001 002package ca.uhn.fhir.jpa.rp.dstu3; 003 004import java.util.*; 005 006import org.apache.commons.lang3.StringUtils; 007 008import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; 009import ca.uhn.fhir.model.api.Include; 010import ca.uhn.fhir.model.api.annotation.*; 011import org.hl7.fhir.dstu3.model.*; 012import ca.uhn.fhir.rest.annotation.*; 013import ca.uhn.fhir.rest.param.*; 014import ca.uhn.fhir.rest.api.SortSpec; 015import ca.uhn.fhir.rest.api.SummaryEnum; 016import ca.uhn.fhir.rest.api.SearchTotalModeEnum; 017import ca.uhn.fhir.rest.api.SearchContainedModeEnum; 018 019public class SequenceResourceProvider extends 020 ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider<Sequence> 021 { 022 023 @Override 024 public Class<Sequence> getResourceType() { 025 return Sequence.class; 026 } 027 028 @Search(allowUnknownParams=true) 029 public ca.uhn.fhir.rest.api.server.IBundleProvider search( 030 jakarta.servlet.http.HttpServletRequest theServletRequest, 031 jakarta.servlet.http.HttpServletResponse theServletResponse, 032 033 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails, 034 035 @Description(shortDefinition="Search the contents of the resource's data using a filter") 036 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_FILTER) 037 StringAndListParam theFtFilter, 038 039 @Description(shortDefinition="Search the contents of the resource's data using a fulltext search") 040 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT) 041 StringAndListParam theFtContent, 042 043 @Description(shortDefinition="Search the contents of the resource's narrative using a fulltext search") 044 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_TEXT) 045 StringAndListParam theFtText, 046 047 @Description(shortDefinition="Search for resources which have the given tag") 048 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_TAG) 049 TokenAndListParam theSearchForTag, 050 051 @Description(shortDefinition="Search for resources which have the given security labels") 052 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_SECURITY) 053 TokenAndListParam theSearchForSecurity, 054 055 @Description(shortDefinition="Search for resources which have the given profile") 056 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_PROFILE) 057 UriAndListParam theSearchForProfile, 058 059 @Description(shortDefinition="Search the contents of the resource's data using a list") 060 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_LIST) 061 StringAndListParam theList, 062 063 @Description(shortDefinition="The language of the resource") 064 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_LANGUAGE) 065 TokenAndListParam theResourceLanguage, 066 067 @Description(shortDefinition="Search for resources which have the given source value (Resource.meta.source)") 068 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE) 069 UriAndListParam theSearchForSource, 070 071 @Description(shortDefinition="Return resources linked to by the given target") 072 @OptionalParam(name="_has") 073 HasAndListParam theHas, 074 075 076 077 @Description(shortDefinition="The ID of the resource") 078 @OptionalParam(name="_id") 079 TokenAndListParam the_id, 080 081 082 @Description(shortDefinition="Chromosome number of the reference sequence") 083 @OptionalParam(name="chromosome") 084 TokenAndListParam theChromosome, 085 086 087 @Description(shortDefinition="Search parameter for region of the reference DNA sequence string. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `coordinate=1$lt345$gt123`, this means it will search for the Sequence resource on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.") 088 @OptionalParam(name="coordinate", compositeTypes= { TokenParam.class, NumberParam.class }) 089 CompositeAndListParam<TokenParam, NumberParam> theCoordinate, 090 091 092 @Description(shortDefinition="End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence.") 093 @OptionalParam(name="end") 094 NumberAndListParam theEnd, 095 096 097 @Description(shortDefinition="The unique identity for a particular sequence") 098 @OptionalParam(name="identifier") 099 TokenAndListParam theIdentifier, 100 101 102 @Description(shortDefinition="The subject that the observation is about") 103 @OptionalParam(name="patient", targetTypes={ } ) 104 ReferenceAndListParam thePatient, 105 106 107 @Description(shortDefinition="Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence.") 108 @OptionalParam(name="start") 109 NumberAndListParam theStart, 110 111 112 @Description(shortDefinition="Amino Acid Sequence/ DNA Sequence / RNA Sequence") 113 @OptionalParam(name="type") 114 TokenAndListParam theType, 115 116 @RawParam 117 Map<String, List<String>> theAdditionalRawParams, 118 119 @Description(shortDefinition="Only return resources which were last updated as specified by the given range") 120 @OptionalParam(name="_lastUpdated") 121 DateRangeParam theLastUpdated, 122 123 @IncludeParam 124 Set<Include> theIncludes, 125 126 @IncludeParam(reverse=true) 127 Set<Include> theRevIncludes, 128 129 @Sort 130 SortSpec theSort, 131 132 @ca.uhn.fhir.rest.annotation.Count 133 Integer theCount, 134 135 @ca.uhn.fhir.rest.annotation.Offset 136 Integer theOffset, 137 138 SummaryEnum theSummaryMode, 139 140 SearchTotalModeEnum theSearchTotalMode, 141 142 SearchContainedModeEnum theSearchContainedMode 143 144 ) { 145 startRequest(theServletRequest); 146 try { 147 SearchParameterMap paramMap = new SearchParameterMap(); 148 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_FILTER, theFtFilter); 149 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, theFtContent); 150 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TEXT, theFtText); 151 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TAG, theSearchForTag); 152 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SECURITY, theSearchForSecurity); 153 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_PROFILE, theSearchForProfile); 154 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE, theSearchForSource); 155 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LIST, theList); 156 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LANGUAGE, theResourceLanguage); 157 158 paramMap.add("_has", theHas); 159 paramMap.add("_id", the_id); 160 paramMap.add("chromosome", theChromosome); 161 paramMap.add("coordinate", theCoordinate); 162 paramMap.add("end", theEnd); 163 paramMap.add("identifier", theIdentifier); 164 paramMap.add("patient", thePatient); 165 paramMap.add("start", theStart); 166 paramMap.add("type", theType); 167 paramMap.setRevIncludes(theRevIncludes); 168 paramMap.setLastUpdated(theLastUpdated); 169 paramMap.setIncludes(theIncludes); 170 paramMap.setSort(theSort); 171 paramMap.setCount(theCount); 172 paramMap.setOffset(theOffset); 173 paramMap.setSummaryMode(theSummaryMode); 174 paramMap.setSearchTotalMode(theSearchTotalMode); 175 paramMap.setSearchContainedMode(theSearchContainedMode); 176 177 getDao().translateRawParameters(theAdditionalRawParams, paramMap); 178 179 ca.uhn.fhir.rest.api.server.IBundleProvider retVal = getDao().search(paramMap, theRequestDetails, theServletResponse); 180 return retVal; 181 } finally { 182 endRequest(theServletRequest); 183 } 184 } 185 186}