From cd9fb56fc3d6a1d0fc77d8c7c7c5363bf2cef091 Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Mon, 17 Jul 2023 12:35:41 +0200
Subject: [PATCH] SSDM-13689: updated docs. obis-0.4.2rc4
---
.../src/python/obis/__init__.py | 2 +-
app-openbis-command-line/src/python/setup.py | 2 +-
docs/app-openbis-command-line/README.md | 65 +++++++++++++------
3 files changed, 48 insertions(+), 21 deletions(-)
diff --git a/app-openbis-command-line/src/python/obis/__init__.py b/app-openbis-command-line/src/python/obis/__init__.py
index 71b93ec62ce..7223e75da21 100644
--- a/app-openbis-command-line/src/python/obis/__init__.py
+++ b/app-openbis-command-line/src/python/obis/__init__.py
@@ -14,6 +14,6 @@
#
__author__ = "ID SIS • ETH Zürich"
__email__ = "openbis-support@id.ethz.ch"
-__version__ = "0.4.2rc3"
+__version__ = "0.4.2rc4"
from .dm import *
diff --git a/app-openbis-command-line/src/python/setup.py b/app-openbis-command-line/src/python/setup.py
index 3c87435cee0..e576159e85e 100644
--- a/app-openbis-command-line/src/python/setup.py
+++ b/app-openbis-command-line/src/python/setup.py
@@ -31,7 +31,7 @@ data_files = [
setup(
name="obis",
- version="0.4.2rc3",
+ version="0.4.2rc4",
description="Local data management with assistance from OpenBIS.",
long_description=long_description,
long_description_content_type="text/markdown",
diff --git a/docs/app-openbis-command-line/README.md b/docs/app-openbis-command-line/README.md
index 4505c3ef8b2..f194d05afbb 100644
--- a/docs/app-openbis-command-line/README.md
+++ b/docs/app-openbis-command-line/README.md
@@ -232,23 +232,44 @@ it comes to integration with other tools.
obis data_set search [OPTIONS]
Options:
- -object_type, --object_type TEXT
- Object type code to filter by
-space, --space TEXT Space code
- -project, --project TEXT Full project identification code
- -experiment, --experiment TEXT Full experiment code
- -object, --object TEXT Object identification information, it can be permId or identifier
- -type, --type TEXT Type code
+ -project, --project TEXT Project identification code
+ -collection, --collection TEXT Collection code
+ -id, --id TEXT Dataset identification information, it can
+ be permId or identifier
+ -type, --type TEXT Dataset type code
+ -property TEXT Property code
+ -property-value TEXT Property value
-registration-date, --registration-date TEXT
Registration date, it can be in the format
- "oYYYY-MM-DD" (e.g. ">2023-01-31", "=2023-01-31", "<2023-01-31")
+ "oYYYY-MM-DD" (e.g. ">2023-01-01")
-modification-date, --modification-date TEXT
Modification date, it can be in the format
- "oYYYY-MM-DD" (e.g. ">2023-01-31", "=2023-01-31", "<2023-01-31")
- -property TEXT Property code
- -property-value TEXT Property value
- -save, --save TEXT Directory name to save results
+ "oYYYY-MM-DD" (e.g. ">2023-01-01")
+ -save, --save TEXT Filename to save results
-r, --recursive Search data recursively
+
+Search by sample object parameters:
+ -object-type, --object-type TEXT
+ Object type code to filter by
+ -object-space, --object-space TEXT
+ Object space code
+ -object-project, --object-project TEXT
+ Full object project identification code
+ -object-collection, --object-collection TEXT
+ Full object collection code
+ -object-id, --object-id TEXT Object identification information, it can be
+ permId or identifier
+ -object-property TEXT Object property code
+ -object-property-value TEXT Object property value
+ -object-registration-date, --object-registration-date TEXT
+ Registration date, it can be in the format
+ "oYYYY-MM-DD" (e.g. ">2023-01-01")
+ -object-modification-date, --object-modification-date TEXT
+ Modification date, it can be in the format
+ "oYYYY-MM-DD" (e.g. ">2023-01-01")
+ --help Show this message and exit.
+
```
With `data_set search` command, obis connects to a configured OpenBIS instance and searches for all
@@ -259,6 +280,10 @@ Search results can be downloaded into a file by using `save` option.
Recursive option enables searching for datasets of children samples or datasets
+-object* filtering parameters allows to search for datasets owned by objects specified by these params,
+i.e. obis will find objects fitting these criterias (as if it was an `object search` command) and then it will extract
+dataset data.
+
*Note: Filtering by `-project` may not work when `Project Samples` are disabled in OpenBIS
configuration.*
@@ -310,21 +335,23 @@ data set is connected directly to an object - gets or sets given properties to i
obis object search [OPTIONS]
Options:
- -type, --type TEXT Type code to filter by
-space, --space TEXT Space code
-project, --project TEXT Full project identification code
- -experiment, --experiment TEXT Full experiment
- -object, --object TEXT Object identification information, it can be permId or identifier
+ -collection, --collection TEXT Full collection code
+ -object, --object TEXT Object identification information, it can be
+ permId or identifier
+ -type, --type TEXT Type code
+ -property TEXT Property code
+ -property-value TEXT Property value
-registration-date, --registration-date TEXT
Registration date, it can be in the format
- "oYYYY-MM-DD" (e.g. ">2023-01-31", "=2023-01-31", "<2023-01-31")
+ "oYYYY-MM-DD" (e.g. ">2023-01-01")
-modification-date, --modification-date TEXT
Modification date, it can be in the format
- "oYYYY-MM-DD" (e.g. ">2023-01-31", "=2023-01-31", "<2023-01-31")
- -property TEXT Property code
- -property-value TEXT Property value
- -save, --save TEXT File name to save results in csv format
+ "oYYYY-MM-DD" (e.g. ">2023-01-01")
+ -save, --save TEXT Filename to save results
-r, --recursive Search data recursively
+
```
With `object search` command, obis connects to a configured OpenBIS instance and searches for all
--
GitLab