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Posted to commits@taverna.apache.org by st...@apache.org on 2017/12/21 19:36:18 UTC
[1/2] incubator-taverna-server git commit: Some table of contents
Repository: incubator-taverna-server
Updated Branches:
refs/heads/master 926419b0b -> e00ba6cbf
Some table of contents
(Generated with https://github.com/ekalinin/github-markdown-toc then
manually pasted into the various sections)
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/commit/7a036cea
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/tree/7a036cea
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/diff/7a036cea
Branch: refs/heads/master
Commit: 7a036ceacbd354e172f4d804a885f6678d9dd05d
Parents: 926419b
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Dec 21 19:33:32 2017 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Thu Dec 21 19:33:32 2017 +0000
----------------------------------------------------------------------
usage.md | 141 ++++++++++++++++++++++++++++++++++++++++++++++++++++++----
1 file changed, 133 insertions(+), 8 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/7a036cea/usage.md
----------------------------------------------------------------------
diff --git a/usage.md b/usage.md
index ee6081f..2514bf2 100644
--- a/usage.md
+++ b/usage.md
@@ -19,6 +19,21 @@ Apache Taverna Server: Usage and API Guide
Note: In this documentation we will assume the Taverna server is installed on http://localhost:8080/taverna-server - unless you are running the server locally you will have to replace `localhost:8080` with the corresponding `servername:port` (optionally switch to `https`). If you have deployed the Taverna Server WAR with a different service name you will also have to replace `/taverna-server`.
+
+* [Conceptual interface](#conceptual-interface)
+* [The (RESTful) Usage Pattern](#the-restful-usage-pattern)
+* [API of the REST Interface](#api-of-the-rest-interface)
+ * [Main Server Resource](#main-server-resource)
+ * [Per-Workflow Run Resource](#per-workflow-run-resource)
+* [API of the SOAP Interface](#api-of-the-soap-interface)
+ * [Global Settings](#global-settings)
+ * [Basic Workflow Operations](#basic-workflow-operations)
+ * [Input and Output Control](#input-and-output-control)
+ * [File Operations](#file-operations)
+ * [Event Listeners](#event-listeners)
+ * [Per-Run Security Configuration](#per-run-security-configuration)
+
+
Conceptual interface
--------------------
@@ -214,6 +229,15 @@ It is important to use the right namespaces for their corresponding elements/att
### Main Server Resource
+* [Resource: /](#resource-)
+* [Resource: /runs](#resource-runs)
+* [Resource: /policy](#resource-policy)
+* [Resource: /policy/capabilities](#resource-policycapabilities)
+* [Resource: /policy/enabledNotificationFabrics](#resource-policyenablednotificationfabrics)
+* [Resource: /policy/permittedListenerTypes](#resource-policypermittedlistenertypes)
+* [Resource: /policy/permittedWorkflows](#resource-policypermittedworkflows)
+* [Resource: /policy/runLimit](#resource-policyrunlimit)
+
#### Resource: /
* * Method: GET
@@ -348,6 +372,40 @@ Gets the maximum number of simultaneous runs that the user may create. Note that
Note that all of these resources require that the user be authenticated and permitted to (at least) see the run.
+* [Resource: /runs/{id}](#resource-runsid)
+* [Resource: /runs/{id}/expiry](#resource-runsidexpiry)
+* [Resource: /runs/{id}/createTime](#resource-runsidcreatetime)
+* [Resource: /runs/{id}/finishTime](#resource-runsidfinishtime)
+* [Resource: /runs/{id}/startTime](#resource-runsidstarttime)
+* [Resource: /runs/{id}/status](#resource-runsidstatus)
+* [Resource: /runs/{id}/workflow](#resource-runsidworkflow)
+* [Resource: /runs/{id}/input](#resource-runsidinput)
+* [Resource: /runs/{id}/input/baclava](#resource-runsidinputbaclava)
+* [Resource: /runs/{id}/input/expected](#resource-runsidinputexpected)
+* [Resource: /runs/{id}/input/input/{name}](#resource-runsidinputinputname)
+* [Resource: /runs/{id}/output](#resource-runsidoutput)
+* [Resource: /runs/{id}/run-bundle](#resource-runsidrun-bundle)
+* [Resource: /runs/{id}/generate-provenance](#resource-runsidgenerate-provenance)
+* [Resource: /runs/{id}/stdout](#resource-runsidstdout)
+* [Resource: /runs/{id}/stderr](#resource-runsidstderr)
+* [Resource: /runs/{id}/log](#resource-runsidlog)
+* [Resource: /runs/{id}/usage](#resource-runsidusage)
+* [Resource: /runs/{id}/listeners](#resource-runsidlisteners)
+* [Resource: /runs/{id}/listeners/{name}](#resource-runsidlistenersname)
+* [Resource: /runs/{id}/listeners/{name}/configuration](#resource-runsidlistenersnameconfiguration)
+* [Resource: /runs/{id}/listeners/{name}/properties](#resource-runsidlistenersnameproperties)
+* [Resource: /runs/{id}/listeners/{name}/properties/{propName}](#resource-runsidlistenersnamepropertiespropname)
+* [Resource: /runs/{id}/security](#resource-runsidsecurity)
+* [Resource: /runs/{id}/security/credentials](#resource-runsidsecuritycredentials)
+* [Resource: /runs/{id}/security/credentials/{credID}](#resource-runsidsecuritycredentialscredid)
+* [Resource: /runs/{id}/security/owner](#resource-runsidsecurityowner)
+* [Resource: /runs/{id}/security/permissions](#resource-runsidsecuritypermissions)
+* [Resource: /runs/{id}/security/permissions/{user}](#resource-runsidsecuritypermissionsuser)
+* [Resource: /runs/{id}/security/trusts](#resource-runsidsecuritytrusts)
+* [Resource: /runs/{id}/security/trusts/{trustID}](#resource-runsidsecuritytruststrustid)
+* [Resource: /runs/{id}/wd and /runs/{id}/wd/{path…}](#resource-runsidwd--and-runsidwdpath)
+
+
#### Resource: /runs/{id}
* Method: GET
@@ -1193,12 +1251,13 @@ API of the SOAP Interface
Taverna Server supports a SOAP interface to the majority of its user-facing functionality. The operations that it supports are divided into a few groups:
-- Global Settings
-- Basic Workflow Operations
-- Input and Output Control
-- File Operations
-- Event Listeners
-- Security Configuration
+ * [Global Settings](#global-settings)
+ * [Basic Workflow Operations](#basic-workflow-operations)
+ * [Input and Output Control](#input-and-output-control)
+ * [File Operations](#file-operations)
+ * [Event Listeners](#event-listeners)
+ * [Per-Run Security Configuration](#per-run-security-configuration)
+
The connection itself is done (under recommended deployment patterns) by HTTPS, and is authenticated via Basic HTTP username and password at the connection level. All information reported is only necessarily true for a particular user; no guarantee is made that it will be the same for any other user.
@@ -1208,6 +1267,13 @@ Note that the information below is just a summary. The WSDL document for the ser
These operations describe things that are across all the workflow runs owned by the connecting user on the server.
+* [getCapabilities](#getcapabilities)
+* [getEnabledNotificationFabrics](#getenablednotificationfabrics)
+* [getMaxSimultaneousRuns](#getmaxsimultaneousruns)
+* [getPermittedWorkflows](#getpermittedworkflows)
+* [getPermittedListenerTypes](#getpermittedlistenertypes)
+* [listRuns](#listruns)
+
#### getCapabilities
This obtains the description of the abstract capabilities (and their versions) of the execution engine that is hosted inside the service.
@@ -1234,7 +1300,25 @@ Get a list of all workflow runs on the server that the user has access to. (Work
### Basic Workflow Operations
-An ID string identifies every workflow run. All operations on a workflow run take the ID as one their arguments. (Implementation note: This ID is a UUID.)
+An ID string identifies every workflow run. All operations on a workflow run take the _run ID_ as one their arguments. (Implementation note: This ID is a UUID.)
+
+* [submitWorkflow](#submitworkflow)
+* [destroyRun](#destroyrun)
+* [getRunExpiry](#getrunexpiry)
+* [setRunExpiry](#setrunexpiry)
+* [getRunCreationTime](#getruncreationtime)
+* [getRunStartTime](#getrunstarttime)
+* [getRunFinishTime](#getrunfinishtime)
+* [getRunWorkflow](#getrunworkflow)
+* [getRunStatus](#getrunstatus)
+* [setRunStatus](#setrunstatus)
+* [getRunBundle](#getrunbundle)
+* [getRunGenerateProvenance](#getrungenerateprovenance)
+* [setRunGenerateProvenance](#setrungenerateprovenance)
+* [getRunStdout](#getrunstdout)
+* [getRunStderr](#getrunstderr)
+* [getRunLog](#getrunlog)
+* [getRunUsageRecord](#getrunusagerecord)
#### submitWorkflow
@@ -1306,6 +1390,17 @@ Get the resource usage description of the execution engine, or *null* when the e
### Input and Output Control
+These operations are used to find and set the required workflow _inputs_, and after the run, the resulting _outputs_.
+
+* [getRunInputDescriptor](#getruninputdescriptor)
+* [getRunInputs](#getruninputs)
+* [setRunInputPortFile](#setruninputportfile)
+* [setRunInputPortValue](#setruninputportvalue)
+* [setRunInputBaclavaFile](#setruninputbaclavafile)
+* [getRunOutputDescription](#getrunoutputdescription)
+* [setRunOutputBaclavaFile](#setrunoutputbaclavafile)
+* [getRunOutputBaclavaFile](#getrunoutputbaclavafile)
+
#### getRunInputDescriptor
Returns a description of what inputs are expected by a particular workflow.
@@ -1342,6 +1437,18 @@ Get the name of the Baclava file that will have the run outputs written to it.
Every workflow run has a working directory that is private to itself. That working directory will be the current directory when the workflow run is executing.
+* [getRunDirectoryContents](#getrundirectorycontents)
+* [destroyRunDirectoryEntry](#destroyrundirectoryentry)
+* [getRunDirectoryAsZip](#getrundirectoryaszip)
+* [makeRunDirectory](#makerundirectory)
+* [getRunFileContents](#getrunfilecontents)
+* [getRunFileContentsMTOM](#getrunfilecontentsmtom)
+* [getRunFileType](#getrunfiletype)
+* [getRunFileLength](#getrunfilelength)
+* [makeRunFile](#makerunfile)
+* [setRunFileContents](#setrunfilecontents)
+* [setRunFileContentsMTOM](#setrunfilecontentsmtom)
+
#### getRunDirectoryContents
List the contents of a directory. The workflow run's working directory is denoted by the empty filename, and only that directory or its subdirectories may be listed.
@@ -1388,9 +1495,17 @@ Set the contents of an existing file. (MTOM-enabled.)
### Event Listeners
+The event listeners can be set up to receive notifications on as the workflow run progresses.
+
+* [getRunListeners](#getrunlisteners)
+* [addRunListener](#addrunlistener)
+* [getRunListenerConfiguration](#getrunlistenerconfiguration)
+* [getRunListenerProperties](#getrunlistenerproperties)
+* [getRunListenerProperty / setRunListenerProperty](#getrunlistenerproperty--setrunlistenerproperty)
+
#### getRunListeners
-**GET** a list of listeners attached to a particular run.
+Get a list of listeners attached to a particular run.
#### addRunListener
@@ -1424,6 +1539,16 @@ There is one standard listener, `io`, which is attached by default. This listene
Note that all of the operations below are restricted to the owner of the run except for discovering the identity of the owner of the run.
+* [getRunOwner](#getrunowner)
+* [listRunPermissions](#listrunpermissions)
+* [setRunPermission](#setrunpermission)
+* [getRunCredentials](#getruncredentials)
+* [setRunCredential](#setruncredential)
+* [deleteRunCredential](#deleteruncredential)
+* [getRunCertificates](#getruncertificates)
+* [setRunCertificates](#setruncertificates)
+* [deleteRunCertificates](#deleteruncertificates)
+
#### getRunOwner
Get the identity of the owner of the run. Note that the owner always has full permission to modify and read the run.
[2/2] incubator-taverna-server git commit: Table of Content
Posted by st...@apache.org.
Table of Content
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/commit/e00ba6cb
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/tree/e00ba6cb
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/diff/e00ba6cb
Branch: refs/heads/master
Commit: e00ba6cbfffdec610e4551b5ba770b8a5d5c5e92
Parents: 7a036ce
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Thu Dec 21 19:35:35 2017 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Thu Dec 21 19:35:35 2017 +0000
----------------------------------------------------------------------
install.md | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/e00ba6cb/install.md
----------------------------------------------------------------------
diff --git a/install.md b/install.md
index cfa829c..c59fef8 100644
--- a/install.md
+++ b/install.md
@@ -18,6 +18,31 @@
Apache Taverna Server Installation and Administration Guide
===========================================================
+* [Known Limitations](#known-limitations)
+* [Installation](#installation)
+ * [Prerequisites](#prerequisites)
+ * [Installation into Tomcat](#installation-into-tomcat)
+ * [Step 1. Configure Tomcat for JMX](#step-1-configure-tomcat-for-jmx)
+ * [Step 2. Configure Tomcat for General Management](#step-2-configure-tomcat-for-general-management)
+ * [Step 3. Prepare for T2Server WebApp Installation](#step-3-prepare-for-t2server-webapp-installation)
+ * [Step 4. Download the Webapp ARchive](#step-4-download-the-webapp-archive)
+ * [Step 5. Install the WebApp](#step-5-install-the-webapp)
+ * [Firewall Requirements](#firewall-requirements)
+ * [Details of Configuration](#details-of-configuration)
+ * [Configuration Property List](#configuration-property-list)
+ * [Enabling Notification Options](#enabling-notification-options)
+ * [User Accounts](#user-accounts)
+ * [Configuration of Impersonation](#configuration-of-impersonation)
+ * [Security in Taverna Server](#security-in-taverna-server)
+ * [General](#general)
+ * [Architecture](#architecture)
+ * [Insecure Mode](#insecure-mode)
+ * [Part-Secure Mode](#part-secure-mode)
+* [Managing the Server](#managing-the-server)
+ * [Component: Taverna/Server/Webapp](#component-tavernaserverwebapp)
+ * [Component: Taverna/Server/RunFactory](#component-tavernaserverrunfactory)
+ * [Component: Taverna/Server/Users](#component-tavernaserverusers)
+
Known Limitations
-----------------