From f2c6fed0308a92436b35b6fba4ec13926046fa57 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jos=C3=A9=20Mar=C3=ADa=20Fern=C3=A1ndez?= Date: Tue, 29 Nov 2022 19:40:01 +0100 Subject: [PATCH] Version bump to 0.9.0 --- CITATION.cff | 2 +- README.md | 17 ++++++++++------- TODO.md | 2 +- wfexs_backend/__init__.py | 2 +- 4 files changed, 13 insertions(+), 10 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 791defff..38b0db1c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -22,4 +22,4 @@ message: "If you use this software, please cite it using these metadata." repository-code: "https://github.com/inab/WfExS-backend" type: software title: "WfExS-backend" -version: 0.5.6 +version: 0.9.0 diff --git a/README.md b/README.md index b057723f..4b6b1be3 100644 --- a/README.md +++ b/README.md @@ -65,7 +65,7 @@ usage: WfExS-backend.py [-h] [--log-file LOGFILENAME] [-q] [-v] [-d] [-L LOCALCO {init,cache,staged-workdir,export,config-validate,stage,mount-workdir,export-stage,offline-execute,execute,export-results,export-crate} ... -WfExS (workflow execution service) backend 0.5.6-29-geb9615b (eb9615ba3668ac21dde4c02286ff3baa34a00e62) +WfExS (workflow execution service) backend 0.6.0 (532266dd5b0945cb1f1801a376428437e1ab3571) optional arguments: -h, --help show this help message and exit @@ -134,12 +134,12 @@ optional arguments: -g, --glob Given cache element names are globs (default: False) Subparser 'staged-workdir' -usage: WfExS-backend.py staged-workdir [-h] [-g] - {offline-exec,ls,mount,rm,shell,status} +usage: WfExS-backend.py staged-workdir [-h] [--full] [-g] + {offline-exec,ls,mount,rm,shell,status,create-staged-crate,create-prov-crate} [staged_workdir_command_args [staged_workdir_command_args ...]] positional arguments: - {offline-exec,ls,mount,rm,shell,status} + {offline-exec,ls,mount,rm,shell,status,create-staged-crate,create-prov-crate} Staged working directory command to perform offline-exec Offline execute the staged instances which match the input pattern @@ -154,11 +154,14 @@ positional arguments: If there is no additional parameters, it launches a shell in the mounted working directory of the instance status Shows staged instances status + create-staged-crateIt creates an RO-Crate from the prospective provenance + create-prov-crateIt creates an RO-Crate from the retrospective provenance (after a workflow execution) staged_workdir_command_args Optional staged working directory element names (default: None) optional arguments: -h, --help show this help message and exit + --full Should the RO-Crate contain a copy of the inputs (and outputs)? (default: False) -g, --glob Given staged workflow names are globs (default: False) Subparser 'export' @@ -278,7 +281,7 @@ WfExS commands are: * `stage`: This command is used to first validate workflow staging and security context configuration files, then fetch all the workflow preconditions and files, staging them for an execution. It honours `-L`, `-W`, `-Z` parameters and `WFEXS_CONFIG_FILE` environment variable, and once the staging is finished it prints the path to the parent execution environment. -* `staged-workdir`: This command is complementary to `stage`. It recognizes both `-L` parameter and `WFEXS_CONFIG_FILE` environment variable. This command has several subcommands which help on the workflow execution lifecycle (list available working directories and their statuses, remove some of them, execute either a shell or a custom command in a working directory context, execute, ...). +* `staged-workdir`: This command is complementary to `stage`. It recognizes both `-L` parameter and `WFEXS_CONFIG_FILE` environment variable. This command has several subcommands which help on the workflow execution lifecycle (list available working directories and their statuses, remove some of them, execute either a shell or a custom command in a working directory context, execute, export prospective and retrospective provenance to RO-Crate, ...). * `export`: This command is complementary to `stage`. It recognizes both `-L` parameter and `WFEXS_CONFIG_FILE` environment variable, and depends on `-J` parameter to locate the execution environment directory to be used, properly staged through `stage`. It also depends on both -E and -Z parameters, to declare the different export patterns and the needed credentials to complete the rules. This command has a couple of subcommands to list previously exported items and to do those exports. @@ -286,9 +289,9 @@ WfExS commands are: * `offline-execute`: This command is complementary to `stage`. It recognizes both `-L` parameter and `WFEXS_CONFIG_FILE` environment variable, and depends on `-J` parameter to locate the execution environment directory to be used, properly staged through `stage`. It executes the workflow, assuming all the preconditions are in place. -* `export-results` _(to be finished)_: This command is complementary to `offline-execute`. It recognizes both `-L` parameter and `WFEXS_CONFIG_FILE` environment variable, and depends on `-J` parameter to locate the execution environment directory to be used, properly staged through `stage` and executed through `offline-execute`. It export the results from an execution at a working directory, assuming there is an execution there. Export rules should be described in the file used in `-W` parameter when the working directory was staged. +* `export-results`: This command is complementary to `offline-execute`. It recognizes both `-L` parameter and `WFEXS_CONFIG_FILE` environment variable, and depends on `-J` parameter to locate the execution environment directory to be used, properly staged through `stage` and executed through `offline-execute`. It export the results from an execution at a working directory, assuming there is an execution there. Export rules should be described in the file used in `-W` parameter when the working directory was staged. -* `export-crate` _(to be finished)_: This command is complementary to `export-results`. It recognizes both `-L` parameter and `WFEXS_CONFIG_FILE` environment variable, and depends on `-J` parameter to locate the execution environment directory to be used, properly staged through `stage` and executed through `offline-execute` and `export-results`. It bundles the metadata and provenance results from an execution at a working directory in an RO-Crate, assuming there is an execution there. +* `export-crate`: This command is complementary to `export-results`. It recognizes both `-L` parameter and `WFEXS_CONFIG_FILE` environment variable, and depends on `-J` parameter to locate the execution environment directory to be used, properly staged through `stage` and executed through `offline-execute` and `export-results`. It bundles the metadata and provenance results from an execution at a working directory in an RO-Crate, assuming there is an execution there. * `mount-workdir`: This command is a helper to inspect encrypted execution environments, as it mounts its working directory for a limited time. As `export-stage`, `offline-execute` or `export-results`, it recognizes both `-L` parameter and `WFEXS_CONFIG_FILE` environment variable, and depends on `-J` parameter. diff --git a/TODO.md b/TODO.md index 57039f08..d7452eba 100644 --- a/TODO.md +++ b/TODO.md @@ -51,7 +51,7 @@ references to the inputs, that we are going to use to instantiate the workflows. - [ ] **Step 7.i**: Upload to osf.io . -- [ ] **Step 8**: Create execution provenance, which includes uploading URLs of results and / or DOIs / URIs. +- [ ] **Step 8**: (partially implemented) Create execution provenance, which includes uploading URLs of results and / or DOIs / URIs. - [x] **Step 9**: Generate RO-Crate from execution provenance and exported results. diff --git a/wfexs_backend/__init__.py b/wfexs_backend/__init__.py index 7b38d363..ac52bf21 100644 --- a/wfexs_backend/__init__.py +++ b/wfexs_backend/__init__.py @@ -20,7 +20,7 @@ __license__ = "Apache 2.0" # https://www.python.org/dev/peps/pep-0396/ -__version__ = "0.5.6" +__version__ = "0.9.0" __url__ = "https://github.com/inab/WfExS-backend" __official_name__ = "WfExS-backend"