From a185c8d55ba99e0666f1a10579320e1fe5101075 Mon Sep 17 00:00:00 2001 From: BryanFauble <17128019+BryanFauble@users.noreply.github.com> Date: Mon, 23 Oct 2023 12:53:51 -0700 Subject: [PATCH] regen docs --- docs/build/html/articles/cli.html | 49 +++++++++++++------ .../html/getting_started/credentials.html | 9 +++- docs/build/html/searchindex.js | 2 +- 3 files changed, 42 insertions(+), 18 deletions(-) diff --git a/docs/build/html/articles/cli.html b/docs/build/html/articles/cli.html index 8f7aaf505..0ffcea8aa 100644 --- a/docs/build/html/articles/cli.html +++ b/docs/build/html/articles/cli.html @@ -158,7 +158,8 @@

Usage 
synapse [command] -h
-
usage: synapse [-h] [--version] [-u SYNAPSEUSER] [-p SYNAPSEPASSWORD] [-c CONFIGPATH] [--debug] [--silent] [-s]
+
usage: synapse [-h] [--version] [-u SYNAPSEUSER] [-p SYNAPSEPASSWORD]
+               [-c CONFIGPATH] [--debug] [--silent] [-s]
                {get,manifest,sync,store,add,mv,cp,get-download-list,associate,delete,query,submit,show,cat,list,config,set-provenance,get-provenance,set-annotations,get-annotations,create,store-table,onweb,login,test-encoding,get-sts-token,migrate}
                ...
 

@@ -208,7 +209,8 @@ 
Sub-commands:
 
get

 
downloads a file from Synapse

-
synapse get [-h] [-q queryString] [-v VERSION] [-r] [--followLink] [--limitSearch projId] [--downloadLocation path] [--multiThreaded]
+
synapse get [-h] [-q queryString] [-v VERSION] [-r] [--followLink]
+            [--limitSearch projId] [--downloadLocation path] [--multiThreaded]
             [--manifest {all,root,suppress}]
             [local path]
 

@@ -318,8 +320,10 @@ 
options

 
uploads and adds a file to Synapse

 
synapse store [-h] (--parentid syn123 | --id syn123 | --type TYPE) [--name NAME]
-              [--description DESCRIPTION | --descriptionFile DESCRIPTION_FILE_PATH] [--used [target ...]] [--executed [target ...]]
-              [--limitSearch projId] [--noForceVersion] [--annotations ANNOTATIONS] [--replace]
+              [--description DESCRIPTION | --descriptionFile DESCRIPTION_FILE_PATH]
+              [--used [target ...]] [--executed [target ...]]
+              [--limitSearch projId] [--noForceVersion]
+              [--annotations ANNOTATIONS] [--replace]
               [FILE]
 

 

@@ -380,8 +384,10 @@ 
options

 
uploads and adds a file to Synapse

 
synapse add [-h] (--parentid syn123 | --id syn123 | --type TYPE) [--name NAME]
-            [--description DESCRIPTION | --descriptionFile DESCRIPTION_FILE_PATH] [--used [target ...]] [--executed [target ...]]
-            [--limitSearch projId] [--noForceVersion] [--annotations ANNOTATIONS] [--replace]
+            [--description DESCRIPTION | --descriptionFile DESCRIPTION_FILE_PATH]
+            [--used [target ...]] [--executed [target ...]]
+            [--limitSearch projId] [--noForceVersion]
+            [--annotations ANNOTATIONS] [--replace]
             [FILE]
 

 

@@ -459,7 +465,8 @@ 
options
 
cp

 
Copies specific versions of synapse content such as files, folders and projects by recursively copying all sub-content

-
synapse cp [-h] --destinationId syn123 [--version 1] [--setProvenance traceback] [--updateExisting] [--skipCopyAnnotations]
+
synapse cp [-h] --destinationId syn123 [--version 1] [--setProvenance traceback]
+           [--updateExisting] [--skipCopyAnnotations]
            [--excludeTypes [file table ...]] [--skipCopyWiki]
            syn123
 

@@ -595,9 +602,11 @@ 
Positional Arguments
 
submit

 
submit an entity or a file for evaluation

-
synapse submit [-h] [--evaluationID EVALUATIONID] [--evaluationName EVALUATIONNAME] [--entity ENTITY] [--file FILE] [--parentId PARENTID]
-               [--name NAME] [--teamName TEAMNAME] [--submitterAlias ALIAS] [--used [target ...]] [--executed [target ...]]
-               [--limitSearch projId]
+
synapse submit [-h] [--evaluationID EVALUATIONID]
+               [--evaluationName EVALUATIONNAME] [--entity ENTITY] [--file FILE]
+               [--parentId PARENTID] [--name NAME] [--teamName TEAMNAME]
+               [--submitterAlias ALIAS] [--used [target ...]]
+               [--executed [target ...]] [--limitSearch projId]
 

 

 

@@ -727,8 +736,10 @@ 
config
 
set-provenance

 
create provenance records

-
synapse set-provenance [-h] --id syn123 [--name NAME] [--description DESCRIPTION] [-o [OUTPUT_FILE]] [--used [target ...]]
-                       [--executed [target ...]] [--limitSearch projId]
+
synapse set-provenance [-h] --id syn123 [--name NAME]
+                       [--description DESCRIPTION] [-o [OUTPUT_FILE]]
+                       [--used [target ...]] [--executed [target ...]]
+                       [--limitSearch projId]
 

 

 

@@ -822,7 +833,9 @@ 
options
 
create

 
Creates folders or projects on Synapse

-
synapse create [-h] [--parentid syn123] --name NAME [--description DESCRIPTION | --descriptionFile DESCRIPTION_FILE_PATH] type
+
synapse create [-h] [--parentid syn123] --name NAME
+               [--description DESCRIPTION | --descriptionFile DESCRIPTION_FILE_PATH]
+               type
 

 

 

@@ -919,7 +932,8 @@ 
test-encoding
 
get-sts-token

 
Get an STS token for access to AWS S3 storage underlying Synapse

-
synapse get-sts-token [-h] [-o {json,boto,shell,bash,cmd,powershell}] id {read_write,read_only}
+
synapse get-sts-token [-h] [-o {json,boto,shell,bash,cmd,powershell}]
+                      id {read_write,read_only}
 

 

 

@@ -946,8 +960,11 @@ 
options
 
migrate

 
Migrate Synapse entities to a different storage location

-
synapse migrate [-h] [--source_storage_location_ids [SOURCE_STORAGE_LOCATION_IDS ...]] [--file_version_strategy FILE_VERSION_STRATEGY]
-                [--include_table_files] [--continue_on_error] [--csv_log_path CSV_LOG_PATH] [--dryRun] [--force]
+
synapse migrate [-h]
+                [--source_storage_location_ids [SOURCE_STORAGE_LOCATION_IDS ...]]
+                [--file_version_strategy FILE_VERSION_STRATEGY]
+                [--include_table_files] [--continue_on_error]
+                [--csv_log_path CSV_LOG_PATH] [--dryRun] [--force]
                 id dest_storage_location_id db_path
 

 

diff --git a/docs/build/html/getting_started/credentials.html b/docs/build/html/getting_started/credentials.html
index 8114c4603..a4dd02000 100644
--- a/docs/build/html/getting_started/credentials.html
+++ b/docs/build/html/getting_started/credentials.html
@@ -153,7 +153,13 @@ 
Use Environment Variable
 
Use .synapseConfig

 
For writing code using the Synapse Python client that is easy to share with others, please do not include your credentials in the code. Instead, please use .synapseConfig file to manage your credentials.

-
When installing the Synapse Python client, the .synapseConfig is added to your home directory. Open the .synapseConfig file and find the following section:

+
When installing the Synapse Python client, the .synapseConfig is added to your home directory.

+
You may also create the ~/.synapseConfig file by utilizing the command line client command and following the interactive prompts:

+
synapse config
+

+

+
The following describes how to add your credentials to the .synapseConfig file without the use of the synapse config command.

+
Open the .synapseConfig file and find the following section:

 
#[authentication]
 #username = <username>
 #authtoken = <authtoken>
@@ -177,6 +183,7 @@ 
Use .synap
 
  • synapseclient.Synapse
    • 
 
  • synapseclient.Synapse.login()
    • 
 
  • synapseclient.Synapse.logout()
    • 
+
  • synapse config
    • 
 
 
    
 
    
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 62ff85719..fabbbb30b 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["api/Activity","api/Annotations","api/Client","api/Entity","api/Evaluation","api/JsonSchema","api/Table","api/Team","api/Views","api/Wiki","api/core","articles/Upload","articles/api","articles/cli","articles/data_storage","articles/permissions","articles/reticulate","articles/synapseutils","articles/tables","articles/validate_annotations","getting_started/basics","getting_started/credentials","getting_started/installation","index","news"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":5,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,sphinx:56},filenames:["api/Activity.rst","api/Annotations.rst","api/Client.rst","api/Entity.rst","api/Evaluation.rst","api/JsonSchema.rst","api/Table.rst","api/Team.rst","api/Views.rst","api/Wiki.rst","api/core.rst","articles/Upload.rst","articles/api.rst","articles/cli.rst","articles/data_storage.rst","articles/permissions.rst","articles/reticulate.rst","articles/synapseutils.rst","articles/tables.rst","articles/validate_annotations.rst","getting_started/basics.rst","getting_started/credentials.rst","getting_started/installation.rst","index.rst","news.rst"],objects:{"":[[17,2,0,"-","synapseutils"]],"synapseclient.Synapse":[[2,1,1,"","clear_download_list"],[2,1,1,"","createColumns"],[2,1,1,"","createStorageLocationSetting"],[2,1,1,"","create_external_s3_file_handle"],[2,1,1,"","create_s3_storage_location"],[2,1,1,"","create_snapshot_version"],[2,1,1,"","delete"],[2,1,1,"","deleteProvenance"],[2,1,1,"","downloadTableColumns"],[2,1,1,"","findEntityId"],[2,1,1,"","get"],[2,1,1,"","getAnnotations"],[2,1,1,"","getChildren"],[2,1,1,"","getColumn"],[2,1,1,"","getColumns"],[2,1,1,"","getConfigFile"],[2,1,1,"","getEvaluation"],[2,1,1,"","getEvaluationByContentSource"],[2,1,1,"","getEvaluationByName"],[2,1,1,"","getMyStorageLocationSetting"],[2,1,1,"","getPermissions"],[2,1,1,"","getProjectSetting"],[2,1,1,"","getProvenance"],[2,1,1,"","getSubmission"],[2,1,1,"","getSubmissionBundles"],[2,1,1,"","getSubmissionStatus"],[2,1,1,"","getSubmissions"],[2,1,1,"","getTableColumns"],[2,1,1,"","getTeam"],[2,1,1,"","getTeamMembers"],[2,1,1,"","getUserProfile"],[2,1,1,"","getWiki"],[2,1,1,"","getWikiAttachments"],[2,1,1,"","getWikiHeaders"],[2,1,1,"","get_annotations"],[2,1,1,"","get_available_services"],[2,1,1,"","get_download_list"],[2,1,1,"","get_download_list_manifest"],[2,1,1,"","get_membership_status"],[2,1,1,"","get_sts_storage_token"],[2,1,1,"","get_team_open_invitations"],[2,1,1,"","invalidateAPIKey"],[2,1,1,"","invite_to_team"],[2,1,1,"","is_certified"],[2,1,1,"","is_synapse_id"],[2,1,1,"","login"],[2,1,1,"","logout"],[2,1,1,"","md5Query"],[2,1,1,"","move"],[2,1,1,"","onweb"],[2,1,1,"","printEntity"],[2,1,1,"","remove_from_download_list"],[2,1,1,"","restDELETE"],[2,1,1,"","restGET"],[2,1,1,"","restPOST"],[2,1,1,"","restPUT"],[2,1,1,"","sendMessage"],[2,1,1,"","send_membership_invitation"],[2,1,1,"","service"],[2,1,1,"","setAnnotations"],[2,1,1,"","setEndpoints"],[2,1,1,"","setPermissions"],[2,1,1,"","setProvenance"],[2,1,1,"","setStorageLocation"],[2,1,1,"","set_annotations"],[2,1,1,"","store"],[2,1,1,"","submit"],[2,1,1,"","tableQuery"],[2,1,1,"","updateActivity"],[2,1,1,"","uploadFileHandle"]],"synapseclient.activity":[[0,0,1,"","Activity"]],"synapseclient.activity.Activity":[[0,1,1,"","executed"],[0,1,1,"","used"]],"synapseclient.annotations":[[1,0,1,"","Annotations"]],"synapseclient.annotations.Annotations":[[1,1,1,"","__init__"]],"synapseclient.core":[[10,2,0,"-","utils"],[10,2,0,"-","version_check"]],"synapseclient.core.upload":[[10,2,0,"-","multipart_upload"]],"synapseclient.core.upload.multipart_upload":[[10,3,1,"","_multipart_upload"],[10,3,1,"","multipart_upload_file"],[10,3,1,"","multipart_upload_string"],[10,3,1,"","shared_executor"]],"synapseclient.core.utils":[[10,3,1,"","as_url"],[10,3,1,"","caller_module_name"],[10,3,1,"","concrete_type_of"],[10,0,1,"","deprecated_keyword_param"],[10,3,1,"","download_file"],[10,3,1,"","equal_paths"],[10,3,1,"","extract_filename"],[10,3,1,"","extract_prefix"],[10,3,1,"","extract_synapse_id_from_query"],[10,3,1,"","extract_user_name"],[10,3,1,"","extract_zip_file_to_directory"],[10,3,1,"","file_url_to_path"],[10,3,1,"","find_data_file_handle"],[10,3,1,"","format_time_interval"],[10,3,1,"","from_unix_epoch_time"],[10,3,1,"","from_unix_epoch_time_secs"],[10,3,1,"","get_properties"],[10,3,1,"","guess_file_name"],[10,3,1,"","id_of"],[10,3,1,"","is_base64_encoded"],[10,3,1,"","is_date"],[10,3,1,"","is_in_path"],[10,3,1,"","is_json"],[10,3,1,"","is_same_base_url"],[10,3,1,"","is_synapse_id_str"],[10,3,1,"","is_url"],[10,3,1,"","itersubclasses"],[10,3,1,"","make_bogus_binary_file"],[10,3,1,"","make_bogus_data_file"],[10,3,1,"","md5_for_file"],[10,3,1,"","normalize_path"],[10,3,1,"","normalize_whitespace"],[10,3,1,"","printTransferProgress"],[10,3,1,"","query_limit_and_offset"],[10,3,1,"","snake_case"],[10,3,1,"","threadsafe_generator"],[10,0,1,"","threadsafe_iter"],[10,3,1,"","to_list"],[10,3,1,"","to_unix_epoch_time"],[10,3,1,"","to_unix_epoch_time_secs"],[10,3,1,"","topolgical_sort"],[10,3,1,"","touch"],[10,3,1,"","unique_filename"]],"synapseclient.core.version_check":[[10,1,1,"","check_for_updates"],[10,1,1,"","release_notes"]],"synapseclient.entity":[[3,0,1,"","DockerRepository"],[3,0,1,"","Entity"],[3,0,1,"","File"],[3,0,1,"","Folder"],[3,0,1,"","Link"],[3,0,1,"","Project"]],"synapseclient.evaluation":[[4,0,1,"","Evaluation"],[4,0,1,"","Submission"],[4,0,1,"","SubmissionStatus"]],"synapseclient.evaluation.Evaluation":[[4,1,1,"","__init__"]],"synapseclient.evaluation.Submission":[[4,1,1,"","__init__"]],"synapseclient.evaluation.SubmissionStatus":[[4,1,1,"","__init__"]],"synapseclient.services":[[5,2,0,"-","json_schema"]],"synapseclient.services.json_schema":[[5,0,1,"","JsonSchema"],[5,0,1,"","JsonSchemaOrganization"],[5,0,1,"","JsonSchemaService"],[5,0,1,"","JsonSchemaVersion"]],"synapseclient.services.json_schema.JsonSchema":[[5,1,1,"","create"],[5,1,1,"","get"],[5,1,1,"","list_versions"]],"synapseclient.services.json_schema.JsonSchemaOrganization":[[5,1,1,"","create"],[5,1,1,"","create_json_schema"],[5,1,1,"","delete"],[5,1,1,"","get"],[5,1,1,"","get_acl"],[5,1,1,"","get_json_schema"],[5,1,1,"","list_json_schemas"],[5,1,1,"","set_acl"],[5,1,1,"","update_acl"]],"synapseclient.services.json_schema.JsonSchemaService":[[5,4,1,"","JsonSchema"],[5,4,1,"","JsonSchemaOrganization"],[5,4,1,"","JsonSchemaVersion"],[5,1,1,"","bind_json_schema"],[5,1,1,"","bind_json_schema_to_entity"],[5,1,1,"","create_json_schema"],[5,1,1,"","create_organization"],[5,1,1,"","delete_json_schema"],[5,1,1,"","delete_json_schema_from_entity"],[5,1,1,"","delete_organization"],[5,1,1,"","get_invalid_json_schema_validation"],[5,1,1,"","get_json_schema"],[5,1,1,"","get_json_schema_body"],[5,1,1,"","get_json_schema_from_entity"],[5,1,1,"","get_json_schema_validation_statistics"],[5,1,1,"","get_organization"],[5,1,1,"","get_organization_acl"],[5,1,1,"","json_schema_validation"],[5,1,1,"","list_json_schema_versions"],[5,1,1,"","list_json_schemas"],[5,1,1,"","list_organizations"],[5,1,1,"","login"],[5,1,1,"","unbind_json_schema"],[5,1,1,"","update_organization_acl"],[5,1,1,"","validate"],[5,1,1,"","validate_children"],[5,1,1,"","validate_entity_with_json_schema"],[5,1,1,"","validation_stats"]],"synapseclient.services.json_schema.JsonSchemaVersion":[[5,1,1,"","bind_to_object"],[5,1,1,"","create"],[5,1,1,"","delete"],[5,1,1,"","expand"],[5,1,1,"","get"]],"synapseclient.table":[[6,0,1,"","Column"],[6,0,1,"","CsvFileTable"],[3,0,1,"","EntityViewSchema"],[6,0,1,"","Row"],[6,0,1,"","RowSet"],[6,0,1,"","RowSetTable"],[3,0,1,"","Schema"],[6,3,1,"","Table"],[6,0,1,"","TableAbstractBaseClass"],[6,0,1,"","TableQueryResult"],[6,3,1,"","as_table_columns"],[6,3,1,"","build_table"]],"synapseclient.table.Column":[[6,1,1,"","__init__"]],"synapseclient.table.CsvFileTable":[[6,1,1,"","asDataFrame"],[6,1,1,"","from_table_query"],[6,1,1,"","iter_row_metadata"],[6,1,1,"","setColumnHeaders"]],"synapseclient.table.Row":[[6,1,1,"","__init__"]],"synapseclient.table.RowSet":[[6,1,1,"","__init__"]],"synapseclient.table.RowSetTable":[[6,1,1,"","iter_row_metadata"]],"synapseclient.table.TableAbstractBaseClass":[[6,0,1,"","RowMetadataTuple"],[6,1,1,"","iter_row_metadata"]],"synapseclient.table.TableAbstractBaseClass.RowMetadataTuple":[[6,4,1,"","row_etag"],[6,4,1,"","row_id"],[6,4,1,"","row_version"]],"synapseclient.table.TableQueryResult":[[6,1,1,"","asDataFrame"],[6,1,1,"","iter_row_metadata"],[6,1,1,"","next"]],"synapseclient.team":[[7,0,1,"","Team"],[7,0,1,"","TeamMember"],[7,0,1,"","UserGroupHeader"],[7,0,1,"","UserProfile"]],"synapseclient.wiki":[[9,0,1,"","Wiki"]],"synapseclient.wiki.Wiki":[[9,1,1,"","__init__"]],"synapseutils.copy_functions":[[17,3,1,"","changeFileMetaData"],[17,3,1,"","copy"],[17,3,1,"","copyFileHandles"],[17,3,1,"","copyWiki"]],"synapseutils.describe_functions":[[17,3,1,"","describe"]],"synapseutils.migrate_functions":[[17,0,1,"","MigrationResult"],[17,3,1,"","index_files_for_migration"],[17,3,1,"","migrate_indexed_files"]],"synapseutils.migrate_functions.MigrationResult":[[17,1,1,"","as_csv"],[17,1,1,"","get_counts_by_status"],[17,1,1,"","get_migrations"]],"synapseutils.monitor":[[17,3,1,"","notifyMe"],[17,3,1,"","with_progress_bar"]],"synapseutils.sync":[[17,3,1,"","generateManifest"],[17,3,1,"","generate_sync_manifest"],[17,3,1,"","readManifestFile"],[17,3,1,"","syncFromSynapse"],[17,3,1,"","syncToSynapse"]],"synapseutils.walk_functions":[[17,3,1,"","walk"]],synapseclient:[[2,0,1,"","Synapse"],[0,2,0,"-","activity"],[1,2,0,"-","annotations"],[2,2,0,"-","client"],[3,2,0,"-","entity"],[4,2,0,"-","evaluation"],[6,2,0,"-","table"],[7,2,0,"-","team"],[9,2,0,"-","wiki"]],synapseutils:[[17,2,0,"-","copy_functions"],[17,2,0,"-","describe_functions"],[17,2,0,"-","migrate_functions"],[17,2,0,"-","monitor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