001
002package ca.uhn.fhir.jpa.rp.r4;
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.r4.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="Only return resources which were last updated as specified by the given range")
083                        @OptionalParam(name="_lastUpdated")
084                        DateRangeParam the_lastUpdated, 
085   
086
087                        @Description(shortDefinition="The profile of the resource")
088                        @OptionalParam(name="_profile")
089                        UriAndListParam the_profile, 
090   
091
092                        @Description(shortDefinition="The security of the resource")
093                        @OptionalParam(name="_security")
094                        TokenAndListParam the_security,
095   
096
097                        @Description(shortDefinition="The tag of the resource")
098                        @OptionalParam(name="_tag")
099                        TokenAndListParam the_tag,
100   
101
102                        @Description(shortDefinition="Chromosome number of the reference sequence")
103                        @OptionalParam(name="chromosome")
104                        TokenAndListParam theChromosome,
105   
106
107                        @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.")
108                        @OptionalParam(name="chromosome-variant-coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
109                        CompositeAndListParam<TokenParam, NumberParam> theChromosome_variant_coordinate,
110   
111
112                        @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.")
113                        @OptionalParam(name="chromosome-window-coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
114                        CompositeAndListParam<TokenParam, NumberParam> theChromosome_window_coordinate,
115   
116
117                        @Description(shortDefinition="The unique identity for a particular sequence")
118                        @OptionalParam(name="identifier")
119                        TokenAndListParam theIdentifier,
120   
121
122                        @Description(shortDefinition="The subject that the observation is about")
123                        @OptionalParam(name="patient", targetTypes={  } )
124                        ReferenceAndListParam thePatient, 
125   
126
127                        @Description(shortDefinition="Reference Sequence of the sequence")
128                        @OptionalParam(name="referenceseqid")
129                        TokenAndListParam theReferenceseqid,
130   
131
132                        @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.")
133                        @OptionalParam(name="referenceseqid-variant-coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
134                        CompositeAndListParam<TokenParam, NumberParam> theReferenceseqid_variant_coordinate,
135   
136
137                        @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.")
138                        @OptionalParam(name="referenceseqid-window-coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
139                        CompositeAndListParam<TokenParam, NumberParam> theReferenceseqid_window_coordinate,
140   
141
142                        @Description(shortDefinition="Amino Acid Sequence/ DNA Sequence / RNA Sequence")
143                        @OptionalParam(name="type")
144                        TokenAndListParam theType,
145   
146
147                        @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.")
148                        @OptionalParam(name="variant-end")
149                        NumberAndListParam theVariant_end, 
150   
151
152                        @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.")
153                        @OptionalParam(name="variant-start")
154                        NumberAndListParam theVariant_start, 
155   
156
157                        @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.")
158                        @OptionalParam(name="window-end")
159                        NumberAndListParam theWindow_end, 
160   
161
162                        @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.")
163                        @OptionalParam(name="window-start")
164                        NumberAndListParam theWindow_start, 
165
166                        @RawParam
167                        Map<String, List<String>> theAdditionalRawParams,
168
169        
170                        @IncludeParam
171                        Set<Include> theIncludes,
172
173                        @IncludeParam(reverse=true)
174                        Set<Include> theRevIncludes,
175
176                        @Sort
177                        SortSpec theSort,
178                        
179                        @ca.uhn.fhir.rest.annotation.Count
180                        Integer theCount,
181
182                        @ca.uhn.fhir.rest.annotation.Offset
183                        Integer theOffset,
184
185                        SummaryEnum theSummaryMode,
186
187                        SearchTotalModeEnum theSearchTotalMode,
188
189                        SearchContainedModeEnum theSearchContainedMode
190
191                        ) {
192                startRequest(theServletRequest);
193                try {
194                        SearchParameterMap paramMap = new SearchParameterMap();
195                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_FILTER, theFtFilter);
196                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, theFtContent);
197                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TEXT, theFtText);
198                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TAG, theSearchForTag);
199                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SECURITY, theSearchForSecurity);
200                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_PROFILE, theSearchForProfile);
201                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE, theSearchForSource);
202                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LIST, theList);
203                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LANGUAGE, theResourceLanguage);
204
205                        paramMap.add("_has", theHas);
206                                paramMap.add("_id", the_id);
207                                                                paramMap.add("_profile", the_profile);
208                                paramMap.add("_security", the_security);
209                                paramMap.add("_tag", the_tag);
210                                paramMap.add("chromosome", theChromosome);
211                                paramMap.add("chromosome-variant-coordinate", theChromosome_variant_coordinate);
212                                paramMap.add("chromosome-window-coordinate", theChromosome_window_coordinate);
213                                paramMap.add("identifier", theIdentifier);
214                                paramMap.add("patient", thePatient);
215                                paramMap.add("referenceseqid", theReferenceseqid);
216                                paramMap.add("referenceseqid-variant-coordinate", theReferenceseqid_variant_coordinate);
217                                paramMap.add("referenceseqid-window-coordinate", theReferenceseqid_window_coordinate);
218                                paramMap.add("type", theType);
219                                paramMap.add("variant-end", theVariant_end);
220                                paramMap.add("variant-start", theVariant_start);
221                                paramMap.add("window-end", theWindow_end);
222                                paramMap.add("window-start", theWindow_start);
223paramMap.setRevIncludes(theRevIncludes);
224                        paramMap.setLastUpdated(the_lastUpdated);
225                        paramMap.setIncludes(theIncludes);
226                        paramMap.setSort(theSort);
227                        paramMap.setCount(theCount);
228                        paramMap.setOffset(theOffset);
229                        paramMap.setSummaryMode(theSummaryMode);
230                        paramMap.setSearchTotalMode(theSearchTotalMode);
231                        paramMap.setSearchContainedMode(theSearchContainedMode);
232
233                        getDao().translateRawParameters(theAdditionalRawParams, paramMap);
234
235                        ca.uhn.fhir.rest.api.server.IBundleProvider retVal = getDao().search(paramMap, theRequestDetails, theServletResponse);
236                        return retVal;
237                } finally {
238                        endRequest(theServletRequest);
239                }
240        }
241
242}