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comparison BiodbEntry.R @ 1:253d531a0193 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b
author prog
date Sat, 03 Sep 2016 17:02:01 -0400
parents e66bb061af06
children 20d69a062da3
comparison
equal deleted inserted replaced
0:e66bb061af06 1:253d531a0193
18 .factory <<- NULL 18 .factory <<- NULL
19 19
20 callSuper(...) # calls super-class initializer with remaining parameters 20 callSuper(...) # calls super-class initializer with remaining parameters
21 }) 21 })
22 22
23 ############# 23 ###################
24 # SET FIELD # 24 # SET FIELD VALUE #
25 ############# 25 ###################
26 26
27 BiodbEntry$methods( setFieldValue = function(field, value) {
28 .self$setField(field, value)
29 })
30
27 BiodbEntry$methods( setField = function(field, value) { 31 BiodbEntry$methods( setField = function(field, value) {
28 32
29 class = .self$getFieldClass(field) 33 class = .self$getFieldClass(field)
30 34
31 # Check cardinality 35 # Check cardinality
32 if (class != 'data.frame' && .self$getFieldCardinality(field) == RBIODB.CARD.ONE && length(value) > 1) 36 if (class != 'data.frame' && .self$getFieldCardinality(field) == BIODB.CARD.ONE && length(value) > 1)
33 stop(paste0('Cannot set more that one value to single value field "', field, '" in BiodEntry.')) 37 stop(paste0('Cannot set more that one value to single value field "', field, '" in BiodEntry.'))
34 38
35 # Check value class 39 # Check value class
36 value <- switch(class, 40 value <- switch(class,
37 'character' = as.character(value), 41 'character' = as.character(value),
43 47
44 .self$.fields[[field]] <- value 48 .self$.fields[[field]] <- value
45 }) 49 })
46 50
47 ################### 51 ###################
52 # GET FIELD NAMES #
53 ###################
54
55 BiodbEntry$methods( getFieldNames = function(field) {
56 return(names(.self$.fields))
57 })
58
59 ###################
48 # GET FIELD CLASS # 60 # GET FIELD CLASS #
49 ################### 61 ###################
50 62
51 BiodbEntry$methods( getFieldClass = function(field) { 63 BiodbEntry$methods( getFieldClass = function(field) {
52 64
53 if ( ! field %in% RBIODB.FIELDS[['name']]) 65 if ( ! field %in% BIODB.FIELDS[['name']])
54 stop(paste0('Unknown field "', field, '" in BiodEntry.')) 66 stop(paste0('Unknown field "', field, '" in BiodEntry.'))
55 67
56 field.class <- RBIODB.FIELDS[which(field == RBIODB.FIELDS[['name']]), 'class'] 68 field.class <- BIODB.FIELDS[which(field == BIODB.FIELDS[['name']]), 'class']
57 69
58 return(field.class) 70 return(field.class)
59 }) 71 })
60 72
61 ######################### 73 #########################
62 # GET FIELD CARDINALITY # 74 # GET FIELD CARDINALITY #
63 ######################### 75 #########################
64 76
65 BiodbEntry$methods( getFieldCardinality = function(field) { 77 BiodbEntry$methods( getFieldCardinality = function(field) {
66 78
67 if ( ! field %in% RBIODB.FIELDS[['name']]) 79 if ( ! field %in% BIODB.FIELDS[['name']])
68 stop(paste0('Unknown field "', field, '" in BiodEntry.')) 80 stop(paste0('Unknown field "', field, '" in BiodEntry.'))
69 81
70 field.card <- RBIODB.FIELDS[which(field == RBIODB.FIELDS[['name']]), 'cardinality'] 82 field.card <- BIODB.FIELDS[which(field == BIODB.FIELDS[['name']]), 'cardinality']
71 83
72 return(field.card) 84 return(field.card)
73 }) 85 })
74 86
75 ############# 87 ###################
76 # GET FIELD # 88 # GET FIELD VALUE #
77 ############# 89 ###################
78 90
91 BiodbEntry$methods( getFieldValue = function(field) {
92 return(.self$getField(field))
93 })
94
79 BiodbEntry$methods( getField = function(field) { 95 BiodbEntry$methods( getField = function(field) {
80 96
81 if ( ! field %in% RBIODB.FIELDS[['name']]) 97 if ( ! field %in% BIODB.FIELDS[['name']])
82 stop(paste0('Unknown field "', field, '" in BiodEntry.')) 98 stop(paste0('Unknown field "', field, '" in BiodEntry.'))
83 99
84 if (field %in% names(.self$.fields)) 100 if (field %in% names(.self$.fields))
85 return(.self$.fields[[field]]) 101 return(.self$.fields[[field]])
86 else if (.self$.compute.field(field)) 102 else if (.self$.compute.field(field))
95 # COMPUTE FIELD # 111 # COMPUTE FIELD #
96 ################## 112 ##################
97 113
98 BiodbEntry$methods( .compute.field = function(field) { 114 BiodbEntry$methods( .compute.field = function(field) {
99 115
100 if ( ! is.null(.self$.factory) && field %in% names(RBIODB.FIELD.COMPUTING)) { 116 if ( ! is.null(.self$.factory) && field %in% names(BIODB.FIELD.COMPUTING)) {
101 for (db in RBIODB.FIELD.COMPUTING[[field]]) { 117 for (db in BIODB.FIELD.COMPUTING[[field]]) {
102 db.id <- .self$getField(paste0(db, 'id')) 118 db.id <- .self$getField(paste0(db, 'id'))
103 if ( ! is.na(db.id)) { 119 if ( ! is.na(db.id)) {
104 db.compound <- .self$.factory$createEntry(db, type = RBIODB.COMPOUND, id = db.id) 120 db.compound <- .self$.factory$createEntry(db, type = BIODB.COMPOUND, id = db.id)
105 if ( ! is.null(db.compound)) { 121 if ( ! is.null(db.compound)) {
106 .self$setField(field, db.compound$getField(field)) 122 .self$setField(field, db.compound$getField(field))
107 return(TRUE) 123 return(TRUE)
108 } 124 }
109 } 125 }
110 } 126 }
111 } 127 }
112 128
113 return(FALSE) 129 return(FALSE)
130 })
131
132 ############################
133 # GET FIELDS AS DATA FRAME #
134 ############################
135
136 BiodbEntry$methods( getFieldsAsDataFrame = function(field) {
137
138 df <- data.frame()
139
140 # Loop on all fields
141 for (f in names(.self$.fields))
142
143 # If field class is a basic type
144 if (.self$getFieldClass(f) %in% c('character', 'logical', 'integer', 'double'))
145 df[1, f] <- .self$getFieldValue(f)
146
147 return(df)
114 }) 148 })
115 149
116 ########### 150 ###########
117 # FACTORY # 151 # FACTORY #
118 ########### 152 ###########