1 | /** |
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2 | * RestController |
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3 | * |
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4 | * This controler provides a REST service. |
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5 | * The names of the RESET resources are the same as the names of this |
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6 | * controller's actions. E.g., the resources called getStudies simply |
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7 | * corresponds to the action getStudies. Some of the resources are parameterized. |
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8 | * The parameters are passed as parameters in the url and are available in the |
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9 | * params respecting Grails' conventions. In this file, we adher to the javadoc |
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10 | * convention for describing parameters ("@param"), but actually we mean |
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11 | * key-value pairs in the params object of each Grails action we comment on. |
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12 | * |
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13 | * @author Jahn-Takeshi Saito |
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14 | * @since 20100601 |
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15 | * |
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16 | */ |
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17 | |
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18 | import dbnp.studycapturing.Study |
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19 | import dbnp.studycapturing.Assay |
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20 | import grails.converters.* |
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21 | import nl.metabolomicscentre.dsp.http.BasicAuthentication |
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22 | |
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23 | |
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24 | class RestController { |
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25 | |
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26 | |
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27 | |
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28 | /**************************************************/ |
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29 | /** Rest resources for Simple Assay Module (SAM) **/ |
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30 | /**************************************************/ |
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31 | |
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32 | def authService |
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33 | def beforeInterceptor = [action:this.&auth,except:["isUser"]] |
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34 | def credentials |
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35 | def requestUser |
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36 | |
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37 | /** |
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38 | * Authorization closure, which is run before executing any of the REST resource actions |
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39 | * It fetches a username/password combination from basic HTTP authentication and checks whether |
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40 | * that is an active (nimble) account |
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41 | * @return |
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42 | */ |
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43 | private def auth() { |
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44 | |
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45 | credentials = BasicAuthentication.credentialsFromRequest(request) |
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46 | requestUser = authService.authUser(credentials.u,credentials.p) |
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47 | if(!requestUser) { |
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48 | response.sendError(403) |
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49 | return false |
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50 | } |
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51 | else { |
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52 | return true |
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53 | } |
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54 | } |
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55 | |
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56 | /** |
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57 | * REST resource for data modules. |
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58 | * Username and password should be supplied via HTTP Basic Authentication. |
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59 | * Determines whether the given user/password combination is a valid GSCF account. |
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60 | * |
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61 | * @return bool {"authenticated":true} when user/password is a valid GSCF account, {"authenticated":false} otherwise. |
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62 | */ |
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63 | def isUser= { |
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64 | boolean isUser |
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65 | credentials = BasicAuthentication.credentialsFromRequest(request) |
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66 | def reqUser = authService.authUser(credentials.u,credentials.p) |
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67 | if (reqUser) { |
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68 | isUser = true |
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69 | } |
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70 | else { |
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71 | isUser = false |
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72 | } |
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73 | def reply = ['authenticated':isUser] |
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74 | render reply as JSON |
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75 | } |
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76 | |
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77 | /** |
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78 | * REST resource for data modules. |
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79 | * Username and password should be supplied via HTTP Basic Authentication. |
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80 | * Provide a list of all studies owned by the supplied user. |
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81 | * |
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82 | * @return JSON object list containing 'studyToken', and 'name' (title) for each study |
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83 | */ |
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84 | def getStudies = { |
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85 | List studies = [] |
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86 | def user = params.user |
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87 | Study.findAllByOwner(requestUser).each { study -> |
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88 | studies.push( [ 'title':study.title, 'studyToken':study.code ] ) |
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89 | } |
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90 | render studies as JSON |
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91 | } |
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92 | |
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93 | |
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94 | /** |
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95 | * REST resource for data modules. |
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96 | * Username and password should be supplied via HTTP Basic Authentication. |
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97 | * Provide a list of all subjects belonging to a study. |
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98 | * |
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99 | * @param studyToken String The external study id (code) of the target GSCF Study object |
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100 | * @return JSON object list of subject names |
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101 | */ |
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102 | def getSubjects = { |
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103 | List subjects = [] |
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104 | if( params.studyToken ) { |
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105 | def id = params.studyToken |
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106 | def study = Study.find( "from Study as s where s.code=?", [id]) |
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107 | if(study) study.subjects.each { subjects.push it.name } |
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108 | } |
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109 | render subjects as JSON |
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110 | } |
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111 | |
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112 | |
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113 | /** |
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114 | * REST resource for data modules. |
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115 | * Username and password should be supplied via HTTP Basic Authentication. |
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116 | * Provide a list of all assays for a given study |
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117 | * |
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118 | * Example call of the getAssays REST resource: |
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119 | * http://localhost:8080/gscf/rest/getAssays?studyToken=PPSH&moduleURL=http://localhost:8182/sam |
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120 | * |
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121 | * @param stuyToken String The external study id (code) of the target GSCF Study object |
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122 | * @param moduleURL String The base URL of the calling dbNP module |
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123 | * @return list of assays in the study as JSON object list, filtered to only contain assays |
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124 | * for the specified module, with 'assayToken' and 'name' for each assay |
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125 | */ |
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126 | def getAssays = { |
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127 | List assays = [] |
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128 | if( params.studyToken ) { |
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129 | def id = params.studyToken |
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130 | def study = Study.find( "from Study as s where s.code=?", [id] ) |
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131 | if(study && study.owner == requestUser) study.assays.each{ assay -> |
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132 | //if (assay.module.url.equals(params.moduleURL)) { |
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133 | def map = ['name':assay.name, 'assayToken':assay.externalAssayID] |
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134 | assays.push( map ) |
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135 | //} |
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136 | } |
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137 | } |
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138 | render assays as JSON |
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139 | } |
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140 | |
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141 | |
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142 | /** |
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143 | * REST resource for data modules. |
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144 | * Username and password should be supplied via HTTP Basic Authentication. |
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145 | * Provide all samples of a given Assay. The result is an enriched list with additional information for each sample. |
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146 | * |
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147 | * @param assayToken String (assayToken of some Assay in GSCF) |
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148 | * @return As a JSON object list, for each sample in that assay: |
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149 | * @return 'name' (Sample name, which is unique) |
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150 | * @return 'material' (Sample material) |
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151 | * @return 'subject' (The name of the subject from which the sample was taken) |
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152 | * @return 'event' (the name of the template of the SamplingEvent describing the sampling) |
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153 | * @return 'startTime' (the time the sample was taken relative to the start of the study, as a string) |
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154 | */ |
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155 | def getSamples = { |
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156 | def items = [] |
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157 | if( params.assayToken ) { |
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158 | def assay = Assay.find( "from Assay as a where externalAssayID=?",[params.assayToken]) |
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159 | assay.getSamples().each { sample -> |
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160 | def item = [ |
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161 | 'sampleToken' : sample.name, |
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162 | 'material' : sample.material.name, |
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163 | 'subject' : sample.parentSubject.name, |
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164 | 'event' : sample.parentEvent.template.name, |
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165 | 'startTime' : sample.parentEvent.getStartTimeString() |
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166 | ] |
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167 | items.push item |
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168 | } |
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169 | } |
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170 | render items as JSON |
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171 | } |
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172 | |
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173 | |
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174 | |
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175 | |
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176 | |
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177 | /** |
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178 | * REST resource for dbNP modules. |
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179 | * |
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180 | * @param studyToken String, the external identifier of the study |
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181 | * @return List of all fields of this study |
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182 | * @return |
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183 | * |
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184 | * Example REST call (without authentication): |
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185 | * http://localhost:8080/gscf/rest/getStudy/study?studyToken=PPSH |
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186 | * |
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187 | * Returns the JSON object: |
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188 | * {"title":"NuGO PPS human study","studyToken":"PPSH","startDate":"2008-01-13T23:00:00Z", |
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189 | * "Description":"Human study performed at RRI; centres involved: RRI, IFR, TUM, Maastricht U.", |
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190 | * "Objectives":null,"Consortium":null,"Cohort name":null,"Lab id":null,"Institute":null, |
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191 | * "Study protocol":null} |
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192 | */ |
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193 | def getStudy = { |
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194 | def items = [:] |
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195 | if( params.studyToken ) { |
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196 | def study = Study.find( "from Study as s where code=?",[params.studyToken]) |
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197 | study.giveFields().each { field -> |
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198 | def name = field.name |
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199 | def value = study.getFieldValue( name ) |
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200 | if(name=="code") { name = "studyToken" } |
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201 | items[name] = value |
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202 | } |
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203 | } |
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204 | render items as JSON |
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205 | } |
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206 | |
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207 | |
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208 | |
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209 | /** |
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210 | * REST resource for dbNP modules. |
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211 | * |
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212 | * @param assayToken String, the external identifier of the study |
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213 | * @return List of all fields of this assay |
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214 | * |
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215 | * Example REST call (without authentication): |
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216 | * http://localhost:8080/gscf/rest/getAssay/assay?assayToken=PPS3_SAM |
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217 | * |
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218 | * Returns the JSON object: {"name":"Lipid profiling","module":{"class":"dbnp.studycapturing.AssayModule","id":1, |
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219 | * "name":"SAM module for clinical data","platform":"clinical measurements","url":"http://sam.nmcdsp.org"}, |
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220 | * "assayToken":"PPS3_SAM","Description":null} |
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221 | */ |
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222 | def getAssay = { |
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223 | def items = [:] |
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224 | if( params.assayToken ) { |
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225 | def assay = Assay.find( "from Assay as a where externalAssayID=?",[params.assayToken]) |
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226 | assay.giveFields().each { field -> |
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227 | def name = field.name |
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228 | def value = assay.getFieldValue( name ) |
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229 | if(name=="externalAssayID") { name = "assayToken" } |
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230 | items[name] = value |
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231 | } |
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232 | } |
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233 | render items as JSON |
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234 | } |
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235 | |
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236 | |
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237 | |
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238 | /** |
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239 | * REST resource for data modules. |
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240 | * Username and password should be supplied via HTTP Basic Authentication. |
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241 | * One specific sample of a given Assay. |
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242 | * |
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243 | * @param assayToken String (id of some Assay in GSCF) |
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244 | * @return As a JSON object list, for each sample in that assay: |
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245 | * @return 'name' (Sample name, which is unique) |
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246 | * @return 'material' (Sample material) |
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247 | * @return 'subject' (The name of the subject from which the sample was taken) |
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248 | * @return 'event' (the name of the template of the SamplingEvent describing the sampling) |
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249 | * @return 'startTime' (the time the sample was taken relative to the start of the study, as a string) |
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250 | * |
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251 | * Example REST call (without authentication): |
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252 | * http://localhost:8080/gscf/rest/getSample/sam?assayToken=PPS3_SAM&sampleToken=A30_B |
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253 | * |
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254 | * Returns the JSON object: |
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255 | * {"subject":"A30","event":"Liver extraction","startTime":"1 week, 1 hour", |
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256 | * "sampleToken":"A30_B","material":{"class":"dbnp.data.Term","id":6,"accession":"BTO:0000131", |
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257 | * "name":"blood plasma","ontology":{"class":"Ontology","id":2}},"Remarks":null, |
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258 | * "Text on vial":"T70.91709057820039","Sample measured volume":null} |
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259 | */ |
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260 | def getSample = { |
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261 | def items = [:] |
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262 | if( params.assayToken && params.sampleToken ) { |
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263 | def assay = Assay.find( "from Assay as a where externalAssayID=?",[params.assayToken]) |
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264 | assay.getSamples().each { sample -> |
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265 | if( sample.name == params.sampleToken ) { |
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266 | items = [ |
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267 | 'subject' : sample.parentSubject.name, |
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268 | 'event' : sample.parentEvent.template.name, |
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269 | 'startTime' : sample.parentEvent.getStartTimeString() |
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270 | ] |
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271 | sample.giveFields().each { field -> |
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272 | def name = field.name |
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273 | def value = sample.getFieldValue( name ) |
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274 | if(name=="name") { name = "sampleToken" } |
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275 | items[name] = value |
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276 | } |
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277 | } |
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278 | } |
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279 | } |
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280 | render items as JSON |
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281 | } |
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282 | } |
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