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}