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comparison BiodbConn.R @ 2:20d69a062da3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
author prog
date Thu, 02 Mar 2017 08:55:00 -0500
parents 253d531a0193
children
comparison
equal deleted inserted replaced
1:253d531a0193 2:20d69a062da3
1 if ( ! exists('BiodbConn')) { 1 #####################
2 # CLASS DECLARATION #
3 #####################
2 4
3 source('biodb-common.R') 5 BiodbConn <- methods::setRefClass("BiodbConn", contains = "BiodbObject", fields = list( .debug = "logical" ))
4 6
5 ##################### 7 ###############
6 # CLASS DECLARATION # 8 # CONSTRUCTOR #
7 ##################### 9 ###############
8
9 BiodbConn <- setRefClass("BiodbConn", fields = list( .debug = "logical" ))
10 10
11 ############### 11 BiodbConn$methods( initialize = function(debug = FALSE, ...) {
12 # CONSTRUCTOR # 12 .debug <<- debug
13 ############### 13 })
14 14
15 BiodbConn$methods( initialize = function(debug = FALSE, ...) { 15 #######################
16 .debug <<- debug 16 # PRINT DEBUG MESSAGE #
17 }) 17 #######################
18 18
19 ####################### 19 BiodbConn$methods( .print.debug.msg = function(msg) {
20 # PRINT DEBUG MESSAGE # 20 if (.self$.debug)
21 ####################### 21 .print.msg(msg = msg, class = class(.self))
22 })
22 23
23 BiodbConn$methods( .print.debug.msg = function(msg) { 24 ##########################
24 if (.self$.debug) 25 # GET ENTRY CONTENT TYPE #
25 .print.msg(msg = msg, class = class(.self)) 26 ##########################
26 })
27 27
28 ###################### 28 BiodbConn$methods( getEntryContentType = function() {
29 # HANDLES ENTRY TYPE # 29 .self$.abstract.method()
30 ###################### 30 })
31 31
32 BiodbConn$methods( handlesEntryType = function(type) { 32 #############
33 return( ! is.null(.self$getEntryContentType(type))) 33 # GET ENTRY #
34 }) 34 #############
35 35
36 ########################## 36 BiodbConn$methods( getEntry = function(id, drop = TRUE) {
37 # GET ENTRY CONTENT TYPE # 37 content <- .self$getEntryContent(id)
38 ########################## 38 return(.self$createEntry(content, drop = drop))
39 })
39 40
40 BiodbConn$methods( getEntryContentType = function(type) { 41 #####################
41 stop("Method getEntryContentType() is not implemented in concrete class.") 42 # GET ENTRY CONTENT #
42 }) 43 #####################
43 44
44 ############# 45 # Download entry content from the public database.
45 # GET ENTRY # 46 # type The entry type.
46 ############# 47 # id The ID of the entry to get.
48 # RETURN An entry content downloaded from database.
49 BiodbConn$methods( getEntryContent = function(id) {
50 .self$.abstract.method()
51 })
47 52
48 BiodbConn$methods( getEntry = function(type, id, drop = TRUE) { 53 #############################
49 content <- .self$getEntryContent(type, id) 54 # CREATE ENTRY FROM CONTENT #
50 return(.self$createEntry(type, content, drop = drop)) 55 #############################
51 })
52 56
53 ##################### 57 # Creates a Compound instance from file content.
54 # GET ENTRY CONTENT # 58 # content A file content, downloaded from the public database.
55 ##################### 59 # RETURN A compound instance.
56 60 BiodbConn$methods( createEntry = function(content, drop = TRUE) {
57 # Download entry content from the public database. 61 .self$.abstract.method()
58 # type The entry type. 62 })
59 # id The ID of the entry to get.
60 # RETURN An entry content downloaded from database.
61 BiodbConn$methods( getEntryContent = function(type, id) {
62 stop("Method getCompound() is not implemented in concrete class.")
63 })
64
65 #############################
66 # CREATE ENTRY FROM CONTENT #
67 #############################
68
69 # Creates a Compound instance from file content.
70 # content A file content, downloaded from the public database.
71 # RETURN A compound instance.
72 BiodbConn$methods( createEntry = function(type, content, drop = TRUE) {
73 stop("Method createEntry() is not implemented in concrete class.")
74 })
75 63
76 ################# 64 #################
77 # GET ENTRY IDS # 65 # GET ENTRY IDS #
78 ################# 66 #################
79
80 # Get a list of IDs of all entries contained in this database.
81 BiodbConn$methods( getEntryIds = function(type) {
82 stop("Method getEntryIds() is not implemented in concrete class.")
83 })
84 67
85 ################## 68 # Get a list of IDs of all entries contained in this database.
86 # GET NB ENTRIES # 69 BiodbConn$methods( getEntryIds = function(max.results = NA_integer_) {
87 ################## 70 .self$.abstract.method()
88 71 })
89 # Get the number of entries contained in this database. 72
90 BiodbConn$methods( getNbEntries = function(type) { 73 ##################
91 stop("Method getNbEntries() is not implemented in concrete class.") 74 # GET NB ENTRIES #
92 }) 75 ##################
93 } 76
77 # Get the number of entries contained in this database.
78 BiodbConn$methods( getNbEntries = function() {
79 .self$.abstract.method()
80 })