From 8b2d310ca11c56d2514fb8d719edeb2a1cecc475 Mon Sep 17 00:00:00 2001 From: thomasyu888 Date: Sat, 9 Sep 2023 18:55:34 -0700 Subject: [PATCH] Update docs --- docs/404.html | 2 +- docs/ISSUE_TEMPLATE.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/docker.html | 4 +- docs/articles/index.html | 2 +- docs/articles/manageSynapseCredentials.html | 4 +- docs/articles/synapser.html | 308 ++++++++---------- docs/articles/systemDependencies.html | 4 +- docs/articles/tables.html | 16 +- docs/articles/troubleshooting.html | 89 ++++- docs/articles/upload.html | 4 +- docs/articles/views.html | 30 +- docs/authors.html | 6 +- docs/index.html | 28 +- docs/news/index.html | 9 +- docs/pkgdown.yml | 4 +- docs/reference/Activity-class.html | 2 +- docs/reference/Activity.html | 2 +- docs/reference/Column-class.html | 2 +- docs/reference/Column.html | 2 +- docs/reference/Dataset-class.html | 2 +- docs/reference/Dataset.html | 2 +- docs/reference/DockerRepository-class.html | 2 +- docs/reference/DockerRepository.html | 2 +- docs/reference/EntityViewSchema-class.html | 2 +- docs/reference/EntityViewSchema.html | 2 +- docs/reference/Evaluation-class.html | 2 +- docs/reference/Evaluation.html | 2 +- docs/reference/File-class.html | 2 +- docs/reference/File.html | 2 +- docs/reference/Folder-class.html | 2 +- docs/reference/Folder.html | 2 +- docs/reference/Link-class.html | 2 +- docs/reference/Link.html | 2 +- .../MaterializedViewSchema-class.html | 2 +- docs/reference/MaterializedViewSchema.html | 2 +- docs/reference/PartialRowset-class.html | 2 +- docs/reference/PartialRowset.html | 2 +- docs/reference/Project-class.html | 2 +- docs/reference/Project.html | 2 +- docs/reference/Row-class.html | 2 +- docs/reference/Row.html | 2 +- docs/reference/RowSet-class.html | 2 +- docs/reference/RowSet.html | 2 +- docs/reference/Schema-class.html | 2 +- docs/reference/Schema.html | 2 +- docs/reference/Submission-class.html | 2 +- docs/reference/Submission.html | 2 +- docs/reference/SubmissionStatus-class.html | 2 +- docs/reference/SubmissionStatus.html | 2 +- .../reference/SubmissionViewSchema-class.html | 2 +- docs/reference/SubmissionViewSchema.html | 2 +- docs/reference/Table.html | 2 +- docs/reference/Team-class.html | 2 +- docs/reference/Team.html | 2 +- docs/reference/TeamMember-class.html | 2 +- docs/reference/TeamMember.html | 2 +- docs/reference/UserGroupHeader-class.html | 2 +- docs/reference/UserGroupHeader.html | 2 +- docs/reference/UserProfile-class.html | 2 +- docs/reference/UserProfile.html | 2 +- docs/reference/Wiki-class.html | 2 +- docs/reference/Wiki.html | 2 +- docs/reference/as.list.html | 2 +- docs/reference/index.html | 2 +- docs/reference/nextElem.html | 2 +- docs/reference/synBuildTable.html | 2 +- docs/reference/synClearDownloadList.html | 2 +- docs/reference/synCreateColumn.html | 2 +- docs/reference/synCreateColumns.html | 2 +- .../synCreateExternalS3FileHandle.html | 2 +- .../reference/synCreateS3StorageLocation.html | 2 +- docs/reference/synCreateSnapshotVersion.html | 2 +- .../synCreateStorageLocationSetting.html | 2 +- docs/reference/synDelete.html | 2 +- docs/reference/synDeleteProvenance.html | 2 +- docs/reference/synDownloadTableColumns.html | 2 +- docs/reference/synFindEntityId.html | 2 +- docs/reference/synGet.html | 2 +- docs/reference/synGetAnnotations.html | 2 +- docs/reference/synGetChildren.html | 2 +- docs/reference/synGetColumn.html | 2 +- docs/reference/synGetColumns.html | 2 +- docs/reference/synGetConfigFile.html | 2 +- docs/reference/synGetDownloadList.html | 2 +- .../reference/synGetDownloadListManifest.html | 2 +- docs/reference/synGetEvaluation.html | 2 +- .../synGetEvaluationByContentSource.html | 2 +- docs/reference/synGetEvaluationByName.html | 2 +- docs/reference/synGetMembershipStatus.html | 2 +- .../synGetMyStorageLocationSetting.html | 2 +- docs/reference/synGetPermissions.html | 2 +- docs/reference/synGetProjectSetting.html | 2 +- docs/reference/synGetProvenance.html | 2 +- docs/reference/synGetStsStorageToken.html | 2 +- docs/reference/synGetSubmission.html | 2 +- docs/reference/synGetSubmissionBundles.html | 2 +- docs/reference/synGetSubmissionStatus.html | 2 +- docs/reference/synGetSubmissions.html | 2 +- docs/reference/synGetTableColumns.html | 2 +- docs/reference/synGetTeam.html | 2 +- docs/reference/synGetTeamMembers.html | 2 +- docs/reference/synGetTeamOpenInvitations.html | 2 +- docs/reference/synGetUserProfile.html | 2 +- docs/reference/synGetWiki.html | 2 +- docs/reference/synGetWikiAttachments.html | 2 +- docs/reference/synGetWikiHeaders.html | 2 +- docs/reference/synInvalidateAPIKey.html | 2 +- docs/reference/synInviteToTeam.html | 2 +- docs/reference/synIsCertified.html | 2 +- docs/reference/synLogin.html | 2 +- docs/reference/synLogout.html | 2 +- docs/reference/synMd5Query.html | 2 +- docs/reference/synMove.html | 2 +- docs/reference/synOnweb.html | 2 +- docs/reference/synPrintEntity.html | 2 +- docs/reference/synRemoveFromDownloadList.html | 2 +- docs/reference/synRestDELETE.html | 2 +- docs/reference/synRestGET.html | 2 +- docs/reference/synRestPOST.html | 2 +- docs/reference/synRestPUT.html | 2 +- .../synSendMembershipInvitation.html | 2 +- docs/reference/synSendMessage.html | 2 +- docs/reference/synSetAnnotations.html | 2 +- docs/reference/synSetEndpoints.html | 2 +- docs/reference/synSetPermissions.html | 2 +- docs/reference/synSetProvenance.html | 2 +- docs/reference/synSetStorageLocation.html | 2 +- docs/reference/synStore.html | 2 +- docs/reference/synSubmit.html | 2 +- docs/reference/synTableQuery.html | 2 +- docs/reference/synUpdateActivity.html | 2 +- docs/reference/synUploadFileHandle.html | 2 +- docs/reference/synapser-package.html | 2 +- 134 files changed, 404 insertions(+), 346 deletions(-) diff --git a/docs/404.html b/docs/404.html index f387370f..82938920 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html index a19f07c6..466250e9 100644 --- a/docs/ISSUE_TEMPLATE.html +++ b/docs/ISSUE_TEMPLATE.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 5411cf91..cde16452 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/articles/docker.html b/docs/articles/docker.html index 1fcf9f09..6a390263 100644 --- a/docs/articles/docker.html +++ b/docs/articles/docker.html @@ -33,7 +33,7 @@ synapser - 1.0.0 + 1.1.0 @@ -102,7 +102,7 @@

Docker

Bruce Hoff

-

2023-02-01

+

2023-09-09

Source: vignettes/docker.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 9b407ac2..e9d2aa96 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/articles/manageSynapseCredentials.html b/docs/articles/manageSynapseCredentials.html index dec6f0bf..9392c3a9 100644 --- a/docs/articles/manageSynapseCredentials.html +++ b/docs/articles/manageSynapseCredentials.html @@ -33,7 +33,7 @@ synapser - 1.0.0 + 1.1.0 @@ -103,7 +103,7 @@

Manage Synapse Credentials

KimYen Ladia

-

2023-02-01

+

2023-09-09

Source: vignettes/manageSynapseCredentials.Rmd diff --git a/docs/articles/synapser.html b/docs/articles/synapser.html index fe9cff12..f7452942 100644 --- a/docs/articles/synapser.html +++ b/docs/articles/synapser.html @@ -33,7 +33,7 @@ synapser - 1.0.0 + 1.1.0 @@ -102,7 +102,7 @@

Synapse R Client Overview

Bruce Hoff

-

2023-02-01

+

2023-09-09

Source: vignettes/synapser.Rmd @@ -218,7 +218,7 @@

Accessing DataView the entity’s metadata in the R console:

 print(fileEntity)
-## File(parentId='syn51038312', path='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpG52o0s/file156f930cb36ad', name='file156f930cb36ad', files=['file156f930cb36ad'], cacheDir='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpG52o0s', etag='c22c30c1-ccb7-493b-a665-e5edeefa6fe1', concreteType='org.sagebionetworks.repo.model.FileEntity', createdOn='2023-02-02T02:15:24.818Z', dataFileHandleId='121216962', versionNumber=1, createdBy='3324230', modifiedOn='2023-02-02T02:15:24.974Z', modifiedBy='3324230', versionLabel='1', _file_handle={'id': '121216962', 'etag': 'db05364c-205e-460f-a79c-a679ca016da6', 'createdBy': '3324230', 'createdOn': '2023-02-02T02:15:25.000Z', 'modifiedOn': '2023-02-02T02:15:25.000Z', 'concreteType': 'org.sagebionetworks.repo.model.file.S3FileHandle', 'contentType': 'application/octet-stream', 'contentMd5': '8465d33d9f407ef250ce519e92f300fb', 'fileName': 'file156f930cb36ad', 'storageLocationId': 1, 'contentSize': 23, 'status': 'AVAILABLE', 'bucketName': 'proddata.sagebase.org', 'key': '3324230/1c78e027-8a1a-49fc-832e-b927417b9e1f/file156f930cb36ad', 'isPreview': False, 'externalURL': None}, isLatestVersion=True, id='syn51038314', synapseStore=True)
+## File(_file_handle={'id': '128470724', 'etag': '7ea66756-bbea-4827-a5d6-86d610952575', 'createdBy': '3324230', 'createdOn': '2023-09-10T01:52:04.000Z', 'modifiedOn': '2023-09-10T01:52:04.000Z', 'concreteType': 'org.sagebionetworks.repo.model.file.S3FileHandle', 'contentType': 'application/octet-stream', 'contentMd5': '8465d33d9f407ef250ce519e92f300fb', 'fileName': 'file335b64fd60c', 'storageLocationId': 1, 'contentSize': 23, 'status': 'AVAILABLE', 'bucketName': 'proddata.sagebase.org', 'key': '3324230/a5f347b4-b614-4740-861f-29db3b84bff6/file335b64fd60c', 'isPreview': False, 'externalURL': None}, createdBy='3324230', modifiedBy='3324230', files=['file335b64fd60c'], synapseStore=True, cacheDir='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpE2HGEb', path='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpE2HGEb/file335b64fd60c', createdOn='2023-09-10T01:52:04.003Z', parentId='syn52417363', etag='d01545de-61aa-4fa3-a770-c7545a46e69e', concreteType='org.sagebionetworks.repo.model.FileEntity', versionNumber=1, id='syn52417364', isLatestVersion=True, modifiedOn='2023-09-10T01:52:04.176Z', name='file335b64fd60c', dataFileHandleId='128470724', versionLabel='1')

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]]$id
-## [1] "syn51038316"
+## [1] "syn52417365"
 ## 
 ## [[1]]$type
 ## [1] "org.sagebionetworks.repo.model.Folder"
@@ -301,13 +301,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[1]]$benefactorId
-## [1] 51038312
+## [1] 52417363
 ## 
 ## [[1]]$createdOn
-## [1] "2023-02-02T02:15:25.912Z"
+## [1] "2023-09-10T01:52:05.690Z"
 ## 
 ## [[1]]$modifiedOn
-## [1] "2023-02-02T02:15:26.070Z"
+## [1] "2023-09-10T01:52:05.840Z"
 ## 
 ## [[1]]$createdBy
 ## [1] "3324230"
@@ -318,10 +318,10 @@ 
Organizing Data in a Project## 
 ## [[2]]
 ## [[2]]$name
-## [1] "file156f930cb36ad"
+## [1] "file335b64fd60c"
 ## 
 ## [[2]]$id
-## [1] "syn51038314"
+## [1] "syn52417364"
 ## 
 ## [[2]]$type
 ## [1] "org.sagebionetworks.repo.model.FileEntity"
@@ -336,13 +336,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[2]]$benefactorId
-## [1] 51038312
+## [1] 52417363
 ## 
 ## [[2]]$createdOn
-## [1] "2023-02-02T02:15:24.818Z"
+## [1] "2023-09-10T01:52:04.003Z"
 ## 
 ## [[2]]$modifiedOn
-## [1] "2023-02-02T02:15:24.974Z"
+## [1] "2023-09-10T01:52:04.176Z"
 ## 
 ## [[2]]$createdBy
 ## [1] "3324230"
@@ -358,7 +358,7 @@ 
Organizing Data in a Project## [1] "Data"
 ## 
 ## [[1]]$id
-## [1] "syn51038316"
+## [1] "syn52417365"
 ## 
 ## [[1]]$type
 ## [1] "org.sagebionetworks.repo.model.Folder"
@@ -373,13 +373,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[1]]$benefactorId
-## [1] 51038312
+## [1] 52417363
 ## 
 ## [[1]]$createdOn
-## [1] "2023-02-02T02:15:25.912Z"
+## [1] "2023-09-10T01:52:05.690Z"
 ## 
 ## [[1]]$modifiedOn
-## [1] "2023-02-02T02:15:26.070Z"
+## [1] "2023-09-10T01:52:05.840Z"
 ## 
 ## [[1]]$createdBy
 ## [1] "3324230"
@@ -390,10 +390,10 @@ 
Organizing Data in a Project## 
 ## [[2]]
 ## [[2]]$name
-## [1] "file156f930cb36ad"
+## [1] "file335b64fd60c"
 ## 
 ## [[2]]$id
-## [1] "syn51038314"
+## [1] "syn52417364"
 ## 
 ## [[2]]$type
 ## [1] "org.sagebionetworks.repo.model.FileEntity"
@@ -408,13 +408,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[2]]$benefactorId
-## [1] 51038312
+## [1] 52417363
 ## 
 ## [[2]]$createdOn
-## [1] "2023-02-02T02:15:24.818Z"
+## [1] "2023-09-10T01:52:04.003Z"
 ## 
 ## [[2]]$modifiedOn
-## [1] "2023-02-02T02:15:24.974Z"
+## [1] "2023-09-10T01:52:04.176Z"
 ## 
 ## [[2]]$createdBy
 ## [1] "3324230"
@@ -437,7 +437,7 @@ 
Organizing Data in a Project## [1] "Data"
 ## 
 ## $id
-## [1] "syn51038316"
+## [1] "syn52417365"
 ## 
 ## $type
 ## [1] "org.sagebionetworks.repo.model.Folder"
@@ -452,13 +452,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## $benefactorId
-## [1] 51038312
+## [1] 52417363
 ## 
 ## $createdOn
-## [1] "2023-02-02T02:15:25.912Z"
+## [1] "2023-09-10T01:52:05.690Z"
 ## 
 ## $modifiedOn
-## [1] "2023-02-02T02:15:26.070Z"
+## [1] "2023-09-10T01:52:05.840Z"
 ## 
 ## $createdBy
 ## [1] "3324230"
@@ -467,10 +467,10 @@ 
Organizing Data in a Project## [1] "3324230"
 ## 
 ## $name
-## [1] "file156f930cb36ad"
+## [1] "file335b64fd60c"
 ## 
 ## $id
-## [1] "syn51038314"
+## [1] "syn52417364"
 ## 
 ## $type
 ## [1] "org.sagebionetworks.repo.model.FileEntity"
@@ -485,13 +485,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## $benefactorId
-## [1] 51038312
+## [1] 52417363
 ## 
 ## $createdOn
-## [1] "2023-02-02T02:15:24.818Z"
+## [1] "2023-09-10T01:52:04.003Z"
 ## 
 ## $modifiedOn
-## [1] "2023-02-02T02:15:24.974Z"
+## [1] "2023-09-10T01:52:04.176Z"
 ## 
 ## $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 syn51038316 is in trash can.
+## Entity syn52417365 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 @@ -574,91 +574,6 @@

Annotating Synapse Entities## [1] 42
-

Type Conversions -

-

The core of the Synapser library is the python client. Reticulate is used to -translate R to Python and back.

-

These are the documented conversions from R to Python: Reticulate -Type Conversions

-

NA values in R do not have a direct equivalent in -Python. This has been a topic of great discussion. Synapser is not -trying to solve this. NA values in R are handled by -Reticulate per the implementation defined in Reticulate.

-

When working with R and Reticulate, NA values in types tables are -converted by Reticulate depending on the data type.

-

For numeric data types, NA values are converted to the corresponding -R value NA_real_. For integer data types, NA values are -converted to NA_integer_. For logical data types, NA values -are converted to NA_logical_. For character data types, NA -values are converted to NA_character_.

-

In addition, Reticulate also converts any values that cannot be -coerced to the specified data type to NA_character_.

-

Reticulate performs these conversions automatically.

-

When Reticulate converts R objects to Python objects, the NA values -in R types tables are converted to Python’s None.

-

R’s NA is a logical constant of length 1 which is used -to represent the absence of a value. In Python, the equivalent of -NA is None, which is a special constant used -to indicate the absence of a value.

-

Reticulate automatically converts NA values in R types -tables to None when converting R objects to Python. This -ensures that the data types and values remain consistent between the two -languages.

-

Examples:

-
    -
  • Reticulate converts logical NAs to Python -True, which convert back to TRUE in R
    • -
-
-na_logical = NA
-class(na_logical)
-## [1] "logical"
-na_py <- reticulate::r_to_py(na_logical)
-na_py
-## True
-na_r <- reticulate::py_to_r(na_py)
-na_r
-## [1] TRUE
-
-na_logical = c(T, F, NA)
-class(na_logical)
-## [1] "logical"
-na_py <- reticulate::r_to_py(na_logical)
-na_py
-## [True, False, True]
-na_r <- reticulate::py_to_r(na_py)
-na_r
-## [1]  TRUE FALSE  TRUE
-
    -
  • Reticulate converts character NAs to Python strings, -which convert back to characters in R
    • -
-
-na_char = c("T", "F", NA)
-class(na_char)
-## [1] "character"
-na_py <- reticulate::r_to_py(na_char)
-na_py
-## ['T', 'F', 'NA']
-na_r <- reticulate::py_to_r(na_py)
-na_r
-## [1] "T"  "F"  "NA"
-
    -
  • Reticulate converts numeric NAs to Python -np.nan, which convert back to NA in R
    • -
-
-na_num = c(1538006762583, 1538006762584, NA)
-class(na_num)
-## [1] "numeric"
-na_py <- reticulate::r_to_py(na_num)
-na_py
-## [1538006762583.0, 1538006762584.0, nan]
-na_r <- reticulate::py_to_r(na_py)
-na_r
-## [1] 1.538007e+12 1.538007e+12           NA
-
-

Provenance

Synapse provides tools for tracking ‘provenance’, or the @@ -672,7 +587,7 @@

Provenance

Creating an activity object:

-
+
 act <- Activity(
   name = "clustering",
   description = "whizzy clustering",
@@ -682,18 +597,18 @@ 
Creating an activity object:
+
 act <- Activity(name = "clustering", description = "whizzy clustering")
 act$used(c("syn12345", "syn12346"))
 act$executed("syn4567")

 
The used and executed can reference entities in Synapse or URLs.

 
Entity examples:

-
+
   act$used("syn12345")
   act$used(project)
   act$used(target = "syn12345", targetVersion = 2)

 
URL examples:

-
+
   act$used("http://mydomain.com/my/awesome/data.RData")
   act$used(url = "http://mydomain.com/my/awesome/data.RData", name = "Awesome Data")
   act$used(url = "https://github.com/joe_hacker/code_repo", name = "Gnarly hacks", wasExecuted = TRUE)

@@ -703,7 +618,7 @@ 
Storing entities with provenance
 
The activity can be passed in when storing an Entity to set the
 Entity’s provenance:

-
+
 project <- synGet(project$properties$id)
 project <- synStore(project, activity = act)

 
We’ve now recorded that ‘project’ is the output of syn4567 applied to
@@ -715,14 +630,14 @@ 
Recording data sourceThe synStore() has shortcuts for specifying the used and executed
 lists directly. For example, when storing a data entity, it’s a good
 idea to record its source:

-
+
 project <- synStore(
   project,
   activityName = "data-r-us",
   activityDescription = "downloaded from data-r-us",
   used = "http://data-r-us.com/excellent/data.xyz")

 
For more information:

-
+
 ?Activity
 ?synDeleteProvenance

 

@@ -741,7 +656,7 @@ 
Wikis
 folder, file, etc). Text and graphics can be composed in markdown and
 rendered in the web view of the object.

 
Creating a Wiki

-
+
 project <- synGet(project$properties$id)
 content <- "
 # My Wiki Page
@@ -760,7 +675,7 @@ 
Wikis
              attachments = list(filePath))
 wiki <- synStore(wiki)

 
Updating a Wiki

-
+
 project <- synGet(project$properties$id)
 wiki <- synGetWiki(project)
 wiki.markdown <- "
@@ -772,7 +687,7 @@ 
Wikis
 
 wiki <- synStore(wiki)

 
For more information:

-
+
 ?Wiki
 ?synGetWiki

 

@@ -783,7 +698,7 @@ 
Evaluations
+
 eval <- Evaluation(
   name = sprintf("My unique evaluation created on %s", format(Sys.time(), "%a %b %d %H%M%OS4 %Y")),
   description = "testing",
@@ -792,22 +707,22 @@ 
Evaluations= "This evaluation only accepts files.")
 eval <- synStore(eval)

 
Retrieving the created Evaluation:

-
+
 eval <- synGetEvaluation(eval$id)
 eval
 ## {
-##   "contentSource": "syn51038321",
-##   "createdOn": "2023-02-02T02:15:38.350Z",
+##   "contentSource": "syn52417370",
+##   "createdOn": "2023-09-10T01:52:19.778Z",
 ##   "description": "testing",
-##   "etag": "ba59943c-7633-41b0-b1c7-cf395a2d2690",
-##   "id": "9615299",
-##   "name": "My unique evaluation created on Wed Feb 01 181538.1668 2023",
+##   "etag": "ab96e0c7-14f2-4ca8-bc6e-343d23e97f9e",
+##   "id": "9615409",
+##   "name": "My unique evaluation created on Sat Sep 09 185219.5925 2023",
 ##   "ownerId": "3324230",
 ##   "submissionInstructionsMessage": "This evaluation only accepts files.",
 ##   "submissionReceiptMessage": "Thank you for your submission!"
 ## }

 
Submitting a file to an existing Evaluation:

-
+
 # first create a file to submit
 filePath <- tempfile()
 connection <- file(filePath)
@@ -818,7 +733,7 @@ 
Evaluations# submit the created file
 submission <- synSubmit(eval, file)

 
List submissions:

-
+
 submissions <- synGetSubmissionBundles(eval)
 as.list(submissions)
 ## [[1]]
@@ -826,73 +741,124 @@ 
Evaluations## {
 ##   "contributors": [
 ##     {
-##       "createdOn": "2023-02-02T02:15:40.563Z",
+##       "createdOn": "2023-09-10T01:52:22.150Z",
 ##       "principalId": "3324230"
 ##     }
 ##   ],
-##   "createdOn": "2023-02-02T02:15:40.563Z",
-##   "entityBundleJSON": "{\"entity\":{\"name\":\"file156f93dd15047\",\"id\":\"syn51038326\",\"etag\":\"144a593a-46fa-4cf9-80e7-a9eb272b462f\",\"createdOn\":\"2023-02-02T02:15:40.020Z\",\"modifiedOn\":\"2023-02-02T02:15:40.169Z\",\"createdBy\":\"3324230\",\"modifiedBy\":\"3324230\",\"parentId\":\"syn51038321\",\"concreteType\":\"org.sagebionetworks.repo.model.FileEntity\",\"versionNumber\":1,\"versionLabel\":\"1\",\"isLatestVersion\":true,\"dataFileHandleId\":\"121216980\"},\"entityType\":\"file\",\"annotations\":{\"id\":\"syn51038326\",\"etag\":\"00000000-0000-0000-0000-000000000000\",\"annotations\":{}},\"fileHandles\":[{\"id\":\"121216980\",\"etag\":\"ed105c86-869d-4acf-a84c-2adadb1d15b4\",\"createdBy\":\"3324230\",\"createdOn\":\"2023-02-02T02:15:40.000Z\",\"modifiedOn\":\"2023-02-02T02:15:40.000Z\",\"concreteType\":\"org.sagebionetworks.repo.model.file.S3FileHandle\",\"contentType\":\"application/octet-stream\",\"contentMd5\":\"3f466b7f85d184292a68cea1c4f7cfc2\",\"fileName\":\"file156f93dd15047\",\"storageLocationId\":1,\"contentSize\":27,\"status\":\"AVAILABLE\",\"bucketName\":\"proddata.sagebase.org\",\"key\":\"3324230/3e54a923-1a7a-426f-b298-40fd6b05fd5a/file156f93dd15047\",\"isPreview\":false}]}",
-##   "entityId": "syn51038326",
-##   "evaluationId": "9615299",
-##   "id": "9731868",
-##   "name": "file156f93dd15047",
+##   "createdOn": "2023-09-10T01:52:22.150Z",
+##   "entityBundleJSON": "{\"entity\":{\"name\":\"file335b1a36cede\",\"id\":\"syn52417371\",\"etag\":\"d842081b-7747-4d4d-908e-5ff7e1e903ce\",\"createdOn\":\"2023-09-10T01:52:21.570Z\",\"modifiedOn\":\"2023-09-10T01:52:21.734Z\",\"createdBy\":\"3324230\",\"modifiedBy\":\"3324230\",\"parentId\":\"syn52417370\",\"concreteType\":\"org.sagebionetworks.repo.model.FileEntity\",\"versionNumber\":1,\"versionLabel\":\"1\",\"isLatestVersion\":true,\"dataFileHandleId\":\"128470731\"},\"entityType\":\"file\",\"annotations\":{\"id\":\"syn52417371\",\"etag\":\"00000000-0000-0000-0000-000000000000\",\"annotations\":{}},\"fileHandles\":[{\"id\":\"128470731\",\"etag\":\"24c712b6-9809-468e-a4a1-f60d1a979b3a\",\"createdBy\":\"3324230\",\"createdOn\":\"2023-09-10T01:52:21.000Z\",\"modifiedOn\":\"2023-09-10T01:52:21.000Z\",\"concreteType\":\"org.sagebionetworks.repo.model.file.S3FileHandle\",\"contentType\":\"application/octet-stream\",\"contentMd5\":\"3f466b7f85d184292a68cea1c4f7cfc2\",\"fileName\":\"file335b1a36cede\",\"storageLocationId\":1,\"contentSize\":27,\"status\":\"AVAILABLE\",\"bucketName\":\"proddata.sagebase.org\",\"key\":\"3324230/5076c7be-528c-412f-8abd-aa8cd1477038/file335b1a36cede\",\"isPreview\":false}]}",
+##   "entityId": "syn52417371",
+##   "evaluationId": "9615409",
+##   "id": "9740517",
+##   "name": "file335b1a36cede",
 ##   "userId": "3324230",
 ##   "versionNumber": 1
 ## }
 ## 
 ## [[1]][[2]]
 ## {
-##   "entityId": "syn51038326",
-##   "etag": "0df85dea-16a7-41f1-8402-3ba8fc5df2d6",
-##   "id": "9731868",
-##   "modifiedOn": "2023-02-02T02:15:40.563Z",
+##   "entityId": "syn52417371",
+##   "etag": "c3b2103e-5a41-4863-b798-7a4077c82aad",
+##   "id": "9740517",
+##   "modifiedOn": "2023-09-10T01:52:22.150Z",
 ##   "status": "RECEIVED",
 ##   "statusVersion": 0,
 ##   "submissionAnnotations": {},
 ##   "versionNumber": 1
 ## }

 
Retrieving submission by id:

-
+
 
Retrieving the submission status:

-
+
 submissionStatus <- synGetSubmissionStatus(submission)
 submissionStatus
 ## {
-##   "entityId": "syn51038326",
-##   "etag": "0df85dea-16a7-41f1-8402-3ba8fc5df2d6",
-##   "id": "9731868",
-##   "modifiedOn": "2023-02-02T02:15:40.563Z",
+##   "entityId": "syn52417371",
+##   "etag": "c3b2103e-5a41-4863-b798-7a4077c82aad",
+##   "id": "9740517",
+##   "modifiedOn": "2023-09-10T01:52:22.150Z",
 ##   "status": "RECEIVED",
 ##   "statusVersion": 0,
 ##   "submissionAnnotations": {},
 ##   "versionNumber": 1
 ## }

 
To view the annotations:

-
+
 submissionStatus$submissionAnnotations
 ## {}

 
To update an annotation:

-
+
 submissionStatus$annotations["doubleAnnos"] <- list(c("rank" = 3))
 synStore(submissionStatus)

 
Query an evaluation:

-
+
 queryString <- sprintf("query=select * from evaluation_%s LIMIT %s OFFSET %s'", eval$id, 10, 0)
 synRestGET(paste("/evaluation/submission/query?", URLencode(queryString), sep = ""))
 ## $headers
-## list()
+##  [1] "scopeId"         "entityId"        "userId"          "createdOn"      
+##  [5] "versionNumber"   "modifiedOn"      "submitterAlias"  "cancelControl"  
+##  [9] "submitterId"     "teamId"          "name"            "cancelRequested"
+## [13] "objectId"        "status"          "canCancel"      
 ## 
 ## $rows
-## list()
+## $rows[[1]]
+## $rows[[1]]$values
+## $rows[[1]]$values[[1]]
+## [1] "9615409"
+## 
+## $rows[[1]]$values[[2]]
+## [1] "syn52417371"
+## 
+## $rows[[1]]$values[[3]]
+## [1] "3324230"
+## 
+## $rows[[1]]$values[[4]]
+## [1] "1694310742150"
+## 
+## $rows[[1]]$values[[5]]
+## [1] "1"
+## 
+## $rows[[1]]$values[[6]]
+## [1] "1694310742150"
+## 
+## $rows[[1]]$values[[7]]
+## NULL
+## 
+## $rows[[1]]$values[[8]]
+## [1] "{\"submissionId\":\"9740517\",\"userId\":\"3324230\",\"canCancel\":false,\"cancelRequested\":false}"
+## 
+## $rows[[1]]$values[[9]]
+## [1] "3324230"
+## 
+## $rows[[1]]$values[[10]]
+## NULL
+## 
+## $rows[[1]]$values[[11]]
+## [1] "file335b1a36cede"
+## 
+## $rows[[1]]$values[[12]]
+## [1] "false"
+## 
+## $rows[[1]]$values[[13]]
+## [1] "9740517"
+## 
+## $rows[[1]]$values[[14]]
+## [1] "RECEIVED"
+## 
+## $rows[[1]]$values[[15]]
+## [1] "false"
+## 
+## 
+## 
 ## 
 ## $totalNumberOfResults
-## [1] 0

+## [1] 1

 
To learn more about writing an evaluation query, please see: http://docs.synapse.org/rest/GET/evaluation/submission/query.html

 
For more information, please see:

-
+
 ?synGetEvaluation
 ?synSubmit
 ?synGetSubmissionBundles
@@ -906,22 +872,22 @@ 
Sharing Access to Content
 
Retrieve the sharing setting on an entity:

-
+
 synGetPermissions(project, principalId = 273950)
 ## list()

 
The first time an entity is shared, an ACL object is created for that
 entity. Let’s make project public:

-
+
 acl <- synSetPermissions(project, principalId = 273949, accessType = list("READ"))
 acl
 ## $id
-## [1] "syn51038321"
+## [1] "syn52417370"
 ## 
 ## $creationDate
-## [1] "2023-02-02T02:15:31.181Z"
+## [1] "2023-09-10T01:52:11.933Z"
 ## 
 ## $etag
-## [1] "45bf1411-d081-4b88-a89c-7378d27f7ca7"
+## [1] "6e48e9be-eb88-4ab9-b91b-271986469f72"
 ## 
 ## $resourceAccess
 ## $resourceAccess[[1]]
@@ -937,17 +903,17 @@ 
Sharing Access to Content## [1] 3324230
 ## 
 ## $resourceAccess[[2]]$accessType
-## [1] "DELETE"             "CHANGE_PERMISSIONS" "CREATE"            
-## [4] "MODERATE"           "UPDATE"             "DOWNLOAD"          
-## [7] "CHANGE_SETTINGS"    "READ"

+## [1] "CHANGE_SETTINGS"    "MODERATE"           "UPDATE"            
+## [4] "DOWNLOAD"           "CHANGE_PERMISSIONS" "READ"              
+## [7] "CREATE"             "DELETE"

 
Now public can read:

-
+
 synGetPermissions(project, principalId = 273950)
 ## list()

-
+
 ?synGetPermissions
 ?synSetPermissions

-
+
 synDelete(project)
 ## NULL

 

@@ -962,7 +928,7 @@ 
Accessing the API Directly
 
These methods enable access to the Synapse REST(ish) API taking care
 of details like endpoints and authentication. See the REST API documentation.

-
+
 ?synRestGET
 ?synRestPOST
 ?synRestPUT
diff --git a/docs/articles/systemDependencies.html b/docs/articles/systemDependencies.html
index 2a199d33..a2294ade 100644
--- a/docs/articles/systemDependencies.html
+++ b/docs/articles/systemDependencies.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.1.0
       
     

 
@@ -103,7 +103,7 @@ 
System Dependencies

                         
KimYen
 Ladia

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/systemDependencies.Rmd
       
diff --git a/docs/articles/tables.html b/docs/articles/tables.html
index a69b933d..012e7d38 100644
--- a/docs/articles/tables.html
+++ b/docs/articles/tables.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.1.0
       
     

 
@@ -102,7 +102,7 @@
       
Tables

                         
Bruce Hoff

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/tables.Rmd
       
@@ -154,7 +154,7 @@ 
Tables
 
 table <- synBuildTable("My Favorite Genes", project, genes)
 table$schema
-## Schema(concreteType='org.sagebionetworks.repo.model.table.TableEntity', columnIds=[], 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'}], parentId='syn51038332', name='My Favorite Genes')

+## Schema(concreteType='org.sagebionetworks.repo.model.table.TableEntity', parentId='syn52417372', 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'}], name='My Favorite Genes', columnIds=[])

 
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
@@ -186,7 +186,7 @@ 
Tables
 
 
We now have a table populated with data. Let’s try to query:

 
-results <- synTableQuery(sprintf("select * from %s where Chromosome='1' and Start < 41000 and End > 20000", tableId))

+results <- synTableQuery(sprintf('select * from %s where Chromosome=1 and Start < 41000 and "End" > 20000', tableId))

 
synTableQuery() downloads the data and saves it to a csv
 file at location:

 
@@ -225,7 +225,7 @@ 
Changing Data= c(F, F),
   Time = as.POSIXlt(c("2070-01-12 03:53:12.169", "2018-05-03 12:03:33.464"), tz = "UTC", format = "%Y-%m-%d %H:%M:%OS"))
 synStore(Table(tableId, moreGenes))
-## <synapseclient.table.CsvFileTable object at 0x12babe740>

+## <synapseclient.table.CsvFileTable object at 0x125cdf430>

 
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 0x12bb405b0>

+## <synapseclient.table.CsvFileTable object at 0x125cdf580>

 
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 0x12bb42140>

+## <synapseclient.table.CsvFileTable object at 0x125d5d2d0>

 
Note that using POSIXlt is strongly preferred over
 POSIXct, because POSIXct does not store values
 with enough precision to reliably recover milliseconds. For more
@@ -419,7 +419,7 @@ 
Table Attached Files# get the filehandle ids
 fileHandleIds <- lapply(files, function(f) f$id)
 newData["covers"] <- fileHandleIds
-## Warning in `[<-.data.frame`(`*tmp*`, "covers", value = list("121215793", :
+## Warning in `[<-.data.frame`(`*tmp*`, "covers", value = list("128470754", :
 ## provided 4 variables to replace 1 variables
 
 newTable <- synStore(Table(newSchema$properties$id, newData))

diff --git a/docs/articles/troubleshooting.html b/docs/articles/troubleshooting.html
index 7409bc0e..d08f03bf 100644
--- a/docs/articles/troubleshooting.html
+++ b/docs/articles/troubleshooting.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.1.0
       
     

 
@@ -103,7 +103,7 @@ 
Troubleshooting

                         
KimYen
 Ladia

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/troubleshooting.Rmd
       
@@ -152,6 +152,91 @@ 
Using Synapser with reticulateSynapse
 Python client through reticulate.

 

+

+
Type Conversions
+

+
The core of the Synapser library is the python client. Reticulate is used to
+translate R to Python and back.

+
These are the documented conversions from R to Python: Reticulate
+Type Conversions

+
NA values in R do not have a direct equivalent in
+Python. This has been a topic of great discussion. Synapser is not
+trying to solve this. NA values in R are handled by
+Reticulate per the implementation defined in Reticulate.

+
When working with R and Reticulate, NA values in types tables are
+converted by Reticulate depending on the data type.

+
For numeric data types, NA values are converted to the corresponding
+R value NA_real_. For integer data types, NA values are
+converted to NA_integer_. For logical data types, NA values
+are converted to NA_logical_. For character data types, NA
+values are converted to NA_character_.

+
In addition, Reticulate also converts any values that cannot be
+coerced to the specified data type to NA_character_.

+
Reticulate performs these conversions automatically.

+
When Reticulate converts R objects to Python objects, the NA values
+in R types tables are converted to Python’s None.

+
R’s NA is a logical constant of length 1 which is used
+to represent the absence of a value. In Python, the equivalent of
+NA is None, which is a special constant used
+to indicate the absence of a value.

+
Reticulate automatically converts NA values in R types
+tables to None when converting R objects to Python. This
+ensures that the data types and values remain consistent between the two
+languages.

+
Examples:

+
    
+
  • Reticulate converts logical NAs to Python
+True, which convert back to TRUE in R
    • 
+

+
+na_logical = NA
+class(na_logical)
+## [1] "logical"
+na_py <- reticulate::r_to_py(na_logical)
+na_py
+## True
+na_r <- reticulate::py_to_r(na_py)
+na_r
+## [1] TRUE

+
+na_logical = c(T, F, NA)
+class(na_logical)
+## [1] "logical"
+na_py <- reticulate::r_to_py(na_logical)
+na_py
+## [True, False, True]
+na_r <- reticulate::py_to_r(na_py)
+na_r
+## [1]  TRUE FALSE  TRUE

+
    
+
  • Reticulate converts character NAs to Python strings,
+which convert back to characters in R
    • 
+

+
+na_char = c("T", "F", NA)
+class(na_char)
+## [1] "character"
+na_py <- reticulate::r_to_py(na_char)
+na_py
+## ['T', 'F', 'NA']
+na_r <- reticulate::py_to_r(na_py)
+na_r
+## [1] "T"  "F"  "NA"

+
    
+
  • Reticulate converts numeric NAs to Python
+np.nan, which convert back to NA in R
    • 
+

+
+na_num = c(1538006762583, 1538006762584, NA)
+class(na_num)
+## [1] "numeric"
+na_py <- reticulate::r_to_py(na_num)
+na_py
+## [1538006762583.0, 1538006762584.0, nan]
+na_r <- reticulate::py_to_r(na_py)
+na_r
+## [1] 1.538007e+12 1.538007e+12           NA

+

 

   

 
diff --git a/docs/articles/upload.html b/docs/articles/upload.html
index 2405c00f..a6797d82 100644
--- a/docs/articles/upload.html
+++ b/docs/articles/upload.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.1.0
       
     

 
@@ -103,7 +103,7 @@ 
File Upload

                         
KimYen
 Ladia

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/upload.Rmd
       
diff --git a/docs/articles/views.html b/docs/articles/views.html
index f9bdd3ce..3d0fb484 100644
--- a/docs/articles/views.html
+++ b/docs/articles/views.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.1.0
       
     

 
@@ -103,7 +103,7 @@ 
Views

                         
KimYen
 Ladia

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/views.Rmd
       
@@ -200,26 +200,26 @@ 
Views
 data <- as.data.frame(queryResults)
 data
 ##     ROW_ID ROW_VERSION                             ROW_ETAG          id
-## 1 51038357           1 31ff56cb-b476-4d8d-bb74-4a14d7ace68f syn51038357
-## 2 51038358           1 56d0f16e-e8ef-4293-9eb0-ba65001f0fdc syn51038358
-##                name description           createdOn createdBy
-## 1 file1583932d4a572          NA 2023-02-01 18:17:17   3324230
-## 2 file1583926b9f970          NA 2023-02-01 18:17:19   3324230
+## 1 52417381           1 4b6521d7-f314-4c67-9a64-0ddef6b6ca26 syn52417381
+## 2 52417382           1 43a889f5-a890-4d8a-8472-d0b7f5b0dbae syn52417382
+##               name description           createdOn createdBy
+## 1  file36303670318          NA 2023-09-09 18:54:16   3324230
+## 2 file36305ffc1e66          NA 2023-09-09 18:54:17   3324230
 ##                                   etag          modifiedOn modifiedBy type
-## 1 31ff56cb-b476-4d8d-bb74-4a14d7ace68f 2023-02-01 18:17:19    3324230 file
-## 2 56d0f16e-e8ef-4293-9eb0-ba65001f0fdc 2023-02-01 18:17:20    3324230 file
+## 1 4b6521d7-f314-4c67-9a64-0ddef6b6ca26 2023-09-09 18:54:18    3324230 file
+## 2 43a889f5-a890-4d8a-8472-d0b7f5b0dbae 2023-09-09 18:54:18    3324230 file
 ##   currentVersion    parentId benefactorId   projectId dataFileHandleId
-## 1              1 syn51038356  syn51038356 syn51038356        121217064
-## 2              1 syn51038356  syn51038356 syn51038356        121217065
+## 1              1 syn52417380  syn52417380 syn52417380        128470769
+## 2              1 syn52417380  syn52417380 syn52417380        128470770
 ##   dataFileSizeBytes                   dataFileMD5Hex
 ## 1                37 47dfe7f5eaa49a5413c7b79b67ab9c43
 ## 2                38 ba01e01b9e3ffea3ebef95efa62998b0
 ##                               dataFileConcreteType        dataFileBucket
 ## 1 org.sagebionetworks.repo.model.file.S3FileHandle proddata.sagebase.org
 ## 2 org.sagebionetworks.repo.model.file.S3FileHandle proddata.sagebase.org
-##                                                      dataFileKey contributor
-## 1 3324230/094122c1-804d-4d5b-84dd-301746556a10/file1583932d4a572        Sage
-## 2 3324230/600e1433-6618-43ae-8970-cfc24033608a/file1583926b9f970          UW
+##                                                     dataFileKey contributor
+## 1  3324230/1707f7f0-0fe1-40c1-a732-089576539347/file36303670318        Sage
+## 2 3324230/868c18c3-a1a7-4dd2-8067-a8d20addc0d6/file36305ffc1e66          UW
 ##   class rank
 ## 1     V   NA
 ## 2    NA    X

@@ -246,7 +246,7 @@ 
Updating Annotations using View
 data$contributor[1] <- c("Sage Bionetworks")
 synStore(Table(view$properties$id, data[1,]))
-## <synapseclient.table.CsvFileTable object at 0x1134a1270>

+## <synapseclient.table.CsvFileTable object at 0x10e2cece0>

 

 

 
Update View’s Content
diff --git a/docs/authors.html b/docs/authors.html
index daaac20b..dfe2cda3 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       
       
         synapser
-        1.0.0
+        1.1.0
       
     

 
@@ -98,13 +98,13 @@ 
Citation

 
     
Hoff B (2023).
 synapser: R Language Bindings for Synapse API.
-R package version 1.0.0, https://www.synapse.org. 
+R package version 1.1.0, https://www.synapse.org. 
 

     
@Manual{,
   title = {synapser: R Language Bindings for Synapse API},
   author = {Bruce Hoff},
   year = {2023},
-  note = {R package version 1.0.0},
+  note = {R package version 1.1.0},
   url = {https://www.synapse.org},
 }

 
diff --git a/docs/index.html b/docs/index.html
index 48844361..88a8edc7 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.1.0
       
     

 
@@ -174,7 +174,7 @@ 
On Windows
python --version

+
python --version

 
 
  • Note If it still shows the old version, you may restart your system. Or uninstall the old version from the control panel.
    • 
 
@@ -185,17 +185,17 @@ 
    On macOS
 
  • 
 
    Both python 2x and 3x can stay installed in a MAC. Mac comes with python 2x version. To check the default python version in your MAC, open the terminal and type
    
-
    python --version
-python3 --version
    
+
    python --version
+python3 --version
    
 
    • 
 
  • If you don’t then go ahead and install it with the installer. Go the the python’s official site here.
    • 
 
  • 
 
    Now restart the terminal and check again with both commands python —version
    
-
    python3 --version
    
+
    python3 --version
    
 
    • 
 
  • 
 
    Or use to install last version
    
-
    brew install python3 && cp /usr/local/bin/python3 /usr/local/bin/python
    
+
    brew install python3 && cp /usr/local/bin/python3 /usr/local/bin/python
    
 
    • 
 
 
    
@@ -205,29 +205,29 @@ 
    On Linux
 
  • 
 
    Add the repository and update
    
-
    sudo add-apt-repository ppa:deadsnakes/ppa
-sudo apt-get update
    
+
    sudo add-apt-repository ppa:deadsnakes/ppa
+sudo apt-get update
    
 
    • 
 
  • 
 
    Update the package list
    
-
    apt-get update
    
+
    apt-get update
    
 
    • 
 
  • 
 
    Verify the updated Python packages list
    
-
    apt list | grep python3.10
    
+
    apt list | grep python3.10
    
 
    • 
 
  • 
 
    Install the Python 3.10 package using apt-get
    
-
    sudo apt-get install python3.10
    
+
    sudo apt-get install python3.10
    
 
    • 
 
  • 
 
    Add Python 3.8 & Python 3.10 to update-alternatives
    
-
    sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
-sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 2
    
+
    sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
+sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 2
    
 
    • 
 
  • 
 
    Update Python 3 for point to Python 3.10
    
-
    sudo update-alternatives --config python3
    
+
    sudo update-alternatives --config python3
    
 
    •
    diff --git a/docs/news/index.html b/docs/news/index.html index 69138517..21e79c36 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0

    @@ -78,6 +78,13 @@

    Changelog

    Source: NEWS.md +
    +

    synapser 1.1.0

    +
    +

    Improvements

    +
    • Python synapsePythonClient dependency updated to 2.7.2
      • +
    +

    synapser 1.0.0

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 278a3317..888a1650 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.19.2 +pandoc: 3.1.2 pkgdown: 2.0.7 pkgdown_sha: ~ articles: @@ -10,5 +10,5 @@ articles: troubleshooting: troubleshooting.html upload: upload.html views: views.html -last_built: 2023-02-02T02:14Z +last_built: 2023-09-10T01:51Z diff --git a/docs/reference/Activity-class.html b/docs/reference/Activity-class.html index e4b79f01..aea1fc05 100644 --- a/docs/reference/Activity-class.html +++ b/docs/reference/Activity-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0
    diff --git a/docs/reference/Activity.html b/docs/reference/Activity.html index 13376aaa..aa330fb7 100644 --- a/docs/reference/Activity.html +++ b/docs/reference/Activity.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0
    diff --git a/docs/reference/Column-class.html b/docs/reference/Column-class.html index ec830991..16823b7c 100644 --- a/docs/reference/Column-class.html +++ b/docs/reference/Column-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Column.html b/docs/reference/Column.html index 9e6a8533..aeeddfa5 100644 --- a/docs/reference/Column.html +++ b/docs/reference/Column.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Dataset-class.html b/docs/reference/Dataset-class.html index 49948172..dd48cd1b 100644 --- a/docs/reference/Dataset-class.html +++ b/docs/reference/Dataset-class.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Dataset.html b/docs/reference/Dataset.html index ac2afe69..77d8fa33 100644 --- a/docs/reference/Dataset.html +++ b/docs/reference/Dataset.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/DockerRepository-class.html b/docs/reference/DockerRepository-class.html index 3218ac16..84e359f8 100644 --- a/docs/reference/DockerRepository-class.html +++ b/docs/reference/DockerRepository-class.html @@ -20,7 +20,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/DockerRepository.html b/docs/reference/DockerRepository.html index 932860d8..3c0795e8 100644 --- a/docs/reference/DockerRepository.html +++ b/docs/reference/DockerRepository.html @@ -20,7 +20,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/EntityViewSchema-class.html b/docs/reference/EntityViewSchema-class.html index b685454d..d1c5b281 100644 --- a/docs/reference/EntityViewSchema-class.html +++ b/docs/reference/EntityViewSchema-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/EntityViewSchema.html b/docs/reference/EntityViewSchema.html index c5556f7c..03cfbfd8 100644 --- a/docs/reference/EntityViewSchema.html +++ b/docs/reference/EntityViewSchema.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Evaluation-class.html b/docs/reference/Evaluation-class.html index 2022e847..b763fade 100644 --- a/docs/reference/Evaluation-class.html +++ b/docs/reference/Evaluation-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Evaluation.html b/docs/reference/Evaluation.html index 698f095e..f49e69ed 100644 --- a/docs/reference/Evaluation.html +++ b/docs/reference/Evaluation.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/File-class.html b/docs/reference/File-class.html index 9e091b03..734825fc 100644 --- a/docs/reference/File-class.html +++ b/docs/reference/File-class.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/File.html b/docs/reference/File.html index ab78af40..2e367037 100644 --- a/docs/reference/File.html +++ b/docs/reference/File.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Folder-class.html b/docs/reference/Folder-class.html index c1528651..52efd030 100644 --- a/docs/reference/Folder-class.html +++ b/docs/reference/Folder-class.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Folder.html b/docs/reference/Folder.html index 32015ce0..3c2fa886 100644 --- a/docs/reference/Folder.html +++ b/docs/reference/Folder.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Link-class.html b/docs/reference/Link-class.html index bec06a9d..8fa74035 100644 --- a/docs/reference/Link-class.html +++ b/docs/reference/Link-class.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Link.html b/docs/reference/Link.html index b455763a..1dda25a4 100644 --- a/docs/reference/Link.html +++ b/docs/reference/Link.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/MaterializedViewSchema-class.html b/docs/reference/MaterializedViewSchema-class.html index 478a379c..68158414 100644 --- a/docs/reference/MaterializedViewSchema-class.html +++ b/docs/reference/MaterializedViewSchema-class.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/MaterializedViewSchema.html b/docs/reference/MaterializedViewSchema.html index ebf56413..4c1c5ee3 100644 --- a/docs/reference/MaterializedViewSchema.html +++ b/docs/reference/MaterializedViewSchema.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/PartialRowset-class.html b/docs/reference/PartialRowset-class.html index f938ad85..cc20e27e 100644 --- a/docs/reference/PartialRowset-class.html +++ b/docs/reference/PartialRowset-class.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/PartialRowset.html b/docs/reference/PartialRowset.html index 6ca9ed98..0d230eb9 100644 --- a/docs/reference/PartialRowset.html +++ b/docs/reference/PartialRowset.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Project-class.html b/docs/reference/Project-class.html index 89a22a62..c530ef20 100644 --- a/docs/reference/Project-class.html +++ b/docs/reference/Project-class.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Project.html b/docs/reference/Project.html index 24f3967a..78a512e2 100644 --- a/docs/reference/Project.html +++ b/docs/reference/Project.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Row-class.html b/docs/reference/Row-class.html index 4a010004..2662783e 100644 --- a/docs/reference/Row-class.html +++ b/docs/reference/Row-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Row.html b/docs/reference/Row.html index 6a44103a..76b8ee32 100644 --- a/docs/reference/Row.html +++ b/docs/reference/Row.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/RowSet-class.html b/docs/reference/RowSet-class.html index 02be4049..03720b1f 100644 --- a/docs/reference/RowSet-class.html +++ b/docs/reference/RowSet-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/RowSet.html b/docs/reference/RowSet.html index b6fb3f39..c4d217ac 100644 --- a/docs/reference/RowSet.html +++ b/docs/reference/RowSet.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Schema-class.html b/docs/reference/Schema-class.html index 0a93b3aa..531242cc 100644 --- a/docs/reference/Schema-class.html +++ b/docs/reference/Schema-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Schema.html b/docs/reference/Schema.html index a236e62e..4e284683 100644 --- a/docs/reference/Schema.html +++ b/docs/reference/Schema.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Submission-class.html b/docs/reference/Submission-class.html index 0bd0baf2..cd45f0f7 100644 --- a/docs/reference/Submission-class.html +++ b/docs/reference/Submission-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Submission.html b/docs/reference/Submission.html index 475ccd0e..19bd3821 100644 --- a/docs/reference/Submission.html +++ b/docs/reference/Submission.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/SubmissionStatus-class.html b/docs/reference/SubmissionStatus-class.html index 9a2810b3..27245462 100644 --- a/docs/reference/SubmissionStatus-class.html +++ b/docs/reference/SubmissionStatus-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/SubmissionStatus.html b/docs/reference/SubmissionStatus.html index 50fb81fb..7f14fae1 100644 --- a/docs/reference/SubmissionStatus.html +++ b/docs/reference/SubmissionStatus.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/SubmissionViewSchema-class.html b/docs/reference/SubmissionViewSchema-class.html index c7bd4a79..c764eb78 100644 --- a/docs/reference/SubmissionViewSchema-class.html +++ b/docs/reference/SubmissionViewSchema-class.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/SubmissionViewSchema.html b/docs/reference/SubmissionViewSchema.html index 7d8a0b11..adfe345d 100644 --- a/docs/reference/SubmissionViewSchema.html +++ b/docs/reference/SubmissionViewSchema.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Table.html b/docs/reference/Table.html index 5cbbb641..48ccde2f 100644 --- a/docs/reference/Table.html +++ b/docs/reference/Table.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Team-class.html b/docs/reference/Team-class.html index 500afc21..cd65bc00 100644 --- a/docs/reference/Team-class.html +++ b/docs/reference/Team-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Team.html b/docs/reference/Team.html index 1ed208a5..8ef22316 100644 --- a/docs/reference/Team.html +++ b/docs/reference/Team.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/TeamMember-class.html b/docs/reference/TeamMember-class.html index 9b1f9861..608ea1d4 100644 --- a/docs/reference/TeamMember-class.html +++ b/docs/reference/TeamMember-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/TeamMember.html b/docs/reference/TeamMember.html index 22992a15..566dc8ba 100644 --- a/docs/reference/TeamMember.html +++ b/docs/reference/TeamMember.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/UserGroupHeader-class.html b/docs/reference/UserGroupHeader-class.html index f25f02c7..4fc59390 100644 --- a/docs/reference/UserGroupHeader-class.html +++ b/docs/reference/UserGroupHeader-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/UserGroupHeader.html b/docs/reference/UserGroupHeader.html index 4e1c9ba1..e0d3b781 100644 --- a/docs/reference/UserGroupHeader.html +++ b/docs/reference/UserGroupHeader.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/UserProfile-class.html b/docs/reference/UserProfile-class.html index cd99c82f..00f8da89 100644 --- a/docs/reference/UserProfile-class.html +++ b/docs/reference/UserProfile-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/UserProfile.html b/docs/reference/UserProfile.html index 84e22870..6bb0cdc1 100644 --- a/docs/reference/UserProfile.html +++ b/docs/reference/UserProfile.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Wiki-class.html b/docs/reference/Wiki-class.html index ace95fde..685bbd57 100644 --- a/docs/reference/Wiki-class.html +++ b/docs/reference/Wiki-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/Wiki.html b/docs/reference/Wiki.html index 56181211..2273cd19 100644 --- a/docs/reference/Wiki.html +++ b/docs/reference/Wiki.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/as.list.html b/docs/reference/as.list.html index 4f74f1ba..063af7b7 100644 --- a/docs/reference/as.list.html +++ b/docs/reference/as.list.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index d57d6ec7..f0a130db 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/nextElem.html b/docs/reference/nextElem.html index dcb02284..92f2b895 100644 --- a/docs/reference/nextElem.html +++ b/docs/reference/nextElem.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synBuildTable.html b/docs/reference/synBuildTable.html index 0f573332..561840ec 100644 --- a/docs/reference/synBuildTable.html +++ b/docs/reference/synBuildTable.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synClearDownloadList.html b/docs/reference/synClearDownloadList.html index 0d8bf3fe..aee01f8f 100644 --- a/docs/reference/synClearDownloadList.html +++ b/docs/reference/synClearDownloadList.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synCreateColumn.html b/docs/reference/synCreateColumn.html index 786f8f33..bd7d1ce3 100644 --- a/docs/reference/synCreateColumn.html +++ b/docs/reference/synCreateColumn.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synCreateColumns.html b/docs/reference/synCreateColumns.html index 00990157..349af277 100644 --- a/docs/reference/synCreateColumns.html +++ b/docs/reference/synCreateColumns.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synCreateExternalS3FileHandle.html b/docs/reference/synCreateExternalS3FileHandle.html index c8edca6a..0b7da2df 100644 --- a/docs/reference/synCreateExternalS3FileHandle.html +++ b/docs/reference/synCreateExternalS3FileHandle.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synCreateS3StorageLocation.html b/docs/reference/synCreateS3StorageLocation.html index 077cc998..30a1008d 100644 --- a/docs/reference/synCreateS3StorageLocation.html +++ b/docs/reference/synCreateS3StorageLocation.html @@ -21,7 +21,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synCreateSnapshotVersion.html b/docs/reference/synCreateSnapshotVersion.html index dc1a2c5e..b1538e0a 100644 --- a/docs/reference/synCreateSnapshotVersion.html +++ b/docs/reference/synCreateSnapshotVersion.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synCreateStorageLocationSetting.html b/docs/reference/synCreateStorageLocationSetting.html index 4dbbe640..3560314b 100644 --- a/docs/reference/synCreateStorageLocationSetting.html +++ b/docs/reference/synCreateStorageLocationSetting.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synDelete.html b/docs/reference/synDelete.html index dcc93024..16fb518a 100644 --- a/docs/reference/synDelete.html +++ b/docs/reference/synDelete.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synDeleteProvenance.html b/docs/reference/synDeleteProvenance.html index 08567dd9..d332c6b9 100644 --- a/docs/reference/synDeleteProvenance.html +++ b/docs/reference/synDeleteProvenance.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synDownloadTableColumns.html b/docs/reference/synDownloadTableColumns.html index 5c1d1521..52d749d9 100644 --- a/docs/reference/synDownloadTableColumns.html +++ b/docs/reference/synDownloadTableColumns.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synFindEntityId.html b/docs/reference/synFindEntityId.html index babda132..edcd0620 100644 --- a/docs/reference/synFindEntityId.html +++ b/docs/reference/synFindEntityId.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGet.html b/docs/reference/synGet.html index 2a8e89f7..0cddaf4f 100644 --- a/docs/reference/synGet.html +++ b/docs/reference/synGet.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetAnnotations.html b/docs/reference/synGetAnnotations.html index 3bd067e5..64f8deed 100644 --- a/docs/reference/synGetAnnotations.html +++ b/docs/reference/synGetAnnotations.html @@ -20,7 +20,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetChildren.html b/docs/reference/synGetChildren.html index aeafb19c..e41fdf83 100644 --- a/docs/reference/synGetChildren.html +++ b/docs/reference/synGetChildren.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetColumn.html b/docs/reference/synGetColumn.html index 937f72e4..3992acd4 100644 --- a/docs/reference/synGetColumn.html +++ b/docs/reference/synGetColumn.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetColumns.html b/docs/reference/synGetColumns.html index af760f45..afae92c2 100644 --- a/docs/reference/synGetColumns.html +++ b/docs/reference/synGetColumns.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetConfigFile.html b/docs/reference/synGetConfigFile.html index 28240c35..8022fc40 100644 --- a/docs/reference/synGetConfigFile.html +++ b/docs/reference/synGetConfigFile.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetDownloadList.html b/docs/reference/synGetDownloadList.html index 95756c14..444a79a2 100644 --- a/docs/reference/synGetDownloadList.html +++ b/docs/reference/synGetDownloadList.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetDownloadListManifest.html b/docs/reference/synGetDownloadListManifest.html index 8e897f11..38495118 100644 --- a/docs/reference/synGetDownloadListManifest.html +++ b/docs/reference/synGetDownloadListManifest.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetEvaluation.html b/docs/reference/synGetEvaluation.html index 08f2a609..26f5273b 100644 --- a/docs/reference/synGetEvaluation.html +++ b/docs/reference/synGetEvaluation.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetEvaluationByContentSource.html b/docs/reference/synGetEvaluationByContentSource.html index 74c10882..66e96cf1 100644 --- a/docs/reference/synGetEvaluationByContentSource.html +++ b/docs/reference/synGetEvaluationByContentSource.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetEvaluationByName.html b/docs/reference/synGetEvaluationByName.html index 6c8a91d5..0d6758ab 100644 --- a/docs/reference/synGetEvaluationByName.html +++ b/docs/reference/synGetEvaluationByName.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetMembershipStatus.html b/docs/reference/synGetMembershipStatus.html index cd81d52d..36ad5706 100644 --- a/docs/reference/synGetMembershipStatus.html +++ b/docs/reference/synGetMembershipStatus.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetMyStorageLocationSetting.html b/docs/reference/synGetMyStorageLocationSetting.html index aa639afd..1388e152 100644 --- a/docs/reference/synGetMyStorageLocationSetting.html +++ b/docs/reference/synGetMyStorageLocationSetting.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetPermissions.html b/docs/reference/synGetPermissions.html index 45ff3bb5..24e94e24 100644 --- a/docs/reference/synGetPermissions.html +++ b/docs/reference/synGetPermissions.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetProjectSetting.html b/docs/reference/synGetProjectSetting.html index 09b2ae7b..04dd670c 100644 --- a/docs/reference/synGetProjectSetting.html +++ b/docs/reference/synGetProjectSetting.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetProvenance.html b/docs/reference/synGetProvenance.html index fbe0f738..76f0d311 100644 --- a/docs/reference/synGetProvenance.html +++ b/docs/reference/synGetProvenance.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetStsStorageToken.html b/docs/reference/synGetStsStorageToken.html index cf5e76ab..9038fa91 100644 --- a/docs/reference/synGetStsStorageToken.html +++ b/docs/reference/synGetStsStorageToken.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetSubmission.html b/docs/reference/synGetSubmission.html index 37fa62c8..b3f02b03 100644 --- a/docs/reference/synGetSubmission.html +++ b/docs/reference/synGetSubmission.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetSubmissionBundles.html b/docs/reference/synGetSubmissionBundles.html index d443563b..4f6e6f3f 100644 --- a/docs/reference/synGetSubmissionBundles.html +++ b/docs/reference/synGetSubmissionBundles.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetSubmissionStatus.html b/docs/reference/synGetSubmissionStatus.html index 5b91077c..36a6f572 100644 --- a/docs/reference/synGetSubmissionStatus.html +++ b/docs/reference/synGetSubmissionStatus.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetSubmissions.html b/docs/reference/synGetSubmissions.html index 807a44e0..60b5b01a 100644 --- a/docs/reference/synGetSubmissions.html +++ b/docs/reference/synGetSubmissions.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetTableColumns.html b/docs/reference/synGetTableColumns.html index a328036b..981b662b 100644 --- a/docs/reference/synGetTableColumns.html +++ b/docs/reference/synGetTableColumns.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetTeam.html b/docs/reference/synGetTeam.html index 96a632e9..e274c92f 100644 --- a/docs/reference/synGetTeam.html +++ b/docs/reference/synGetTeam.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetTeamMembers.html b/docs/reference/synGetTeamMembers.html index 8325209c..c02fe079 100644 --- a/docs/reference/synGetTeamMembers.html +++ b/docs/reference/synGetTeamMembers.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetTeamOpenInvitations.html b/docs/reference/synGetTeamOpenInvitations.html index 69eb3dc1..33f1e511 100644 --- a/docs/reference/synGetTeamOpenInvitations.html +++ b/docs/reference/synGetTeamOpenInvitations.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetUserProfile.html b/docs/reference/synGetUserProfile.html index 61b715b2..f1e45a0e 100644 --- a/docs/reference/synGetUserProfile.html +++ b/docs/reference/synGetUserProfile.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetWiki.html b/docs/reference/synGetWiki.html index e1bcbae6..ef481555 100644 --- a/docs/reference/synGetWiki.html +++ b/docs/reference/synGetWiki.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetWikiAttachments.html b/docs/reference/synGetWikiAttachments.html index 8dfd2c7a..43833d82 100644 --- a/docs/reference/synGetWikiAttachments.html +++ b/docs/reference/synGetWikiAttachments.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synGetWikiHeaders.html b/docs/reference/synGetWikiHeaders.html index 1aed301c..852da150 100644 --- a/docs/reference/synGetWikiHeaders.html +++ b/docs/reference/synGetWikiHeaders.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synInvalidateAPIKey.html b/docs/reference/synInvalidateAPIKey.html index d974e1c2..4c0c7e14 100644 --- a/docs/reference/synInvalidateAPIKey.html +++ b/docs/reference/synInvalidateAPIKey.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synInviteToTeam.html b/docs/reference/synInviteToTeam.html index bd359d07..4b91850a 100644 --- a/docs/reference/synInviteToTeam.html +++ b/docs/reference/synInviteToTeam.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synIsCertified.html b/docs/reference/synIsCertified.html index 44b095ab..26eb1f15 100644 --- a/docs/reference/synIsCertified.html +++ b/docs/reference/synIsCertified.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synLogin.html b/docs/reference/synLogin.html index 3c4cfc6f..818758d5 100644 --- a/docs/reference/synLogin.html +++ b/docs/reference/synLogin.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synLogout.html b/docs/reference/synLogout.html index 00847b5c..a6d2d7a7 100644 --- a/docs/reference/synLogout.html +++ b/docs/reference/synLogout.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synMd5Query.html b/docs/reference/synMd5Query.html index 0a6be8a4..d31fcf1f 100644 --- a/docs/reference/synMd5Query.html +++ b/docs/reference/synMd5Query.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synMove.html b/docs/reference/synMove.html index db7a5ceb..ce381c2d 100644 --- a/docs/reference/synMove.html +++ b/docs/reference/synMove.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synOnweb.html b/docs/reference/synOnweb.html index d482d8c6..f11c682a 100644 --- a/docs/reference/synOnweb.html +++ b/docs/reference/synOnweb.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synPrintEntity.html b/docs/reference/synPrintEntity.html index 59f1cd55..019d1862 100644 --- a/docs/reference/synPrintEntity.html +++ b/docs/reference/synPrintEntity.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synRemoveFromDownloadList.html b/docs/reference/synRemoveFromDownloadList.html index 6a0f5192..b2b98096 100644 --- a/docs/reference/synRemoveFromDownloadList.html +++ b/docs/reference/synRemoveFromDownloadList.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synRestDELETE.html b/docs/reference/synRestDELETE.html index e7cc4797..51a310de 100644 --- a/docs/reference/synRestDELETE.html +++ b/docs/reference/synRestDELETE.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synRestGET.html b/docs/reference/synRestGET.html index 957cef88..ad7eedec 100644 --- a/docs/reference/synRestGET.html +++ b/docs/reference/synRestGET.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synRestPOST.html b/docs/reference/synRestPOST.html index 37451566..0b4b6237 100644 --- a/docs/reference/synRestPOST.html +++ b/docs/reference/synRestPOST.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synRestPUT.html b/docs/reference/synRestPUT.html index 897cda5d..c64dfab6 100644 --- a/docs/reference/synRestPUT.html +++ b/docs/reference/synRestPUT.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synSendMembershipInvitation.html b/docs/reference/synSendMembershipInvitation.html index 96a346a9..d8b8884a 100644 --- a/docs/reference/synSendMembershipInvitation.html +++ b/docs/reference/synSendMembershipInvitation.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synSendMessage.html b/docs/reference/synSendMessage.html index befd27c7..2c9f2431 100644 --- a/docs/reference/synSendMessage.html +++ b/docs/reference/synSendMessage.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synSetAnnotations.html b/docs/reference/synSetAnnotations.html index a578114e..a56eda43 100644 --- a/docs/reference/synSetAnnotations.html +++ b/docs/reference/synSetAnnotations.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synSetEndpoints.html b/docs/reference/synSetEndpoints.html index 5aff31a8..74702bb8 100644 --- a/docs/reference/synSetEndpoints.html +++ b/docs/reference/synSetEndpoints.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synSetPermissions.html b/docs/reference/synSetPermissions.html index 1eca59db..fae30bd4 100644 --- a/docs/reference/synSetPermissions.html +++ b/docs/reference/synSetPermissions.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synSetProvenance.html b/docs/reference/synSetProvenance.html index dda8f5a3..3cdc5c95 100644 --- a/docs/reference/synSetProvenance.html +++ b/docs/reference/synSetProvenance.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synSetStorageLocation.html b/docs/reference/synSetStorageLocation.html index e83b2c5a..8cd04849 100644 --- a/docs/reference/synSetStorageLocation.html +++ b/docs/reference/synSetStorageLocation.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synStore.html b/docs/reference/synStore.html index 5de68679..204a2248 100644 --- a/docs/reference/synStore.html +++ b/docs/reference/synStore.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synSubmit.html b/docs/reference/synSubmit.html index 5190f067..6a650237 100644 --- a/docs/reference/synSubmit.html +++ b/docs/reference/synSubmit.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synTableQuery.html b/docs/reference/synTableQuery.html index 66f767f1..0de9d51c 100644 --- a/docs/reference/synTableQuery.html +++ b/docs/reference/synTableQuery.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synUpdateActivity.html b/docs/reference/synUpdateActivity.html index 91853ff6..eb33b445 100644 --- a/docs/reference/synUpdateActivity.html +++ b/docs/reference/synUpdateActivity.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synUploadFileHandle.html b/docs/reference/synUploadFileHandle.html index 32751bf9..cd9cbf3c 100644 --- a/docs/reference/synUploadFileHandle.html +++ b/docs/reference/synUploadFileHandle.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.1.0 diff --git a/docs/reference/synapser-package.html b/docs/reference/synapser-package.html index d9515e2c..2401f011 100644 --- a/docs/reference/synapser-package.html +++ b/docs/reference/synapser-package.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.1.0