print(fileEntity)
-## File(name='filec7f2483a1da5', isLatestVersion=True, concreteType='org.sagebionetworks.repo.model.FileEntity', cacheDir='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/Rtmp1fbwe6', modifiedOn='2023-09-10T05:47:56.465Z', versionLabel='1', path='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/Rtmp1fbwe6/filec7f2483a1da5', _file_handle={'id': '128471083', 'etag': '3c5bfff5-bca6-45f0-ab2e-aacad4b7c2d8', 'createdBy': '3324230', 'createdOn': '2023-09-10T05:47:56.000Z', 'modifiedOn': '2023-09-10T05:47:56.000Z', 'concreteType': 'org.sagebionetworks.repo.model.file.S3FileHandle', 'contentType': 'application/octet-stream', 'contentMd5': '8465d33d9f407ef250ce519e92f300fb', 'fileName': 'filec7f2483a1da5', 'storageLocationId': 1, 'contentSize': 23, 'status': 'AVAILABLE', 'bucketName': 'proddata.sagebase.org', 'key': '3324230/f732db23-673e-4cd2-93fd-09561c8c485b/filec7f2483a1da5', 'isPreview': False, 'externalURL': None}, versionNumber=1, dataFileHandleId='128471083', createdOn='2023-09-10T05:47:56.272Z', id='syn52417540', modifiedBy='3324230', files=['filec7f2483a1da5'], etag='7750a89c-7606-4bcb-8e47-6c99da678425', createdBy='3324230', synapseStore=True, parentId='syn52417539')This is one simple way to read in a small matrix (we load just the first few rows):
@@ -286,7 +286,7 @@Organizing Data in a Project## [1] "Data" ## ## [[1]]$id -## [1] "syn52417541" +## [1] "syn52417560" ## ## [[1]]$type ## [1] "org.sagebionetworks.repo.model.Folder" @@ -301,13 +301,13 @@
Organizing Data in a Project## [1] TRUE ## ## [[1]]$benefactorId -## [1] 52417539 +## [1] 52417558 ## ## [[1]]$createdOn -## [1] "2023-09-10T05:47:57.793Z" +## [1] "2023-09-10T05:57:35.816Z" ## ## [[1]]$modifiedOn -## [1] "2023-09-10T05:47:57.958Z" +## [1] "2023-09-10T05:57:36.006Z" ## ## [[1]]$createdBy ## [1] "3324230" @@ -318,10 +318,10 @@
Organizing Data in a Project## ## [[2]] ## [[2]]$name -## [1] "filec7f2483a1da5" +## [1] "filed50b25528b1" ## ## [[2]]$id -## [1] "syn52417540" +## [1] "syn52417559" ## ## [[2]]$type ## [1] "org.sagebionetworks.repo.model.FileEntity" @@ -336,13 +336,13 @@
Organizing Data in a Project## [1] TRUE ## ## [[2]]$benefactorId -## [1] 52417539 +## [1] 52417558 ## ## [[2]]$createdOn -## [1] "2023-09-10T05:47:56.272Z" +## [1] "2023-09-10T05:57:33.808Z" ## ## [[2]]$modifiedOn -## [1] "2023-09-10T05:47:56.465Z" +## [1] "2023-09-10T05:57:34.009Z" ## ## [[2]]$createdBy ## [1] "3324230" @@ -358,7 +358,7 @@
Organizing Data in a Project## [1] "Data" ## ## [[1]]$id -## [1] "syn52417541" +## [1] "syn52417560" ## ## [[1]]$type ## [1] "org.sagebionetworks.repo.model.Folder" @@ -373,13 +373,13 @@
Organizing Data in a Project## [1] TRUE ## ## [[1]]$benefactorId -## [1] 52417539 +## [1] 52417558 ## ## [[1]]$createdOn -## [1] "2023-09-10T05:47:57.793Z" +## [1] "2023-09-10T05:57:35.816Z" ## ## [[1]]$modifiedOn -## [1] "2023-09-10T05:47:57.958Z" +## [1] "2023-09-10T05:57:36.006Z" ## ## [[1]]$createdBy ## [1] "3324230" @@ -390,10 +390,10 @@
Organizing Data in a Project## ## [[2]] ## [[2]]$name -## [1] "filec7f2483a1da5" +## [1] "filed50b25528b1" ## ## [[2]]$id -## [1] "syn52417540" +## [1] "syn52417559" ## ## [[2]]$type ## [1] "org.sagebionetworks.repo.model.FileEntity" @@ -408,13 +408,13 @@
Organizing Data in a Project## [1] TRUE ## ## [[2]]$benefactorId -## [1] 52417539 +## [1] 52417558 ## ## [[2]]$createdOn -## [1] "2023-09-10T05:47:56.272Z" +## [1] "2023-09-10T05:57:33.808Z" ## ## [[2]]$modifiedOn -## [1] "2023-09-10T05:47:56.465Z" +## [1] "2023-09-10T05:57:34.009Z" ## ## [[2]]$createdBy ## [1] "3324230" @@ -437,7 +437,7 @@
Organizing Data in a Project## [1] "Data" ## ## $id -## [1] "syn52417541" +## [1] "syn52417560" ## ## $type ## [1] "org.sagebionetworks.repo.model.Folder" @@ -452,13 +452,13 @@
Organizing Data in a Project## [1] TRUE ## ## $benefactorId -## [1] 52417539 +## [1] 52417558 ## ## $createdOn -## [1] "2023-09-10T05:47:57.793Z" +## [1] "2023-09-10T05:57:35.816Z" ## ## $modifiedOn -## [1] "2023-09-10T05:47:57.958Z" +## [1] "2023-09-10T05:57:36.006Z" ## ## $createdBy ## [1] "3324230" @@ -467,10 +467,10 @@
Organizing Data in a Project## [1] "3324230" ## ## $name -## [1] "filec7f2483a1da5" +## [1] "filed50b25528b1" ## ## $id -## [1] "syn52417540" +## [1] "syn52417559" ## ## $type ## [1] "org.sagebionetworks.repo.model.FileEntity" @@ -485,13 +485,13 @@
Organizing Data in a Project## [1] TRUE ## ## $benefactorId -## [1] 52417539 +## [1] 52417558 ## ## $createdOn -## [1] "2023-09-10T05:47:56.272Z" +## [1] "2023-09-10T05:57:33.808Z" ## ## $modifiedOn -## [1] "2023-09-10T05:47:56.465Z" +## [1] "2023-09-10T05:57:34.009Z" ## ## $createdBy ## [1] "3324230" @@ -524,7 +524,7 @@
Organizing Data in a Project= TRUE ) ## Retrieving a deleted folder causes: Error in value[[3L]](cond): 404 Client Error: -## Entity syn52417541 is in trash can.
In addition to simple data storage, Synapse entities can be annotated with key/value metadata, described in markdown documents (wikis), and linked together in provenance graphs to create a reproducible record of @@ -711,12 +711,12 @@
table <- synBuildTable("My Favorite Genes", project, genes)
table$schema
-## Schema(name='My Favorite Genes', parentId='syn52417546', columnIds=[], concreteType='org.sagebionetworks.repo.model.table.TableEntity', columns_to_store=[{'name': 'Name', 'columnType': 'STRING', 'maximumSize': 30, 'defaultValue': '', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Chromosome', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Start', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'End', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Strand', 'columnType': 'STRING', 'maximumSize': 30, 'defaultValue': '', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'TranscriptionFactor', 'columnType': 'BOOLEAN', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Time', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}])synBuildTable creates a Table Schema based on the data
and returns a Table object that can be stored in Synapse using
synStore(). To create a custom Table Schema, defines the
@@ -225,7 +225,7 @@
For example, let’s update the names of some of our favorite genes:
@@ -367,14 +367,14 @@Notes on Dates and Timesdf <- as.data.frame(results) df$Time <- as.POSIXlt("2015-07-04 05:22", tz = "UTC", format = "%Y-%m-%d %H:%M") synStore(Table(tableId, moreGenes)) -## <synapseclient.table.CsvFileTable object at 0x11ff40d90>
Dates may also be submitted in timestamp milliseconds:
results <- synTableQuery(sprintf("select * from %s where Name='zap'", tableId))
df <- as.data.frame(results)
df$Time <- timestamp
synStore(Table(tableId, moreGenes))
-## <synapseclient.table.CsvFileTable object at 0x11fefb7f0>Note that using POSIXlt is strongly preferred over
POSIXct, because POSIXct does not store values
with enough precision to reliably recover milliseconds. For more
diff --git a/docs/articles/views.html b/docs/articles/views.html
index e076efa1..e1b16855 100644
--- a/docs/articles/views.html
+++ b/docs/articles/views.html
@@ -200,17 +200,17 @@
data$contributor[1] <- c("Sage Bionetworks")
synStore(Table(view$properties$id, data[1,]))
-## <synapseclient.table.CsvFileTable object at 0x115009390>
+## <synapseclient.table.CsvFileTable object at 0x11a6d1390>