From 2579befead1982b2913325f95a9bc311c5f9ee9d Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Thu, 12 Sep 2019 11:48:13 +0200
Subject: [PATCH] lots of bugfixes in search, added _subcriteria_for method
---
pybis/src/python/pybis/pybis.py | 206 +++++++++++++++++++++++---------
1 file changed, 148 insertions(+), 58 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 398cf56cda8..e65ecd7eca2 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -381,9 +381,9 @@ def _subcriteria_for_tags(tags):
if not isinstance(tags, list):
tags = [tags]
- criterias = []
+ criteria = []
for tag in tags:
- criterias.append({
+ criteria.append({
"fieldName": "code",
"fieldType": "ATTRIBUTE",
"fieldValue": {
@@ -396,7 +396,7 @@ def _subcriteria_for_tags(tags):
return {
"@type": "as.dto.tag.search.TagSearchCriteria",
"operator": "AND",
- "criteria": criterias
+ "criteria": criteria
}
@@ -423,14 +423,99 @@ def _subcriteria_for_properties(prop, val):
}
}
+def _subcriteria_for(thing, entity, parents_or_children='', operator='AND'):
+ """Returns the sub-search criteria for «thing», which can be either:
+ - a python object (sample, dataSet, experiment)
+ - a permId
+ - an identifier
+ - a code
+ """
+
+ if isinstance(thing, str):
+ if is_permid(thing):
+ return _subcriteria_for_permid(
+ thing,
+ entity=entity,
+ parents_or_children=parents_or_children,
+ operator=operator
+ )
+ elif is_identifier(thing):
+ return _subcriteria_for_identifier(
+ thing,
+ entity=entity,
+ parents_or_children=parents_or_children,
+ operator=operator
+ )
+ else:
+ # look for code
+ return _subcriteria_for_code_new(
+ thing,
+ entity=entity,
+ parents_or_children=parents_or_children,
+ operator=operator
+ )
+
+ elif isinstance(thing, list):
+ criteria = []
+ for element in thing:
+ crit = _subcriteria_for(element, entity, parents_or_children, operator)
+ criteria += crit["criteria"]
+
+ return {
+ "criteria": criteria,
+ "@type": crit["@type"],
+ "operator": "OR"
+ }
+ elif thing is None:
+ # we just need the type
+ search_type = get_type_for_entity(entity, 'search', parents_or_children)
+ return {
+ "criteria": [],
+ **search_type,
+ "operator": operator
+ }
+ else:
+ # we passed an object
+ return _subcriteria_for_permid(
+ thing.permId,
+ entity=entity,
+ parents_or_children=parents_or_children,
+ operator=operator
+ )
+
+
+def _subcriteria_for_identifier(ids, entity, parents_or_children='', operator='AND'):
+ if not isinstance(ids, list):
+ ids = [ids]
+
+ criteria = []
+ for id in ids:
+ criteria.append({
+ "@type": "as.dto.common.search.IdentifierSearchCriteria",
+ "fieldValue": {
+ "value": id,
+ "@type": "as.dto.common.search.StringEqualToValue"
+ },
+ "fieldType": "ATTRIBUTE",
+ "fieldName": "identifier"
+ })
+
+ search_type = get_type_for_entity(entity, 'search', parents_or_children)
+ return {
+ "criteria": criteria,
+ **search_type,
+ "operator": operator
+ }
+ return criteria
+
def _subcriteria_for_permid(permids, entity, parents_or_children='', operator='AND'):
if not isinstance(permids, list):
permids = [permids]
- criterias = []
+ criteria = []
for permid in permids:
- criterias.append({
+ criteria.append({
"@type": "as.dto.common.search.PermIdSearchCriteria",
"fieldValue": {
"value": permid,
@@ -440,14 +525,36 @@ def _subcriteria_for_permid(permids, entity, parents_or_children='', operator='A
"fieldName": "code"
})
- criteria = {
- "criteria": criterias,
- "@type": "as.dto.{}.search.{}{}SearchCriteria".format(
- entity.lower(), entity, parents_or_children
- ),
+ search_type = get_type_for_entity(entity, 'search', parents_or_children)
+ return {
+ "criteria": criteria,
+ **search_type,
+ "operator": operator
+ }
+
+
+def _subcriteria_for_code_new(codes, entity, parents_or_children='', operator='AND'):
+ if not isinstance(codes, list):
+ codes = [codes]
+
+ criteria = []
+ for code in codes:
+ criteria.append({
+ "@type": "as.dto.common.search.CodeSearchCriteria",
+ "fieldValue": {
+ "value": code,
+ "@type": "as.dto.common.search.StringEqualToValue"
+ },
+ "fieldType": "ATTRIBUTE",
+ "fieldName": "code"
+ })
+
+ search_type = get_type_for_entity(entity, 'search', parents_or_children)
+ return {
+ "criteria": criteria,
+ **search_type,
"operator": operator
}
- return criteria
def _subcriteria_for_code(code, entity):
@@ -1403,37 +1510,34 @@ class Openbis:
def get_samples(
self, identifier=None, code=None, permId=None,
- space=None, project=None, experiment=None, type=None,
+ space=None, project=None, experiment=None, collection=None, type=None,
start_with=None, count=None,
withParents=None, withChildren=None, tags=None, props=None, **properties
):
""" Get a list of all samples for a given space/project/experiment (or any combination)
"""
+ if collection is not None:
+ experiment = collection
+
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))
+ crit = _subcriteria_for(identifier, 'sample')
+ sub_criteria += crit['criteria']
if space:
- sub_criteria.append(_subcriteria_for_code(space, 'space'))
+ sub_criteria.append(_subcriteria_for(space, 'space'))
if project:
- proj_crit = _subcriteria_for_code(project, 'project')
- sub_criteria.append(proj_crit)
+ sub_criteria.append(_subcriteria_for(project, 'project'))
if experiment:
- sub_criteria.append(_subcriteria_for_code(experiment, 'experiment'))
+ sub_criteria.append(_subcriteria_for(experiment, 'experiment'))
+
+ if withParents:
+ sub_criteria.append(_subcriteria_for(withParents, 'sample', 'Parents'))
+ if withChildren:
+ sub_criteria.append(_subcriteria_for(withChildren, 'sample', 'Children'))
+
if properties is not None:
for prop in properties:
sub_criteria.append(_subcriteria_for_properties(prop, properties[prop]))
@@ -1445,26 +1549,6 @@ class Openbis:
sub_criteria.append(_criteria_for_code(code))
if permId:
sub_criteria.append(_common_search("as.dto.common.search.PermIdSearchCriteria", permId))
- if withParents:
- if not isinstance(withParents, list):
- withParents = [withParents]
- for parent in withParents:
- sub_criteria.append(
- _gen_search_criteria({
- "sample": "SampleParents",
- "identifier": parent
- })
- )
- if withChildren:
- if not isinstance(withChildren, list):
- withChildren = [withChildren]
- for child in withChildren:
- sub_criteria.append(
- _gen_search_criteria({
- "sample": "SampleChildren",
- "identifier": child
- })
- )
criteria = {
"criteria": sub_criteria,
@@ -1596,29 +1680,35 @@ class Openbis:
def get_datasets(
self, code=None, type=None, withParents=None, withChildren=None,
start_with=None, count=None, kind=None,
- status=None, sample=None, experiment=None, project=None,
+ status=None, sample=None, experiment=None, collection=None, project=None,
tags=None, props=None, **properties
):
+ if 'object' in properties:
+ sample = properties['object']
+ if collection is not None:
+ experiment = collection
+
sub_criteria = []
if code:
sub_criteria.append(_criteria_for_code(code))
if type:
- sub_criteria.append(_subcriteria_for_type(type, 'DataSet'))
+ sub_criteria.append(_subcriteria_for_type(type, 'dataSet'))
+
if withParents:
- sub_criteria.append(_subcriteria_for_permid(withParents, 'DataSet', 'Parents'))
+ sub_criteria.append(_subcriteria_for(withParents, 'dataSet', 'Parents'))
if withChildren:
- sub_criteria.append(_subcriteria_for_permid(withChildren, 'DataSet', 'Children'))
+ sub_criteria.append(_subcriteria_for(withChildren, 'dataSet', 'Children'))
if sample:
- sub_criteria.append(_subcriteria_for_code(sample, 'Sample'))
+ sub_criteria.append(_subcriteria_for(sample, 'sample'))
if experiment:
- sub_criteria.append(_subcriteria_for_code(experiment, 'Experiment'))
+ sub_criteria.append(_subcriteria_for(experiment, 'experiment'))
+
if project:
- exp_crit = _subcriteria_for_code(experiment, 'Experiment')
- proj_crit = _subcriteria_for_code(project, 'Project')
- exp_crit['criteria'] = []
+ exp_crit = _subcriteria_for(experiment, 'experiment')
+ proj_crit = _subcriteria_for(project, 'project')
exp_crit['criteria'].append(proj_crit)
sub_criteria.append(exp_crit)
if tags:
--
GitLab