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
048                        @Description(shortDefinition="Search the contents of the resource's data using a list")
049                        @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_LIST)
050                        StringAndListParam theList,
051
052                        @Description(shortDefinition="The language of the resource")
053                        @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_LANGUAGE)
054                        TokenAndListParam theResourceLanguage,
055
056                        @Description(shortDefinition="Search for resources which have the given source value (Resource.meta.source)")
057                        @OptionalParam(name=ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE)
058                        UriAndListParam theSearchForSource,
059
060                        @Description(shortDefinition="Return resources linked to by the given target")
061                        @OptionalParam(name="_has")
062                        HasAndListParam theHas, 
063
064   
065
066                        @Description(shortDefinition="The ID of the resource")
067                        @OptionalParam(name="_id")
068                        TokenAndListParam the_id,
069   
070
071                        @Description(shortDefinition="Only return resources which were last updated as specified by the given range")
072                        @OptionalParam(name="_lastUpdated")
073                        DateRangeParam the_lastUpdated, 
074   
075
076                        @Description(shortDefinition="The profile of the resource")
077                        @OptionalParam(name="_profile")
078                        UriAndListParam the_profile, 
079   
080
081                        @Description(shortDefinition="The security of the resource")
082                        @OptionalParam(name="_security")
083                        TokenAndListParam the_security,
084   
085
086                        @Description(shortDefinition="The tag of the resource")
087                        @OptionalParam(name="_tag")
088                        TokenAndListParam the_tag,
089   
090
091                        @Description(shortDefinition="Search on the narrative of the resource")
092                        @OptionalParam(name="_text")
093                        StringAndListParam the_text, 
094   
095
096                        @Description(shortDefinition="Chromosome number of the reference sequence")
097                        @OptionalParam(name="chromosome")
098                        TokenAndListParam theChromosome,
099   
100
101                        @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.")
102                        @OptionalParam(name="chromosome-variant-coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
103                        CompositeAndListParam<TokenParam, NumberParam> theChromosome_variant_coordinate,
104   
105
106                        @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.")
107                        @OptionalParam(name="chromosome-window-coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
108                        CompositeAndListParam<TokenParam, NumberParam> theChromosome_window_coordinate,
109   
110
111                        @Description(shortDefinition="The unique identity for a particular sequence")
112                        @OptionalParam(name="identifier")
113                        TokenAndListParam theIdentifier,
114   
115
116                        @Description(shortDefinition="The subject that the observation is about")
117                        @OptionalParam(name="patient", targetTypes={  } )
118                        ReferenceAndListParam thePatient, 
119   
120
121                        @Description(shortDefinition="Reference Sequence of the sequence")
122                        @OptionalParam(name="referenceseqid")
123                        TokenAndListParam theReferenceseqid,
124   
125
126                        @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.")
127                        @OptionalParam(name="referenceseqid-variant-coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
128                        CompositeAndListParam<TokenParam, NumberParam> theReferenceseqid_variant_coordinate,
129   
130
131                        @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.")
132                        @OptionalParam(name="referenceseqid-window-coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
133                        CompositeAndListParam<TokenParam, NumberParam> theReferenceseqid_window_coordinate,
134   
135
136                        @Description(shortDefinition="Amino Acid Sequence/ DNA Sequence / RNA Sequence")
137                        @OptionalParam(name="type")
138                        TokenAndListParam theType,
139   
140
141                        @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.")
142                        @OptionalParam(name="variant-end")
143                        NumberAndListParam theVariant_end, 
144   
145
146                        @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.")
147                        @OptionalParam(name="variant-start")
148                        NumberAndListParam theVariant_start, 
149   
150
151                        @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.")
152                        @OptionalParam(name="window-end")
153                        NumberAndListParam theWindow_end, 
154   
155
156                        @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.")
157                        @OptionalParam(name="window-start")
158                        NumberAndListParam theWindow_start, 
159
160                        @RawParam
161                        Map<String, List<String>> theAdditionalRawParams,
162
163        
164                        @IncludeParam
165                        Set<Include> theIncludes,
166
167                        @IncludeParam(reverse=true)
168                        Set<Include> theRevIncludes,
169
170                        @Sort
171                        SortSpec theSort,
172                        
173                        @ca.uhn.fhir.rest.annotation.Count
174                        Integer theCount,
175
176                        @ca.uhn.fhir.rest.annotation.Offset
177                        Integer theOffset,
178
179                        SummaryEnum theSummaryMode,
180
181                        SearchTotalModeEnum theSearchTotalMode,
182
183                        SearchContainedModeEnum theSearchContainedMode
184
185                        ) {
186                startRequest(theServletRequest);
187                try {
188                        SearchParameterMap paramMap = new SearchParameterMap();
189                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_FILTER, theFtFilter);
190                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, theFtContent);
191                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TEXT, theFtText);
192                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE, theSearchForSource);
193                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LIST, theList);
194                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LANGUAGE, theResourceLanguage);
195
196                        paramMap.add("_has", theHas);
197                                paramMap.add("_id", the_id);
198                                                                paramMap.add("_profile", the_profile);
199                                paramMap.add("_security", the_security);
200                                paramMap.add("_tag", the_tag);
201                                paramMap.add("_text", the_text);
202                                paramMap.add("chromosome", theChromosome);
203                                paramMap.add("chromosome-variant-coordinate", theChromosome_variant_coordinate);
204                                paramMap.add("chromosome-window-coordinate", theChromosome_window_coordinate);
205                                paramMap.add("identifier", theIdentifier);
206                                paramMap.add("patient", thePatient);
207                                paramMap.add("referenceseqid", theReferenceseqid);
208                                paramMap.add("referenceseqid-variant-coordinate", theReferenceseqid_variant_coordinate);
209                                paramMap.add("referenceseqid-window-coordinate", theReferenceseqid_window_coordinate);
210                                paramMap.add("type", theType);
211                                paramMap.add("variant-end", theVariant_end);
212                                paramMap.add("variant-start", theVariant_start);
213                                paramMap.add("window-end", theWindow_end);
214                                paramMap.add("window-start", theWindow_start);
215paramMap.setRevIncludes(theRevIncludes);
216                        paramMap.setLastUpdated(the_lastUpdated);
217                        paramMap.setIncludes(theIncludes);
218                        paramMap.setSort(theSort);
219                        paramMap.setCount(theCount);
220                        paramMap.setOffset(theOffset);
221                        paramMap.setSummaryMode(theSummaryMode);
222                        paramMap.setSearchTotalMode(theSearchTotalMode);
223                        paramMap.setSearchContainedMode(theSearchContainedMode);
224
225                        getDao().translateRawParameters(theAdditionalRawParams, paramMap);
226
227                        ca.uhn.fhir.rest.api.server.IBundleProvider retVal = getDao().search(paramMap, theRequestDetails, theServletResponse);
228                        return retVal;
229                } finally {
230                        endRequest(theServletRequest);
231                }
232        }
233
234}