
001 002package ca.uhn.fhir.jpa.rp.r5; 003 004import java.util.*; 005 006import org.apache.commons.lang3.StringUtils; 007 008import ca.uhn.fhir.jpa.provider.r5.*; 009import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; 010import ca.uhn.fhir.model.api.Include; 011import ca.uhn.fhir.model.api.annotation.*; 012import org.hl7.fhir.r5.model.*; 013import ca.uhn.fhir.rest.annotation.*; 014import ca.uhn.fhir.rest.param.*; 015import ca.uhn.fhir.rest.api.SortSpec; 016import ca.uhn.fhir.rest.api.SummaryEnum; 017import ca.uhn.fhir.rest.api.SearchTotalModeEnum; 018import ca.uhn.fhir.rest.api.SearchContainedModeEnum; 019 020public class MolecularSequenceResourceProvider extends 021 JpaResourceProviderR5<MolecularSequence> 022 { 023 024 @Override 025 public Class<MolecularSequence> getResourceType() { 026 return MolecularSequence.class; 027 } 028 029 @Search(allowUnknownParams=true) 030 public ca.uhn.fhir.rest.api.server.IBundleProvider search( 031 javax.servlet.http.HttpServletRequest theServletRequest, 032 javax.servlet.http.HttpServletResponse theServletResponse, 033 034 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails, 035 036 @Description(shortDefinition="Search the contents of the resource's data using a filter") 037 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_FILTER) 038 StringAndListParam theFtFilter, 039 040 @Description(shortDefinition="Search the contents of the resource's data using a fulltext search") 041 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT) 042 StringAndListParam theFtContent, 043 044 @Description(shortDefinition="Search the contents of the resource's narrative using a fulltext search") 045 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_TEXT) 046 StringAndListParam theFtText, 047 048 @Description(shortDefinition="Search for resources which have the given tag") 049 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_TAG) 050 TokenAndListParam theSearchForTag, 051 052 @Description(shortDefinition="Search for resources which have the given security labels") 053 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_SECURITY) 054 TokenAndListParam theSearchForSecurity, 055 056 @Description(shortDefinition="Search for resources which have the given profile") 057 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_PROFILE) 058 UriAndListParam theSearchForProfile, 059 060 @Description(shortDefinition="Search for resources which have the given source value (Resource.meta.source)") 061 @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE) 062 UriAndListParam theSearchForSource, 063 064 @Description(shortDefinition="Return resources linked to by the given target") 065 @OptionalParam(name="_has") 066 HasAndListParam theHas, 067 068 069 070 @Description(shortDefinition="The ID of the resource") 071 @OptionalParam(name="_id") 072 TokenAndListParam the_id, 073 074 075 @Description(shortDefinition="Search on the narrative of the resource") 076 @OptionalParam(name="_text") 077 SpecialAndListParam the_text, 078 079 080 @Description(shortDefinition="Chromosome number of the reference sequence") 081 @OptionalParam(name="chromosome") 082 TokenAndListParam theChromosome, 083 084 085 @Description(shortDefinition="Search parameter by chromosome and variant coordinate. 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 `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants 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.") 086 @OptionalParam(name="chromosome-variant-coordinate", compositeTypes= { TokenParam.class, NumberParam.class }) 087 CompositeAndListParam<TokenParam, NumberParam> theChromosome_variant_coordinate, 088 089 090 @Description(shortDefinition="Search parameter by chromosome and window. 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 `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window 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.") 091 @OptionalParam(name="chromosome-window-coordinate", compositeTypes= { TokenParam.class, NumberParam.class }) 092 CompositeAndListParam<TokenParam, NumberParam> theChromosome_window_coordinate, 093 094 095 @Description(shortDefinition="The unique identity for a particular sequence") 096 @OptionalParam(name="identifier") 097 TokenAndListParam theIdentifier, 098 099 100 @Description(shortDefinition="The subject that the observation is about") 101 @OptionalParam(name="patient", targetTypes={ } ) 102 ReferenceAndListParam thePatient, 103 104 105 @Description(shortDefinition="Reference Sequence of the sequence") 106 @OptionalParam(name="referenceseqid") 107 TokenAndListParam theReferenceseqid, 108 109 110 @Description(shortDefinition="Search parameter by reference sequence and variant coordinate. 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 `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.") 111 @OptionalParam(name="referenceseqid-variant-coordinate", compositeTypes= { TokenParam.class, NumberParam.class }) 112 CompositeAndListParam<TokenParam, NumberParam> theReferenceseqid_variant_coordinate, 113 114 115 @Description(shortDefinition="Search parameter by reference sequence and window. 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 `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.") 116 @OptionalParam(name="referenceseqid-window-coordinate", compositeTypes= { TokenParam.class, NumberParam.class }) 117 CompositeAndListParam<TokenParam, NumberParam> theReferenceseqid_window_coordinate, 118 119 120 @Description(shortDefinition="Amino Acid Sequence/ DNA Sequence / RNA Sequence") 121 @OptionalParam(name="type") 122 TokenAndListParam theType, 123 124 125 @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 variant.") 126 @OptionalParam(name="variant-end") 127 NumberAndListParam theVariant_end, 128 129 130 @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 variant.") 131 @OptionalParam(name="variant-start") 132 NumberAndListParam theVariant_start, 133 134 135 @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.") 136 @OptionalParam(name="window-end") 137 NumberAndListParam theWindow_end, 138 139 140 @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.") 141 @OptionalParam(name="window-start") 142 NumberAndListParam theWindow_start, 143 144 @RawParam 145 Map<String, List<String>> theAdditionalRawParams, 146 147 @Description(shortDefinition="Only return resources which were last updated as specified by the given range") 148 @OptionalParam(name="_lastUpdated") 149 DateRangeParam theLastUpdated, 150 151 @IncludeParam 152 Set<Include> theIncludes, 153 154 @IncludeParam(reverse=true) 155 Set<Include> theRevIncludes, 156 157 @Sort 158 SortSpec theSort, 159 160 @ca.uhn.fhir.rest.annotation.Count 161 Integer theCount, 162 163 @ca.uhn.fhir.rest.annotation.Offset 164 Integer theOffset, 165 166 SummaryEnum theSummaryMode, 167 168 SearchTotalModeEnum theSearchTotalMode, 169 170 SearchContainedModeEnum theSearchContainedMode 171 172 ) { 173 startRequest(theServletRequest); 174 try { 175 SearchParameterMap paramMap = new SearchParameterMap(); 176 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_FILTER, theFtFilter); 177 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, theFtContent); 178 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TEXT, theFtText); 179 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TAG, theSearchForTag); 180 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SECURITY, theSearchForSecurity); 181 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_PROFILE, theSearchForProfile); 182 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE, theSearchForSource); 183 paramMap.add("_has", theHas); 184 paramMap.add("_id", the_id); 185 paramMap.add("_text", the_text); 186 paramMap.add("chromosome", theChromosome); 187 paramMap.add("chromosome-variant-coordinate", theChromosome_variant_coordinate); 188 paramMap.add("chromosome-window-coordinate", theChromosome_window_coordinate); 189 paramMap.add("identifier", theIdentifier); 190 paramMap.add("patient", thePatient); 191 paramMap.add("referenceseqid", theReferenceseqid); 192 paramMap.add("referenceseqid-variant-coordinate", theReferenceseqid_variant_coordinate); 193 paramMap.add("referenceseqid-window-coordinate", theReferenceseqid_window_coordinate); 194 paramMap.add("type", theType); 195 paramMap.add("variant-end", theVariant_end); 196 paramMap.add("variant-start", theVariant_start); 197 paramMap.add("window-end", theWindow_end); 198 paramMap.add("window-start", theWindow_start); 199 paramMap.setRevIncludes(theRevIncludes); 200 paramMap.setLastUpdated(theLastUpdated); 201 paramMap.setIncludes(theIncludes); 202 paramMap.setSort(theSort); 203 paramMap.setCount(theCount); 204 paramMap.setOffset(theOffset); 205 paramMap.setSummaryMode(theSummaryMode); 206 paramMap.setSearchTotalMode(theSearchTotalMode); 207 paramMap.setSearchContainedMode(theSearchContainedMode); 208 209 getDao().translateRawParameters(theAdditionalRawParams, paramMap); 210 211 ca.uhn.fhir.rest.api.server.IBundleProvider retVal = getDao().search(paramMap, theRequestDetails, theServletResponse); 212 return retVal; 213 } finally { 214 endRequest(theServletRequest); 215 } 216 } 217 218}