001
002package ca.uhn.fhir.jpa.rp.dstu3;
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.dstu3.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 SequenceResourceProvider extends 
020        ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider<Sequence>
021        {
022
023        @Override
024        public Class<Sequence> getResourceType() {
025                return Sequence.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="Chromosome number of the reference sequence")
092                        @OptionalParam(name="chromosome")
093                        TokenAndListParam theChromosome,
094   
095
096                        @Description(shortDefinition="Search parameter for region of the reference DNA sequence string. 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 `coordinate=1$lt345$gt123`, this means it will search for the Sequence resource 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.")
097                        @OptionalParam(name="coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
098                        CompositeAndListParam<TokenParam, NumberParam> theCoordinate,
099   
100
101                        @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.")
102                        @OptionalParam(name="end")
103                        NumberAndListParam theEnd, 
104   
105
106                        @Description(shortDefinition="The unique identity for a particular sequence")
107                        @OptionalParam(name="identifier")
108                        TokenAndListParam theIdentifier,
109   
110
111                        @Description(shortDefinition="The subject that the observation is about")
112                        @OptionalParam(name="patient", targetTypes={  } )
113                        ReferenceAndListParam thePatient, 
114   
115
116                        @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.")
117                        @OptionalParam(name="start")
118                        NumberAndListParam theStart, 
119   
120
121                        @Description(shortDefinition="Amino Acid Sequence/ DNA Sequence / RNA Sequence")
122                        @OptionalParam(name="type")
123                        TokenAndListParam theType,
124
125                        @RawParam
126                        Map<String, List<String>> theAdditionalRawParams,
127
128        
129                        @IncludeParam
130                        Set<Include> theIncludes,
131
132                        @IncludeParam(reverse=true)
133                        Set<Include> theRevIncludes,
134
135                        @Sort
136                        SortSpec theSort,
137                        
138                        @ca.uhn.fhir.rest.annotation.Count
139                        Integer theCount,
140
141                        @ca.uhn.fhir.rest.annotation.Offset
142                        Integer theOffset,
143
144                        SummaryEnum theSummaryMode,
145
146                        SearchTotalModeEnum theSearchTotalMode,
147
148                        SearchContainedModeEnum theSearchContainedMode
149
150                        ) {
151                startRequest(theServletRequest);
152                try {
153                        SearchParameterMap paramMap = new SearchParameterMap();
154                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_FILTER, theFtFilter);
155                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, theFtContent);
156                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TEXT, theFtText);
157                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE, theSearchForSource);
158                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LIST, theList);
159                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LANGUAGE, theResourceLanguage);
160
161                        paramMap.add("_has", theHas);
162                                paramMap.add("_id", the_id);
163                                                                paramMap.add("_profile", the_profile);
164                                paramMap.add("_security", the_security);
165                                paramMap.add("_tag", the_tag);
166                                paramMap.add("chromosome", theChromosome);
167                                paramMap.add("coordinate", theCoordinate);
168                                paramMap.add("end", theEnd);
169                                paramMap.add("identifier", theIdentifier);
170                                paramMap.add("patient", thePatient);
171                                paramMap.add("start", theStart);
172                                paramMap.add("type", theType);
173paramMap.setRevIncludes(theRevIncludes);
174                        paramMap.setLastUpdated(the_lastUpdated);
175                        paramMap.setIncludes(theIncludes);
176                        paramMap.setSort(theSort);
177                        paramMap.setCount(theCount);
178                        paramMap.setOffset(theOffset);
179                        paramMap.setSummaryMode(theSummaryMode);
180                        paramMap.setSearchTotalMode(theSearchTotalMode);
181                        paramMap.setSearchContainedMode(theSearchContainedMode);
182
183                        getDao().translateRawParameters(theAdditionalRawParams, paramMap);
184
185                        ca.uhn.fhir.rest.api.server.IBundleProvider retVal = getDao().search(paramMap, theRequestDetails, theServletResponse);
186                        return retVal;
187                } finally {
188                        endRequest(theServletRequest);
189                }
190        }
191
192}