( 99 fields = list(
100 name="TEXT", 100 name = "TEXT",
101 comment="TEXT" 101 comment = "TEXT"
102 ), 102 ),
103 one=list("sample") 103 one = list("sample")
104 ), 104 ),
105 sample=DBModelR::ModelDefinition( 105 sample = DBModelR::ModelDefinition(
106 table="sample", 106 table = "sample",
107 fields=list( 107 fields = list(
108 name="TEXT", 108 name = "TEXT",
109 path="TEXT", 109 path = "TEXT",
110 polarity="TEXT", 110 polarity = "TEXT",
111 kind="TEXT", ## rdata or mxml or enriched_rdata 111 kind = "TEXT", ## rdata or mxml or enriched_rdata
112 raw="BLOB" 112 raw = "BLOB"
113 ), 113 ),
114 one=list( 114 one = list(
115 "peak_picking_parameters", 115 "peak_picking_parameters",
116 "pairing_parameters", 116 "pairing_parameters",
117 "alignmenmt_parameters", 117 "alignmenmt_parameters",
118 "camera_parameters", 118 "camera_parameters",
119 "instrument", 119 "instrument",
120 "instrument_config", 120 "instrument_config",
121 "software", 121 "software",
122 "smol_xcms_set" 122 "smol_xcms_set"
123 ) 123 )
124 ), 124 ),
125 smol_xcms_set=DBModelR::ModelDefinition( 125 smol_xcms_set = DBModelR::ModelDefinition(
126 table="smol_xcms_set", 126 table = "smol_xcms_set",
127 fields=list( 127 fields = list(
128 raw="BLOB" 128 raw = "BLOB"
129 ) 129 )
130 ), 130 ),
131 software=DBModelR::ModelDefinition( 131 software = DBModelR::ModelDefinition(
132 table="software", 132 table = "software",
133 fields=list( 133 fields = list(
134 name="TEXT", 134 name = "TEXT",
135 version="TEXT" 135 version = "TEXT"
136 ) 136 )
137 ), 137 ),
138 # camera_parameters=DBModelR::ModelDefinition( 138 peak_picking_parameters = DBModelR::ModelDefinition(
139 # table="camera_parameters", 139 table = "peak_picking_parameters",
140 # fields=list() 140 fields = list(
141 # ), 141 ppm = "FLOAT",
142 # pairing_parameters=DBModelR::ModelDefinition( 142 peakwidth = "TEXT",
143 # table="pairing_parameters", 143 snthresh = "TEXT",
144 # fields=list() 144 prefilterStep = "TEXT",
145 # ), 145 prefilterLevel = "TEXT",
146 peak_picking_parameters=DBModelR::ModelDefinition( 146 mzdiff = "TEXT",
147 table="peak_picking_parameters", 147 fitgauss = "TEXT",
148 fields=list( 148 noise = "TEXT",
149 ppm="FLOAT", 149 mzCenterFun = "TEXT",
150 peakwidth="TEXT", 150 integrate = "INTEGER",
151 snthresh="TEXT", 151 firstBaselineCheck = "TEXT",
152 prefilterStep="TEXT", 152 snthreshIsoROIs = "TEXT",
153 prefilterLevel="TEXT", 153 maxCharge = "INTEGER",
154 mzdiff="TEXT", 154 maxIso = "INTEGER",
155 fitgauss="TEXT", 155 mzIntervalExtension = "TEXT"
156 noise="TEXT",
157 mzCenterFun="TEXT",
158 integrate="INTEGER",
159 firstBaselineCheck="TEXT",
160 snthreshIsoROIs="TEXT",
161 maxCharge="INTEGER",
162 maxIso="INTEGER",
163 mzIntervalExtension="TEXT"
164 ) 156 )
165 ), 157 ),
166 alignmenmt_parameters=DBModelR::ModelDefinition( 158 alignmenmt_parameters = DBModelR::ModelDefinition(
167 table="alignmenmt_parameters", 159 table = "alignmenmt_parameters",
168 fields=list( 160 fields = list(
169 binSize="TEXT", 161 binSize = "TEXT",
170 centerSample="TEXT", 162 centerSample = "TEXT",
171 response="TEXT", 163 response = "TEXT",
172 distFun="TEXT", 164 distFun = "TEXT",
173 gapInit="TEXT", 165 gapInit = "TEXT",
174 gapExtend="TEXT", 166 gapExtend = "TEXT",
175 factorDiag="TEXT", 167 factorDiag = "TEXT",
176 factorGap="TEXT", 168 factorGap = "TEXT",
177 localAlignment="INTEGER", 169 localAlignment = "INTEGER",
178 initPenalty="TEXT", 170 initPenalty = "TEXT",
179 bw="TEXT", 171 bw = "TEXT",
180 minFraction="TEXT", 172 minFraction = "TEXT",
181 minSamples="TEXT", 173 minSamples = "TEXT",
182 maxFeatures="TEXT" 174 maxFeatures = "TEXT"
183 ) 175 )
184 ) 176 )
185 ) 177 )