| Lines 3-41 were replaced by line 3 |
| - To help scientists manage and share data sets, workflows, and workflow |
| - computation steps (i.e., actors) as well as semantic descriptions (i.e., |
| - metadata and ontology-based annotations) of each of these, we propose |
| - adding a new file-management middleware subsystem to Kepler. |
| - |
| - The main goals of the file-management subsystem are listed below. In |
| - particular, the subsystem should provide the infrastructure for |
| - enabling scientists to: |
| - |
| - * Search for all known items of interest, including actors, workflows, |
| - and data sets. |
| - |
| - * Easily organize actors, workflows, and data sets of interest using the |
| - file-directory metaphor (called "actor libraries" in Ptolemy). For |
| - example, by allowing a scientist to create and persist a personal |
| - library, and to browse and search that library. Allow items to be |
| - organized into multiple local actor libraries, and in multiple |
| - locations within a library. |
| - |
| - * Persist actors, workflows, and data sets in a network-accesible |
| - repository (i.e., in the EcoGrid). |
| - |
| - * Retrieve new actors, workflows, and data sets from a network-accessible |
| - repository (from the EcoGrid) and update changes to existing items. |
| - |
| - * Track both revisions of actors, workflows, and data sets as well as new |
| - versions (off-shoots or branches) of an item. |
| - |
| - * Store semantic annotations of actors, workflows, and data sets and |
| - publish those annotations to a network repository (the |
| - EcoGrid). Retrieve annotations from the network repository. |
| - |
| - |
| - The figure below outlines the architectural components of the |
| - subsystem. The subsystem assumes the use of [Life-Sciences Identifiers|http://www.i3c.org/wgr/ta/resources/lsid/docs/index.asp] |
| - (LSIDs) as logical identifiers for actors, workflows, data sets, and |
| - annotations (and possibly for local "libraries"?). Thus, particular |
| - files (representing actors, workflows, data sets, or annotations) are |
| - assigned LSIDs and are accessed via LSIDs. |
| + To help scientists manage and share data sets, workflows, and workflow computation steps (i.e., actors) as well as semantic descriptions (i.e., metadata and ontology-based annotations) of each of these, we propose adding a new file-management middleware subsystem to Kepler. |
| At line 42 added 12 lines. |
| + The main goals of the file-management subsystem are listed below. We use the term "Kepler item" loosely below to refer to actors, workflows, and data sets, and "annotations" to refer to metadata (like EML) and semantic descriptions. The subsystem should provide the infrastructure for enabling scientists to: |
| + |
| + * Search for all known Kepler items of interest. |
| + * Organize Kepler items of interest using a file-directory metaphor (currently called "actor libraries" in Ptolemy). For example, a scientist should be able to create and persist a personal library, and to browse and search that library. |
| + * Allow Kepler items to be organized into multiple libraries, and in multiple places within a library. |
| + * Persist Kepler items in a network-accesible repository (i.e., in the EcoGrid). |
| + * Retrieve new Kepler items from a network-accessible repository (the EcoGrid) and update changes to local items. |
| + * Track both revisions of Kepler items as well as new versions (off-shoots or branches) of an item. |
| + * Provide similar functionality for annotations, i.e., store annotations of actors, workflows, and data sets and publish those annotations to a network repository (the EcoGrid), and retrieve new annotations from the network repository. |
| + |
| + The figure below outlines the architectural components of the subsystem. We treat annotations and Kepler items uniformly below. That is, the management subsystem does not have separate storage components for managing annotations and items. The subsystem assumes the use of [Life-Sciences Identifiers|http://www.i3c.org/wgr/ta/resources/lsid/docs/index.asp] (LSIDs) as logical identifiers for items and annotations. (QUESTION: and also for local "libraries" -- do these need to be stored in the EcoGrid, e.g.?). Thus, relevant files are assigned LSIDs and are accessed via LSIDs. We assume that an LSID will store the type of file (e.g., the type of annotation, or the type of Kepler item) associated with the ID. |
| + |
| At line 43 added 1 line. |
| + |
| Lines 46-69 were replaced by line 21 |
| - The main components provide operations over a local data store of |
| - files. The remote manager provides the operations required to interact |
| - with the EcoGrid. It also may provide a local cache for |
| - performance. The LSID manager is used to assign unique identifiers for |
| - items, e.g., serving as logical identifiers for actors, workflows, |
| - data sets, and semantic annotations. The logical/physical index |
| - manager provides operations to related physical files to LSIDs, and to |
| - access files based on LSIDs. The directory/view manager provides |
| - operations for local organizations of items into libraries. |
| - |
| - The following are a set of possible supported operations (note that |
| - these are half-baked, if that): |
| - |
| - * {{Retrieve(ID)}}. Given an id, the subsystem returns the files |
| - associated with the item. |
| - |
| - * {{LocalIDs(IDMetadata)}}. Retrieve a list of local LSIDs, based on LSID |
| - metadata. |
| - |
| - * {{RemoteIDs(IDMetadata)}}. Retrieve a list of remote LSIDs, based on LSID |
| - metadata. |
| - |
| - * {{Store(ItemHandle, IDMetadata)}}. Construct an LSID with the given |
| - metadata for the item, and store the item in the local repository. |
| + The remote manager component provides the operations required to interact with the EcoGrid. It also may provide a local cache for better performance. The LSID manager creates and assigns unique identifiers for items and annotations. The logical/physical index manager provides operations to relate physical files to LSIDs, and to access physical files based on LSIDs. The directory/view manager provides operations to support the creation and retrieval of local, customized libraries. |
| Lines 71-72 were replaced by line 23 |
| - * {{GetRemoteUpdates()}}. Retrieve a list of new or updated LSIDs from a remote |
| - source. |
| + The following are operations (these are very half-baked!) may be provided by the Kepler file-management subsystem: |
| Lines 74-75 were replaced by lines 25-32 |
| - * {{Update(LSID)}}. Update the given LSID item from a remote source. This |
| - retrieves a new revision if one exists. |
| + * {{Retrieve(ID)}}. Given an LSID, returns the relevant files associated with the item. |
| + * {{LocalIDs(IDMetadata)}}. Retrieve a list of local LSIDs, based on LSID metadata. |
| + * {{RemoteIDs(IDMetadata)}}. Retrieve a list of remote LSIDs, based on LSID metadata. |
| + * {{Store(ItemHandle, IDMetadata)}}. Construct an LSID with the given metadata for the item, and store the item in the local repository. |
| + * {{GetRemoteUpdates()}}. Retrieve a list of new or updated LSIDs from a remote source. |
| + * {{Update(LSID)}}. Update the given LSID item from a remote source. This retrieves a new revision if one exists. |
| + * {{Branch(LSID)}}. Create a new version of an item. This creates and returns a new LSID for the item. |
| + * {{CommitToRemoteServer(LSID)}}. Update this item in a remote server. |
| Removed lines 77-78 |
| - * {{Branch(LSID)}}. Create a new version of an item. This creates and |
| - returns a new LSID for the item. |
| Line 80 was replaced by line 35 |
| - * {{CommitToRemoteServer(LSID)}}. Update this item in a remote server. |
| + Another feature that we may consider is support for change management. In particular, when a file within the subsystem is changed, a notification can be cached/stored of the change, for use by components within Kepler. (Isn't there already a change api in Kepler; and can we piggy-back on this?) |
