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                        @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 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.")
108                        @OptionalParam(name="coordinate", compositeTypes= { TokenParam.class, NumberParam.class })
109                        CompositeAndListParam<TokenParam, NumberParam> theCoordinate,
110   
111
112                        @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.")
113                        @OptionalParam(name="end")
114                        NumberAndListParam theEnd, 
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="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.")
128                        @OptionalParam(name="start")
129                        NumberAndListParam theStart, 
130   
131
132                        @Description(shortDefinition="Amino Acid Sequence/ DNA Sequence / RNA Sequence")
133                        @OptionalParam(name="type")
134                        TokenAndListParam theType,
135
136                        @RawParam
137                        Map<String, List<String>> theAdditionalRawParams,
138
139        
140                        @IncludeParam
141                        Set<Include> theIncludes,
142
143                        @IncludeParam(reverse=true)
144                        Set<Include> theRevIncludes,
145
146                        @Sort
147                        SortSpec theSort,
148                        
149                        @ca.uhn.fhir.rest.annotation.Count
150                        Integer theCount,
151
152                        @ca.uhn.fhir.rest.annotation.Offset
153                        Integer theOffset,
154
155                        SummaryEnum theSummaryMode,
156
157                        SearchTotalModeEnum theSearchTotalMode,
158
159                        SearchContainedModeEnum theSearchContainedMode
160
161                        ) {
162                startRequest(theServletRequest);
163                try {
164                        SearchParameterMap paramMap = new SearchParameterMap();
165                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_FILTER, theFtFilter);
166                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, theFtContent);
167                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TEXT, theFtText);
168                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_TAG, theSearchForTag);
169                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SECURITY, theSearchForSecurity);
170                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_PROFILE, theSearchForProfile);
171                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_SOURCE, theSearchForSource);
172                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LIST, theList);
173                        paramMap.add(ca.uhn.fhir.rest.api.Constants.PARAM_LANGUAGE, theResourceLanguage);
174
175                        paramMap.add("_has", theHas);
176                                paramMap.add("_id", the_id);
177                                                                paramMap.add("_profile", the_profile);
178                                paramMap.add("_security", the_security);
179                                paramMap.add("_tag", the_tag);
180                                paramMap.add("chromosome", theChromosome);
181                                paramMap.add("coordinate", theCoordinate);
182                                paramMap.add("end", theEnd);
183                                paramMap.add("identifier", theIdentifier);
184                                paramMap.add("patient", thePatient);
185                                paramMap.add("start", theStart);
186                                paramMap.add("type", theType);
187paramMap.setRevIncludes(theRevIncludes);
188                        paramMap.setLastUpdated(the_lastUpdated);
189                        paramMap.setIncludes(theIncludes);
190                        paramMap.setSort(theSort);
191                        paramMap.setCount(theCount);
192                        paramMap.setOffset(theOffset);
193                        paramMap.setSummaryMode(theSummaryMode);
194                        paramMap.setSearchTotalMode(theSearchTotalMode);
195                        paramMap.setSearchContainedMode(theSearchContainedMode);
196
197                        getDao().translateRawParameters(theAdditionalRawParams, paramMap);
198
199                        ca.uhn.fhir.rest.api.server.IBundleProvider retVal = getDao().search(paramMap, theRequestDetails, theServletResponse);
200                        return retVal;
201                } finally {
202                        endRequest(theServletRequest);
203                }
204        }
205
206}