From ba29d3857187ce1d97e55def9ba2d6948320fd19 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Mon, 3 Dec 2018 15:12:48 +0100
Subject: [PATCH] search samples with identifier added
---
pybis/src/python/pybis/pybis.py | 29 ++++++++++++++++++++++-------
1 file changed, 22 insertions(+), 7 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 8400dab9846..c1a3e2ac23b 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -121,6 +121,7 @@ def get_attrs_for_entity(entity):
def _type_for_id(ident, entity):
+ ident = ident.strip()
"""Returns the data type for a given identifier/permId for use with the API call, e.g.
{
"identifier": "/DEFAULT/SAMPLE_NAME",
@@ -161,6 +162,9 @@ def _type_for_id(ident, entity):
entity_capitalize = entity.capitalize()
if is_identifier(ident):
+ # people tend to omit the / prefix of an identifier...
+ if not ident.startswith('/'):
+ ident = '/'+ident
search_request = {
"identifier": ident.upper(),
"@type": "as.dto.{}.id.{}Identifier".format(entity.lower(), entity_capitalize)
@@ -1310,7 +1314,7 @@ class Openbis:
def get_samples(
- self, code=None, permId=None, space=None, project=None, experiment=None, type=None,
+ self, identifier=None, code=None, permId=None, space=None, project=None, experiment=None, type=None,
start_with=None, count=None,
withParents=None, withChildren=None, tags=None, props=None, **properties
):
@@ -1318,13 +1322,24 @@ class Openbis:
"""
sub_criteria = []
+
+ # v3 API does not offer a search for identifiers. We need to do a combined search instead:
+ # space && code or
+ # space && project && code
+ if identifier:
+ identifier = identifier.lstrip('/')
+ elements = identifier.split('/')
+ if len(elements) == 2:
+ space = elements[0]
+ code = elements[1]
+ elif len(elements) == 3:
+ space = elements[0]
+ code = elements[2]
+ else:
+ raise ValueError("{} is not a valid sample identifier.".format(identifier))
+
if space:
- sub_criteria.append(_gen_search_criteria({
- "space": "Space",
- "operator": "AND",
- "code": space
- })
- )
+ sub_criteria.append(_subcriteria_for_code(space, 'space'))
if project:
proj_crit = _subcriteria_for_code(project, 'project')
sub_criteria.append(proj_crit)
--
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