001 002package ca.uhn.fhir.jpa.rp.r4b; 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.r4b.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 MolecularSequenceResourceProvider extends 020 ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider<MolecularSequence> 021 { 022 023 @Override 024 public Class<MolecularSequence> getResourceType() { 025 return MolecularSequence.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="Search on the narrative of the resource") 083 @OptionalParam(name="_text") 084 StringAndListParam the_text, 085 086 087 @Description(shortDefinition="Chromosome number of the reference sequence") 088 @OptionalParam(name="chromosome") 089 TokenAndListParam theChromosome, 090 091 092 @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.") 093 @OptionalParam(name="chromosome-variant-coordinate", compositeTypes= { TokenParam.class, NumberParam.class }) 094 CompositeAndListParam<TokenParam, NumberParam> theChromosome_variant_coordinate, 095 096 097 @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.") 098 @OptionalParam(name="chromosome-window-coordinate", compositeTypes= { TokenParam.class, NumberParam.class }) 099 CompositeAndListParam<TokenParam, NumberParam> theChromosome_window_coordinate, 100 101 102 @Description(shortDefinition="The unique identity for a particular sequence") 103 @OptionalParam(name="identifier") 104 TokenAndListParam theIdentifier, 105 106 107 @Description(shortDefinition="The subject that the observation is about") 108 @OptionalParam(name="patient", targetTypes={ } ) 109 ReferenceAndListParam thePatient, 110 111 112 @Description(shortDefinition="Reference Sequence of the sequence") 113 @OptionalParam(name="referenceseqid") 114 TokenAndListParam theReferenceseqid, 115 116 117 @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.") 118 @OptionalParam(name="referenceseqid-variant-coordinate", compositeTypes= { TokenParam.class, NumberParam.class }) 119 CompositeAndListParam<TokenParam, NumberParam> theReferenceseqid_variant_coordinate, 120 121 122 @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.") 123 @OptionalParam(name="referenceseqid-window-coordinate", compositeTypes= { TokenParam.class, NumberParam.class }) 124 CompositeAndListParam<TokenParam, NumberParam> theReferenceseqid_window_coordinate, 125 126 127 @Description(shortDefinition="Amino Acid Sequence/ DNA Sequence / RNA Sequence") 128 @OptionalParam(name="type") 129 TokenAndListParam theType, 130 131 132 @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.") 133 @OptionalParam(name="variant-end") 134 NumberAndListParam theVariant_end, 135 136 137 @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.") 138 @OptionalParam(name="variant-start") 139 NumberAndListParam theVariant_start, 140 141 142 @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.") 143 @OptionalParam(name="window-end") 144 NumberAndListParam theWindow_end, 145 146 147 @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.") 148 @OptionalParam(name="window-start") 149 NumberAndListParam theWindow_start, 150 151 @RawParam 152 Map<String, List<String>> theAdditionalRawParams, 153 154 @Description(shortDefinition="Only return resources which were last updated as specified by the given range") 155 @OptionalParam(name="_lastUpdated") 156 DateRangeParam theLastUpdated, 157 158 @IncludeParam 159 Set<Include> theIncludes, 160 161 @IncludeParam(reverse=true) 162 Set<Include> theRevIncludes, 163 164 @Sort 165 SortSpec theSort, 166 167 @ca.uhn.fhir.rest.annotation.Count 168 Integer theCount, 169 170 @ca.uhn.fhir.rest.annotation.Offset 171 Integer theOffset, 172 173 SummaryEnum theSummaryMode, 174 175 SearchTotalModeEnum theSearchTotalMode, 176 177 SearchContainedModeEnum theSearchContainedMode 178 179 ) { 180 startRequest(theServletRequest); 181 try { 182 SearchParameterMap paramMap = new SearchParameterMap(); 183 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_FILTER, theFtFilter); 184 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, theFtContent); 185 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TEXT, theFtText); 186 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TAG, theSearchForTag); 187 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SECURITY, theSearchForSecurity); 188 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_PROFILE, theSearchForProfile); 189 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE, theSearchForSource); 190 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LIST, theList); 191 paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LANGUAGE, theResourceLanguage); 192 193 paramMap.add("_has", theHas); 194 paramMap.add("_id", the_id); 195 paramMap.add("_text", the_text); 196 paramMap.add("chromosome", theChromosome); 197 paramMap.add("chromosome-variant-coordinate", theChromosome_variant_coordinate); 198 paramMap.add("chromosome-window-coordinate", theChromosome_window_coordinate); 199 paramMap.add("identifier", theIdentifier); 200 paramMap.add("patient", thePatient); 201 paramMap.add("referenceseqid", theReferenceseqid); 202 paramMap.add("referenceseqid-variant-coordinate", theReferenceseqid_variant_coordinate); 203 paramMap.add("referenceseqid-window-coordinate", theReferenceseqid_window_coordinate); 204 paramMap.add("type", theType); 205 paramMap.add("variant-end", theVariant_end); 206 paramMap.add("variant-start", theVariant_start); 207 paramMap.add("window-end", theWindow_end); 208 paramMap.add("window-start", theWindow_start); 209 paramMap.setRevIncludes(theRevIncludes); 210 paramMap.setLastUpdated(theLastUpdated); 211 paramMap.setIncludes(theIncludes); 212 paramMap.setSort(theSort); 213 paramMap.setCount(theCount); 214 paramMap.setOffset(theOffset); 215 paramMap.setSummaryMode(theSummaryMode); 216 paramMap.setSearchTotalMode(theSearchTotalMode); 217 paramMap.setSearchContainedMode(theSearchContainedMode); 218 219 getDao().translateRawParameters(theAdditionalRawParams, paramMap); 220 221 ca.uhn.fhir.rest.api.server.IBundleProvider retVal = getDao().search(paramMap, theRequestDetails, theServletResponse); 222 return retVal; 223 } finally { 224 endRequest(theServletRequest); 225 } 226 } 227 228}