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