From f62aff4cc3fe30bd6fd063f705961b1fa5bf7552 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Thu, 30 Oct 2025 11:38:17 +0000 Subject: [PATCH 1/4] Update documentation --- man/ds.colnames.Rd | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/man/ds.colnames.Rd b/man/ds.colnames.Rd index e73910812..9460a567f 100644 --- a/man/ds.colnames.Rd +++ b/man/ds.colnames.Rd @@ -9,20 +9,20 @@ ds.colnames(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string providing the name of the input data frame or matrix.} -\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ -\code{ds.colnames} returns the column names of +\code{ds.colnames} returns the column names of the specified server-side data frame or matrix. } \description{ -Retrieves column names of an R object on the server-side. +Retrieves column names of an R object on the server-side. This function is similar to R function \code{colnames}. } \details{ -The input is restricted to the object of type \code{data.frame} or \code{matrix}. +The input is restricted to the object of type \code{data.frame} or \code{matrix}. Server function called: \code{colnamesDS} } @@ -37,28 +37,28 @@ Server function called: \code{colnamesDS} require('dsBaseClient') builder <- DSI::newDSLoginBuilder() - builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", + builder$append(server = "study1", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM1", driver = "OpalDriver") - builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", + builder$append(server = "study2", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM2", driver = "OpalDriver") builder$append(server = "study3", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", + url = "http://192.168.56.100:8080/", + user = "administrator", password = "datashield_test&", table = "CNSIM.CNSIM3", driver = "OpalDriver") logindata <- builder$build() - + # Log onto the remote Opal training servers - connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") + connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Getting column names of the R objects stored in the server-side ds.colnames(x = "D", datasources = connections[1]) #only the first server ("study1") is used # Clear the Datashield R sessions and logout - datashield.logout(connections) + datashield.logout(connections) } } \seealso{ From fc5fee8bc3e2d483c720c9eb5676e8cc6a33370b Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Thu, 30 Oct 2025 11:49:57 +0000 Subject: [PATCH 2/4] Version update --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index f87cb256d..96e359aaa 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: dsBaseClient Title: 'DataSHIELD' Client Side Base Functions -Version: 6.3.5-9000 +Version: 7.0.0-9000 Description: Base 'DataSHIELD' functions for the client side. 'DataSHIELD' is a software package which allows you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have been designed to only share non disclosive summary statistics, with built in automated output From afee3619fef99211e9d0f1e54951474247ad84c6 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 3 Nov 2025 16:21:43 +0000 Subject: [PATCH 3/4] Updated perf profile --- tests/testthat/perf_files/default_perf_profile.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/perf_files/default_perf_profile.csv b/tests/testthat/perf_files/default_perf_profile.csv index d75711a36..9a649b884 100644 --- a/tests/testthat/perf_files/default_perf_profile.csv +++ b/tests/testthat/perf_files/default_perf_profile.csv @@ -6,7 +6,7 @@ "ds.asNumeric::perf:0","2.185","0.5","2" "ds.assign::perf::0","5.490","0.5","2" "ds.class::perf::combine:0","4.760","0.5","2" -"ds.colnames::perf:0","4.159","0.5","2" +"ds.colnames::perf:0","9.942","0.5","2" "ds.exists::perf::combine:0","11.09","0.5","2" "ds.length::perf::combine:0","9.479","0.5","2" "ds.mean::perf::combine:0","9.650","0.5","2" From 1fd30e16aae9ffe06fec79fe20e8fabc676d04ba Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 14 Nov 2025 18:44:07 +0000 Subject: [PATCH 4/4] Update documents --- docs/404.html | 2 +- docs/LICENSE.html | 2 +- docs/authors.html | 6 +++--- docs/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/checkClass.html | 2 +- docs/reference/colPercent.html | 2 +- docs/reference/computeWeightedMeans.html | 2 +- docs/reference/dot-pool_md_patterns.html | 2 +- docs/reference/ds.Boole.html | 2 +- docs/reference/ds.abs.html | 2 +- docs/reference/ds.asCharacter.html | 2 +- docs/reference/ds.asDataMatrix.html | 2 +- docs/reference/ds.asFactor.html | 2 +- docs/reference/ds.asFactorSimple.html | 2 +- docs/reference/ds.asInteger.html | 2 +- docs/reference/ds.asList.html | 2 +- docs/reference/ds.asLogical.html | 2 +- docs/reference/ds.asMatrix.html | 2 +- docs/reference/ds.asNumeric.html | 2 +- docs/reference/ds.assign.html | 2 +- docs/reference/ds.auc.html | 2 +- docs/reference/ds.boxPlot.html | 2 +- docs/reference/ds.boxPlotGG.html | 2 +- docs/reference/ds.boxPlotGG_data_Treatment.html | 2 +- docs/reference/ds.boxPlotGG_data_Treatment_numeric.html | 2 +- docs/reference/ds.boxPlotGG_numeric.html | 2 +- docs/reference/ds.boxPlotGG_table.html | 2 +- docs/reference/ds.bp_standards.html | 2 +- docs/reference/ds.c.html | 2 +- docs/reference/ds.cbind.html | 2 +- docs/reference/ds.changeRefGroup.html | 2 +- docs/reference/ds.class.html | 2 +- docs/reference/ds.colnames.html | 2 +- docs/reference/ds.completeCases.html | 2 +- docs/reference/ds.contourPlot.html | 2 +- docs/reference/ds.cor.html | 2 +- docs/reference/ds.corTest.html | 2 +- docs/reference/ds.cov.html | 2 +- docs/reference/ds.dataFrame.html | 2 +- docs/reference/ds.dataFrameFill.html | 2 +- docs/reference/ds.dataFrameSort.html | 2 +- docs/reference/ds.dataFrameSubset.html | 2 +- docs/reference/ds.densityGrid.html | 2 +- docs/reference/ds.dim.html | 2 +- docs/reference/ds.dmtC2S.html | 2 +- docs/reference/ds.elspline.html | 2 +- docs/reference/ds.exists.html | 2 +- docs/reference/ds.exp.html | 2 +- docs/reference/ds.extractQuantiles.html | 2 +- docs/reference/ds.forestplot.html | 2 +- docs/reference/ds.gamlss.html | 2 +- docs/reference/ds.getWGSR.html | 2 +- docs/reference/ds.glm.html | 2 +- docs/reference/ds.glmPredict.html | 2 +- docs/reference/ds.glmSLMA.html | 2 +- docs/reference/ds.glmSummary.html | 2 +- docs/reference/ds.glmerSLMA.html | 2 +- docs/reference/ds.heatmapPlot.html | 2 +- docs/reference/ds.hetcor.html | 2 +- docs/reference/ds.histogram.html | 2 +- docs/reference/ds.igb_standards.html | 2 +- docs/reference/ds.isNA.html | 2 +- docs/reference/ds.isValid.html | 2 +- docs/reference/ds.kurtosis.html | 2 +- docs/reference/ds.length.html | 2 +- docs/reference/ds.levels.html | 2 +- docs/reference/ds.lexis.html | 2 +- docs/reference/ds.list.html | 2 +- docs/reference/ds.listClientsideFunctions.html | 2 +- docs/reference/ds.listDisclosureSettings.html | 2 +- docs/reference/ds.listOpals.html | 2 +- docs/reference/ds.listServersideFunctions.html | 2 +- docs/reference/ds.lmerSLMA.html | 2 +- docs/reference/ds.log.html | 2 +- docs/reference/ds.look.html | 2 +- docs/reference/ds.ls.html | 2 +- docs/reference/ds.lspline.html | 2 +- docs/reference/ds.make.html | 2 +- docs/reference/ds.matrix.html | 2 +- docs/reference/ds.matrixDet.html | 2 +- docs/reference/ds.matrixDet.report.html | 2 +- docs/reference/ds.matrixDiag.html | 2 +- docs/reference/ds.matrixDimnames.html | 2 +- docs/reference/ds.matrixInvert.html | 2 +- docs/reference/ds.matrixMult.html | 2 +- docs/reference/ds.matrixTranspose.html | 2 +- docs/reference/ds.mdPattern.html | 2 +- docs/reference/ds.mean.html | 2 +- docs/reference/ds.meanByClass.html | 2 +- docs/reference/ds.meanSdGp.html | 2 +- docs/reference/ds.merge.html | 2 +- docs/reference/ds.message.html | 2 +- docs/reference/ds.metadata.html | 2 +- docs/reference/ds.mice.html | 2 +- docs/reference/ds.names.html | 2 +- docs/reference/ds.ns.html | 2 +- docs/reference/ds.numNA.html | 2 +- docs/reference/ds.qlspline.html | 2 +- docs/reference/ds.quantileMean.html | 2 +- docs/reference/ds.rBinom.html | 2 +- docs/reference/ds.rNorm.html | 2 +- docs/reference/ds.rPois.html | 2 +- docs/reference/ds.rUnif.html | 2 +- docs/reference/ds.ranksSecure.html | 2 +- docs/reference/ds.rbind.html | 2 +- docs/reference/ds.reShape.html | 2 +- docs/reference/ds.recodeLevels.html | 2 +- docs/reference/ds.recodeValues.html | 2 +- docs/reference/ds.rep.html | 2 +- docs/reference/ds.replaceNA.html | 2 +- docs/reference/ds.rm.html | 2 +- docs/reference/ds.rowColCalc.html | 2 +- docs/reference/ds.sample.html | 2 +- docs/reference/ds.scatterPlot.html | 2 +- docs/reference/ds.seq.html | 2 +- docs/reference/ds.setDefaultOpals.html | 2 +- docs/reference/ds.setSeed.html | 2 +- docs/reference/ds.skewness.html | 2 +- docs/reference/ds.sqrt.html | 2 +- docs/reference/ds.subset.html | 2 +- docs/reference/ds.subsetByClass.html | 2 +- docs/reference/ds.summary.html | 2 +- docs/reference/ds.table.html | 2 +- docs/reference/ds.table1D.html | 2 +- docs/reference/ds.table2D.html | 2 +- docs/reference/ds.tapply.assign.html | 2 +- docs/reference/ds.tapply.html | 2 +- docs/reference/ds.testObjExists.html | 2 +- docs/reference/ds.unList.html | 2 +- docs/reference/ds.unique.html | 2 +- docs/reference/ds.var.html | 2 +- docs/reference/ds.vectorCalc.html | 2 +- docs/reference/extract.html | 2 +- docs/reference/getPooledMean.html | 2 +- docs/reference/getPooledVar.html | 2 +- docs/reference/glmChecks.html | 2 +- docs/reference/index.html | 2 +- docs/reference/isAssigned.html | 2 +- docs/reference/isDefined.html | 2 +- docs/reference/logical2int.html | 2 +- docs/reference/meanByClassHelper0a.html | 2 +- docs/reference/meanByClassHelper0b.html | 2 +- docs/reference/meanByClassHelper1.html | 2 +- docs/reference/meanByClassHelper2.html | 2 +- docs/reference/meanByClassHelper3.html | 2 +- docs/reference/meanByClassHelper4.html | 2 +- docs/reference/rowPercent.html | 2 +- docs/reference/subsetHelper.html | 2 +- 149 files changed, 151 insertions(+), 151 deletions(-) diff --git a/docs/404.html b/docs/404.html index 76de734e6..0679d8def 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index e721df6e3..8c771da38 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/authors.html b/docs/authors.html index ea2155cdc..564ece67f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 @@ -102,12 +102,12 @@

Citation

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà-Montagut X, Wheater S (????). dsBaseClient: 'DataSHIELD' Client Side Base Functions. -R package version 6.3.5-9000. +R package version 7.0.0-9000. 

@Manual{,
   title = {dsBaseClient: 'DataSHIELD' Client Side Base Functions},
   author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Tom Bishop and Amadou Gaye and Xavier Escribà-Montagut and Stuart Wheater},
-  note = {R package version 6.3.5-9000},
+  note = {R package version 7.0.0-9000},
 }

Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking the analysis to the data, not the data to the analysis.” diff --git a/docs/index.html b/docs/index.html index f76381f01..7841b0d65 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 87290833d..3ed574488 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,4 +2,4 @@ pandoc: 3.1.3 pkgdown: 2.2.0 pkgdown_sha: ~ articles: {} -last_built: 2025-11-14T05:59Z +last_built: 2025-11-14T18:39Z diff --git a/docs/reference/checkClass.html b/docs/reference/checkClass.html index 3ccfc4dd7..c46de990a 100644 --- a/docs/reference/checkClass.html +++ b/docs/reference/checkClass.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/colPercent.html b/docs/reference/colPercent.html index f4057a4fc..cbd981310 100644 --- a/docs/reference/colPercent.html +++ b/docs/reference/colPercent.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/computeWeightedMeans.html b/docs/reference/computeWeightedMeans.html index 075bcbd78..679684919 100644 --- a/docs/reference/computeWeightedMeans.html +++ b/docs/reference/computeWeightedMeans.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/dot-pool_md_patterns.html b/docs/reference/dot-pool_md_patterns.html index 6ab173a63..f25e02d13 100644 --- a/docs/reference/dot-pool_md_patterns.html +++ b/docs/reference/dot-pool_md_patterns.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.Boole.html b/docs/reference/ds.Boole.html index c048a7c57..640649fd5 100644 --- a/docs/reference/ds.Boole.html +++ b/docs/reference/ds.Boole.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.abs.html b/docs/reference/ds.abs.html index 1ea400369..3861996eb 100644 --- a/docs/reference/ds.abs.html +++ b/docs/reference/ds.abs.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.asCharacter.html b/docs/reference/ds.asCharacter.html index 5cd2add91..451b75340 100644 --- a/docs/reference/ds.asCharacter.html +++ b/docs/reference/ds.asCharacter.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.asDataMatrix.html b/docs/reference/ds.asDataMatrix.html index 4047f2d44..c1e781d66 100644 --- a/docs/reference/ds.asDataMatrix.html +++ b/docs/reference/ds.asDataMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.asFactor.html b/docs/reference/ds.asFactor.html index 01c06a1b2..bca23a519 100644 --- a/docs/reference/ds.asFactor.html +++ b/docs/reference/ds.asFactor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.asFactorSimple.html b/docs/reference/ds.asFactorSimple.html index 57359dce4..db97ca6da 100644 --- a/docs/reference/ds.asFactorSimple.html +++ b/docs/reference/ds.asFactorSimple.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.asInteger.html b/docs/reference/ds.asInteger.html index a8627c315..39687a0a2 100644 --- a/docs/reference/ds.asInteger.html +++ b/docs/reference/ds.asInteger.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.asList.html b/docs/reference/ds.asList.html index d96e01750..d9326df29 100644 --- a/docs/reference/ds.asList.html +++ b/docs/reference/ds.asList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.asLogical.html b/docs/reference/ds.asLogical.html index 0e7f466c9..e8cd5be2e 100644 --- a/docs/reference/ds.asLogical.html +++ b/docs/reference/ds.asLogical.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.asMatrix.html b/docs/reference/ds.asMatrix.html index 2fdb38cc1..bc02ef019 100644 --- a/docs/reference/ds.asMatrix.html +++ b/docs/reference/ds.asMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.asNumeric.html b/docs/reference/ds.asNumeric.html index 92568451f..a925237c8 100644 --- a/docs/reference/ds.asNumeric.html +++ b/docs/reference/ds.asNumeric.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.assign.html b/docs/reference/ds.assign.html index 9147ef7dc..4d45c9e3d 100644 --- a/docs/reference/ds.assign.html +++ b/docs/reference/ds.assign.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.auc.html b/docs/reference/ds.auc.html index 5cb42031f..9d5e5ec26 100644 --- a/docs/reference/ds.auc.html +++ b/docs/reference/ds.auc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.boxPlot.html b/docs/reference/ds.boxPlot.html index c45fad727..623dce9f3 100644 --- a/docs/reference/ds.boxPlot.html +++ b/docs/reference/ds.boxPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.boxPlotGG.html b/docs/reference/ds.boxPlotGG.html index 6fcb7dfe1..859eb74e5 100644 --- a/docs/reference/ds.boxPlotGG.html +++ b/docs/reference/ds.boxPlotGG.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.boxPlotGG_data_Treatment.html b/docs/reference/ds.boxPlotGG_data_Treatment.html index f67256075..7e047545b 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html index 3ef53fd40..86b7e274b 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.boxPlotGG_numeric.html b/docs/reference/ds.boxPlotGG_numeric.html index 1c398f12b..14bc256c0 100644 --- a/docs/reference/ds.boxPlotGG_numeric.html +++ b/docs/reference/ds.boxPlotGG_numeric.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.boxPlotGG_table.html b/docs/reference/ds.boxPlotGG_table.html index 0e413ec3a..602669afc 100644 --- a/docs/reference/ds.boxPlotGG_table.html +++ b/docs/reference/ds.boxPlotGG_table.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.5-9000 + 7.0.0-9000 diff --git a/docs/reference/ds.bp_standards.html b/docs/reference/ds.bp_standards.html index 632874234..a059e099d 100644 --- a/docs/reference/ds.bp_standards.html +++ b/docs/reference/ds.bp_standards.html @@ -20,7 +20,7 @@ dsBaseClient - 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