From f40e7a7fbb35db57016699affe96f8cdf5a8da69 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 18 Jun 2014 12:01:03 -0500
Subject: [PATCH] Rework transient data handling to match Galaxy's.
---
.hgignore | 3 ++-
docs/source/files/job_conf_sample_mq.xml | 2 +-
docs/source/upgrading.rst | 1 +
{persisted_data => files/persisted_data}/info.txt | 0
pulsar/core.py | 5 +++--
server.ini.sample | 6 +++---
6 files changed, 10 insertions(+), 7 deletions(-)
rename {persisted_data => files/persisted_data}/info.txt (100%)
diff --git a/.hgignore b/.hgignore
index 1ab15e04..79942641 100644
--- a/.hgignore
+++ b/.hgignore
@@ -6,7 +6,8 @@ cache
.coverage
local_env.sh
coverage_html_report
-lwr_staging
+files/staging
+files/persisted_data
server.ini
job_managers.ini
*.pem
diff --git a/docs/source/files/job_conf_sample_mq.xml b/docs/source/files/job_conf_sample_mq.xml
index 80607c41..cac3dbff 100644
--- a/docs/source/files/job_conf_sample_mq.xml
+++ b/docs/source/files/job_conf_sample_mq.xml
@@ -21,7 +21,7 @@
<!-- Tell Galaxy where files are being store on remote system, no
web server it can simply ask for this information.
-->
- <param id="jobs_directory">/path/to/remote/lwr/lwr_staging/</param>
+ <param id="jobs_directory">/path/to/remote/pulsar/files/staging/</param>
<!-- Invert file transfers - have LWR initiate downloads during preprocessing
and uploads during postprocessing. -->
<param id="default_file_action">remote_transfer</param>
diff --git a/docs/source/upgrading.rst b/docs/source/upgrading.rst
index 5235e1de..d81b0b98 100644
--- a/docs/source/upgrading.rst
+++ b/docs/source/upgrading.rst
@@ -10,3 +10,4 @@ Rough plan:
- Rebuild dependencies (and/or virtualenv) if needed.
- Copy the LWR's server.ini to Pulsar's root directory.
- Update ``app_factory`` property: ``paste.app_factory = pulsar.web.wsgi:app_factory``
+- If you were using the default values for ``persistence_directory`` and ``staging_directory`` you may wish to update those to the new defaults as well.
diff --git a/persisted_data/info.txt b/files/persisted_data/info.txt
similarity index 100%
rename from persisted_data/info.txt
rename to files/persisted_data/info.txt
diff --git a/pulsar/core.py b/pulsar/core.py
index df1f53bb..c07fcf71 100644
--- a/pulsar/core.py
+++ b/pulsar/core.py
@@ -17,8 +17,9 @@ from logging import getLogger
log = getLogger(__name__)
DEFAULT_PRIVATE_KEY = None
-DEFAULT_STAGING_DIRECTORY = "lwr_staging"
-DEFAULT_PERSISTENCE_DIRECTORY = "persisted_data"
+DEFAULT_FILES_DIRECTORY = "files"
+DEFAULT_STAGING_DIRECTORY = os.path.join(DEFAULT_FILES_DIRECTORY, "staging")
+DEFAULT_PERSISTENCE_DIRECTORY = os.path.join(DEFAULT_FILES_DIRECTORY, "persisted_data")
NOT_WHITELIST_WARNING = "Starting the LWR without a toolbox to white-list." + \
diff --git a/server.ini.sample b/server.ini.sample
index 6592dd76..a246dae0 100644
--- a/server.ini.sample
+++ b/server.ini.sample
@@ -20,8 +20,8 @@ host = localhost
paste.app_factory = pulsar.web.wsgi:app_factory
## Directory to stage files to. This should likely be updated to point
-## to an absolute path, such as /tmp/lwr_staging or C:\\lwr_staging
-staging_directory = lwr_staging
+## to an absolute path, such as /tmp/pulsar_staging or C:\\pulsar_staging
+staging_directory = files/staging
## Private key or password that must be sent as part of the request to
## authorize use. If security is important, please use this in
@@ -35,7 +35,7 @@ staging_directory = lwr_staging
## do this). If user the LWR runs as cannot write to the LWR root
## directory, this should be updated to point to some directory which
## it can write to.
-persistence_directory = persisted_data
+persistence_directory = files/persisted_data
## How are ids assigned. galaxy (default) just passes through ids as
## is. Setting this uuid assigns each job a UUID, this is strongly
--
GitLab