diff --git a/pybis/src/python/pybis/attachment.py b/pybis/src/python/pybis/attachment.py
index 2d53d3d3bae3aa15f2d88a243bbffa9a3a3ab1b7..23df70ae93424316616d53759c3ca47761c7fcf4 100644
--- a/pybis/src/python/pybis/attachment.py
+++ b/pybis/src/python/pybis/attachment.py
@@ -5,7 +5,7 @@ import os
class Attachment:
def __init__(self, filename, title=None, description=None):
if not os.path.exists(filename):
- raise ValueError("File not found: {}".format(filename))
+ raise ValueError(f"File not found: {filename}")
self.fileName = filename
self.title = title
self.description = description
diff --git a/pybis/src/python/pybis/attribute.py b/pybis/src/python/pybis/attribute.py
index 880886870c072117ce8831f76e70d9650b7c1668..bf767fc3626b541b99c1b51a8c156f1ea3174f11 100644
--- a/pybis/src/python/pybis/attribute.py
+++ b/pybis/src/python/pybis/attribute.py
@@ -257,9 +257,7 @@ class AttrHolder:
"@type": "as.dto.person.id.PersonPermId",
}
],
- "@type": "as.dto.common.update.ListUpdateAction{}".format(
- self.__dict__["_changed_users"][userId]["action"]
- ),
+ "@type": f'as.dto.common.update.ListUpdateAction{self.__dict__["_changed_users"][userId]["action"]}',
}
)
@@ -453,16 +451,12 @@ class AttrHolder:
if self._is_new:
if name not in self._defs["attrs_new"]:
raise ValueError(
- "No such attribute: 芦{}禄 for entity: {}. Allowed attributes are: {}".format(
- name, self.entity, self._defs["attrs_new"]
- )
+ f'No such attribute: 芦{name}禄 for entity: {self.entity}. Allowed attributes are: {self._defs["attrs_new"]}'
)
else:
if name not in self._defs["attrs_up"]:
raise ValueError(
- "No such attribute: 芦{}禄 for entity: {}. Allowed attributes are: {}".format(
- name, self.entity, self._defs["attrs_up"]
- )
+ f'No such attribute: 芦{name}禄 for entity: {self.entity}. Allowed attributes are: {self._defs["attrs_up"]}'
)
if name in ["parents", "children", "components"]:
@@ -579,14 +573,12 @@ class AttrHolder:
self.__dict__["_" + name]["isModified"] = True
elif name in ["identifier"]:
- raise KeyError("you can not modify the {}".format(name))
+ raise KeyError(f"you can not modify the {name}")
elif name == "code":
try:
if self._type["autoGeneratedCode"]:
raise KeyError(
- "This {}Type has auto-generated code. You cannot set a code".format(
- self.entity
- )
+ f"This {self.entity}Type has auto-generated code. You cannot set a code"
)
except KeyError:
pass
@@ -606,7 +598,7 @@ class AttrHolder:
# enum: check whether value is a valid constant
if value and value not in self._defs[name]:
raise ValueError(
- "Allowed values for enum {} are: {}".format(name, self._defs[name])
+ f"Allowed values for enum {name} are: {self._defs[name]}"
)
else:
self.__dict__["_" + name] = value
@@ -985,9 +977,7 @@ class AttrHolder:
for attr in attrs:
if attr == "attachments":
continue
- html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
- attr, nvl(getattr(self, attr, ""), "")
- )
+ html += f'<tr> <td>{attr}</td> <td>{nvl(getattr(self, attr, ""), "")}</td> </tr>'
if getattr(self, "_attachments") is not None:
html += "<tr><td>attachments</td><td>"
html += "<br/>".join(att["fileName"] for att in self._attachments)
@@ -1017,9 +1007,7 @@ class AttrHolder:
for role in self._roleAssignments:
if role.get("space") is not None:
roles.append(
- "{} ({})".format(
- role.get("role"), role.get("space").get("code")
- )
+ f'{role.get("role")} ({role.get("space").get("code")})'
)
else:
roles.append(role.get("role"))
diff --git a/pybis/src/python/pybis/data_set.py b/pybis/src/python/pybis/data_set.py
index 96167971c43fabb0d0e9c1e99aa6f5ee15258cf2..0bb13be90a0b4c02c0520a738fff17a0682c264c 100644
--- a/pybis/src/python/pybis/data_set.py
+++ b/pybis/src/python/pybis/data_set.py
@@ -115,9 +115,7 @@ class GitDataSetCreation(object):
def data_store_url(self, dss_code):
data_stores = self.openbis.get_datastores()
data_store = data_stores[data_stores["code"] == dss_code]
- return "{}/datastore_server/rmi-data-store-server-v3.json".format(
- data_store["downloadUrl"][0]
- )
+ return f'{data_store["downloadUrl"][0]}/datastore_server/rmi-data-store-server-v3.json'
def data_set_metadata_creation(self):
"""Create the respresentation of the data set metadata."""
@@ -339,6 +337,4 @@ class GitDataSetFileSearch(object):
if self.dss_code is None:
self.dss_code = self.openbis.get_datastores()["code"][0]
data_store = data_stores[data_stores["code"] == self.dss_code]
- return "{}/datastore_server/rmi-data-store-server-v3.json".format(
- data_store["downloadUrl"][0]
- )
+ return f'{data_store["downloadUrl"][0]}/datastore_server/rmi-data-store-server-v3.json'
diff --git a/pybis/src/python/pybis/dataset.py b/pybis/src/python/pybis/dataset.py
index 9bcb253bbd49f80d2c18ede731586757dbe3f3e6..5225f19d46646ed13a2445c401fd50abc24c4646 100644
--- a/pybis/src/python/pybis/dataset.py
+++ b/pybis/src/python/pybis/dataset.py
@@ -76,7 +76,7 @@ class DataSet(
for file in files:
if not os.path.exists(file):
- raise ValueError("File {} does not exist".format(file))
+ raise ValueError(f"File {file} does not exist")
self.__dict__["files"] = files
@@ -99,7 +99,7 @@ class DataSet(
allowed_kinds = ["PHYSICAL", "CONTAINER", "LINK"]
if kind not in allowed_kinds:
raise ValueError(
- "only these values are allowed for kind: {}".format(allowed_kinds)
+ f"only these values are allowed for kind: {allowed_kinds}"
)
self.a.__dict__["_kind"] = kind
@@ -332,13 +332,13 @@ class DataSet(
}
self.archive_unarchive("archiveDataSets", fetchopts)
if VERBOSE:
- print("DataSet {} archived".format(self.permId))
+ print(f"DataSet {self.permId} archived")
def unarchive(self):
fetchopts = {"@type": "as.dto.dataset.unarchive.DataSetUnarchiveOptions"}
self.archive_unarchive("unarchiveDataSets", fetchopts)
if VERBOSE:
- print("DataSet {} unarchived".format(self.permId))
+ print(f"DataSet {self.permId} unarchived")
def archive_unarchive(self, method, fetchopts):
payload = {}
@@ -493,7 +493,7 @@ class DataSet(
content_copy_index,
)
else:
- raise ValueError("Can't download data set of kind {}.".format(kind))
+ raise ValueError(f"Can't download data set of kind {kind}.")
def _download_physical(
self, files, destination, create_default_folders, wait_until_finished, workers
@@ -545,7 +545,7 @@ class DataSet(
queue.join()
if VERBOSE:
- print("Files downloaded to: {}".format(os.path.join(final_destination)))
+ print(f"Files downloaded to: {os.path.join(final_destination)}")
return final_destination
def _download_link(
@@ -800,9 +800,7 @@ class DataSet(
or getattr(self.props, prop_name) == ""
):
raise ValueError(
- "Property '{}' is mandatory and must not be None".format(
- prop_name
- )
+ f"Property '{prop_name}' is mandatory and must not be None"
)
if self.is_new:
@@ -1172,39 +1170,29 @@ class DataSetDownloadQueue:
r = requests.get(url, stream=True, verify=verify_certificates)
if r.ok == False:
raise ValueError(
- "Could not download from {}: HTTP {}. Reason: {}".format(
- url, r.status_code, r.reason
- )
+ f"Could not download from {url}: HTTP {r.status_code}. Reason: {r.reason}"
)
with open(filename_dest, write_mode) as fh:
for chunk in r.iter_content(chunk_size=1024 * 1024):
- # size += len(chunk)
- # print("WRITE ", datetime.now(), len(chunk))
if chunk: # filter out keep-alive new chunks
fh.write(chunk)
- # print("DONE WRITE", datetime.now())
-
- # print("DONE", datetime.now())
r.raise_for_status()
- # print("{} bytes written".format(size))
actual_file_size = os.path.getsize(filename_dest)
if actual_file_size != int(file_size):
if self.collect_files_with_wrong_length:
self.files_with_wrong_length.append(filename)
else:
print(
- "WARNING! File {} has the wrong length: Expected: {} Actual size: {}".format(
- filename_dest, int(file_size), actual_file_size
- )
+ f"WARNING! File {filename_dest} has the wrong length: Expected: {int(file_size)} Actual size: {actual_file_size}"
)
print(
"REASON: The connection has been silently dropped upstreams.",
"Please check the http timeout settings of the openBIS datastore server",
)
except Exception as err:
- print("ERROR while writing file {}: {}".format(filename_dest, err))
+ print(f"ERROR while writing file {filename_dest}: {err}")
finally:
self.download_queue.task_done()
@@ -1255,9 +1243,7 @@ class PhysicalData:
"""
for attr in self.attrs:
- html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
- attr, getattr(self, attr, "")
- )
+ html += f"<tr> <td>{attr}</td> <td>{getattr(self, attr, '')}</td> </tr>"
html += """
</tbody>
diff --git a/pybis/src/python/pybis/definitions.py b/pybis/src/python/pybis/definitions.py
index 3fa68259bbddd448d3a6b9e2c74bc4f3b7448a07..a04bd8e33f8cf1b9c557b2dd5332c2fbc4688854 100644
--- a/pybis/src/python/pybis/definitions.py
+++ b/pybis/src/python/pybis/definitions.py
@@ -475,7 +475,7 @@ def get_fetchoption_for_entity(entity):
def get_type_for_entity(entity, action, parents_or_children=""):
if action not in "create update delete search".split():
- raise ValueError("unknown action: {}".format(action))
+ raise ValueError(f"unknown action: {action}")
definition = openbis_definitions(entity)
if action in definition and not parents_or_children:
@@ -492,19 +492,11 @@ def get_type_for_entity(entity, action, parents_or_children=""):
if parents_or_children:
return {
- "@type": "as.dto.{}.{}.{}{}{}".format(
- entity.lower(),
- action,
- cap_entity,
- parents_or_children,
- noun[action],
- )
+ "@type": f"as.dto.{entity.lower()}.{action}.{cap_entity}{parents_or_children}{noun[action]}"
}
else:
return {
- "@type": "as.dto.{}.{}.{}{}".format(
- entity.lower(), action, cap_entity, noun[action]
- )
+ "@type": f"as.dto.{entity.lower()}.{action}.{cap_entity}{noun[action]}"
}
@@ -523,12 +515,12 @@ def get_fetchoptions(entity, including=None):
return fo
-def get_method_for_entity(entity, action):
+def get_method_for_entity(entity: str, action: str) -> str:
action = action.lower()
if entity == "vocabulary":
- return "{}Vocabularies".format(action)
+ return f"{action}Vocabularies"
cap_entity = entity[:1].upper() + entity[1:]
- return "{}{}s".format(action, cap_entity)
+ return f"{action}{cap_entity}s"
diff --git a/pybis/src/python/pybis/entity_type.py b/pybis/src/python/pybis/entity_type.py
index a4a5de41bb9047efa7d36f7c24175adf9e6cf5af..60a97b954db4a9fed27156663968dfa91ba5b060 100644
--- a/pybis/src/python/pybis/entity_type.py
+++ b/pybis/src/python/pybis/entity_type.py
@@ -155,7 +155,7 @@ class EntityType:
芦initialValueForExistingEntities禄 too.
"""
if self.is_new:
- raise ValueError("Please save {} first".format(self.entity))
+ raise ValueError(f"Please save {self.entity} first")
if isinstance(prop, str):
property_type = self.openbis.get_property_type(prop.upper())
diff --git a/pybis/src/python/pybis/experiment.py b/pybis/src/python/pybis/experiment.py
index b9dd9c64f88e4b7e577a68fbdf1b9df1c24f9661..488418cdacfd6d5f526b9a1a0f31c69db1ac7fb2 100644
--- a/pybis/src/python/pybis/experiment.py
+++ b/pybis/src/python/pybis/experiment.py
@@ -108,9 +108,7 @@ class Experiment(
# a sample can only belong to exactly one experiment
if obj.experiment is not None:
raise ValueError(
- "sample {} already belongs to experiment {}".format(
- obj.code, obj.experiment
- )
+ f"sample {obj.code} already belongs to experiment {obj.experiment}"
)
else:
if self.is_new:
diff --git a/pybis/src/python/pybis/group.py b/pybis/src/python/pybis/group.py
index d1ec21c1702d2bf7277ff6c3250274f21bebb91a..c48221d3700cf7a7a94780abbaff729a75afdf32 100644
--- a/pybis/src/python/pybis/group.py
+++ b/pybis/src/python/pybis/group.py
@@ -89,15 +89,11 @@ class Group(
try:
self.openbis.assign_role(role=role, group=self, **kwargs)
if VERBOSE:
- print(
- "Role {} successfully assigned to group {}".format(role, self.code)
- )
+ print(f"Role {role} successfully assigned to group {self.code}")
except ValueError as e:
if "exists" in str(e):
if VERBOSE:
- print(
- "Role {} already assigned to group {}".format(role, self.code)
- )
+ print(f"Role {role} already assigned to group {self.code}")
else:
raise ValueError(str(e))
@@ -120,9 +116,7 @@ class Group(
query["project"] = project.upper()
# build a query string for dataframe
- querystr = " & ".join(
- '{} == "{}"'.format(key, value) for key, value in query.items()
- )
+ querystr = " & ".join(f'{key} == "{value}"' for key, value in query.items())
roles = self.get_roles().df
if len(roles) == 0:
if VERBOSE:
diff --git a/pybis/src/python/pybis/material.py b/pybis/src/python/pybis/material.py
index e891dc953f42c573920ff5771519d1e70f731772..c229a442efd953d91eb8fe815a02262457f4372a 100644
--- a/pybis/src/python/pybis/material.py
+++ b/pybis/src/python/pybis/material.py
@@ -36,9 +36,7 @@ class Material(OpenBisObject):
or getattr(self.props, prop_name) == ""
):
raise ValueError(
- "Property '{}' is mandatory and must not be None".format(
- prop_name
- )
+ f"Property '{prop_name}' is mandatory and must not be None"
)
props = self.p._all_props()
@@ -66,4 +64,4 @@ class Material(OpenBisObject):
def delete(self, reason="no reason"):
self.openbis.delete_entity(entity=self.entity, id=self.permId, reason=reason)
if VERBOSE:
- print("Material {} successfully deleted.".format(self.permId))
+ print(f"Material {self.permId} successfully deleted.")
diff --git a/pybis/src/python/pybis/openbis_object.py b/pybis/src/python/pybis/openbis_object.py
index 0dc2b8ce3cd612c3476485e1b4c9358497be1bf7..ff94cde0b8e9d4564281f537944f410a037039f4 100644
--- a/pybis/src/python/pybis/openbis_object.py
+++ b/pybis/src/python/pybis/openbis_object.py
@@ -150,7 +150,7 @@ class OpenBisObject:
entity=self._entity, objectId=self.data["permId"], reason=reason
)
if VERBOSE:
- print("{} {} successfully deleted.".format(self._entity, self.permId))
+ print(f"{self._entity} {self.permId} successfully deleted.")
def _get_single_item_method(self):
single_item_method = None
@@ -174,9 +174,7 @@ class OpenBisObject:
or getattr(self.props, prop_name) == ""
):
raise ValueError(
- "Property '{}' is mandatory and must not be None".format(
- prop_name
- )
+ f"Property '{prop_name}' is mandatory and must not be None"
)
props = self.p._all_props()
@@ -190,7 +188,7 @@ class OpenBisObject:
resp = self.openbis._post_request(self.openbis.as_v3, request)
if VERBOSE:
- print("{} successfully created.".format(self.entity))
+ print(f"{self.entity} successfully created.")
new_entity_data = get_single_item(resp[0]["permId"], only_data=True)
self._set_data(new_entity_data)
return self
@@ -204,7 +202,7 @@ class OpenBisObject:
resp = self.openbis._post_request(self.openbis.as_v3, request)
if VERBOSE:
- print("{} successfully updated.".format(self.entity))
+ print(f"{self.entity} successfully updated.")
new_entity_data = get_single_item(
self.permId, only_data=True, use_cache=False
)
@@ -290,9 +288,7 @@ class Transaction:
or getattr(entity.props, prop_name) == ""
):
raise ValueError(
- "Property '{}' is mandatory and must not be None".format(
- prop_name
- )
+ f"Property '{prop_name}' is mandatory and must not be None"
)
props = entity.p._all_props()
diff --git a/pybis/src/python/pybis/person.py b/pybis/src/python/pybis/person.py
index 4bd8ae72ef6cc355ae41bdc502a588cc781db579..ccd9020f8cafa681c8cd5dbfd6453b5e4d03bd86 100644
--- a/pybis/src/python/pybis/person.py
+++ b/pybis/src/python/pybis/person.py
@@ -1,3 +1,4 @@
+from regex import F
from .attribute import AttrHolder
from .openbis_object import OpenBisObject
from .utils import VERBOSE
@@ -50,19 +51,11 @@ class Person(OpenBisObject):
try:
self.openbis.assign_role(role=role, person=self, **kwargs)
if VERBOSE:
- print(
- "Role {} successfully assigned to person {}".format(
- role, self.userId
- )
- )
+ print(f"Role {role} successfully assigned to person {self.userId}")
except ValueError as e:
if "exists" in str(e):
if VERBOSE:
- print(
- "Role {} already assigned to person {}".format(
- role, self.userId
- )
- )
+ print(f"Role {role} already assigned to person {self.userId}")
else:
raise ValueError(str(e))
@@ -91,9 +84,7 @@ class Person(OpenBisObject):
query["project"] = project.code.upper()
# build a query string for dataframe
- querystr = " & ".join(
- '{} == "{}"'.format(key, value) for key, value in query.items()
- )
+ querystr = " & ".join(f'{key} == "{value}"' for key, value in query.items())
roles = self.get_roles().df
if len(roles) == 0:
if VERBOSE:
@@ -107,11 +98,11 @@ class Person(OpenBisObject):
ra = self.openbis.get_role_assignment(techId)
ra.delete(reason)
if VERBOSE:
- print("Role {} successfully revoked from person {}".format(role, self.code))
+ print(f"Role {role} successfully revoked from person {self.code}")
return
def __str__(self):
- return "{} {}".format(self.get("firstName"), self.get("lastName"))
+ return f'{self.get("firstName")} {self.get("lastName")}'
def delete(self, reason):
raise ValueError("Persons cannot be deleted")
diff --git a/pybis/src/python/pybis/property.py b/pybis/src/python/pybis/property.py
index c252148b088dceb37285be6ca227d0c4b7ff2099..a677fd77f01631226d3bbf55ec6f77ffbcca3965 100644
--- a/pybis/src/python/pybis/property.py
+++ b/pybis/src/python/pybis/property.py
@@ -122,9 +122,7 @@ class PropertyHolder:
"""
if name not in self._property_names:
raise KeyError(
- "No such property: '{}'. Allowed properties are: {}".format(
- name, ", ".join(self._property_names.keys())
- )
+ f"No such property: 芦{name}禄. Allowed properties are: {', '.join(self._property_names.keys())}"
)
property_type = self._property_names[name]
data_type = property_type["dataType"]
@@ -133,13 +131,11 @@ class PropertyHolder:
value = str(value).upper()
if value not in terms.df["code"].values:
raise ValueError(
- "Value for attribute {} must be one of these terms: {}".format(
- name, ", ".join(terms.df["code"].values)
- )
+ f"Value for attribute 芦{name}禄 must be one of these terms: {', '.join(terms.df['code'].values)}"
)
elif data_type in ("INTEGER", "BOOLEAN", "VARCHAR"):
if not check_datatype(data_type, value):
- raise ValueError("Value must be of type {}".format(data_type))
+ raise ValueError(f"Value must be of type {data_type}")
self.__dict__[name] = value
def __setitem__(self, key, value):
@@ -176,13 +172,18 @@ class PropertyHolder:
"""
for prop_name, prop in self._property_names.items():
- html += "<tr> <td>{}</td><td>{}</td><td>{}</td><td>{}</td><td>{}</td> </tr>".format(
- prop_name,
- nvl(getattr(self, prop_name, ""), ""),
- prop.get("description"),
- prop.get("dataType"),
- prop.get("mandatory"),
+ html += "<tr>"
+ html += "".join(
+ f"<td>{item}</td>"
+ for item in [
+ prop_name,
+ nvl(getattr(self, prop_name, ""), ""),
+ prop.get("description"),
+ prop.get("dataType"),
+ prop.get("mandatory"),
+ ]
)
+ html += "</tr>"
html += """
</tbody>
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 6f0c6a1314d642170751cef7286e0f5b2f1f6d76..50cf3e9a15938a37c22364318932a9ffd5004097 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -200,14 +200,12 @@ def _type_for_id(ident, entity):
search_request = {
"identifier": ident.upper(),
- "@type": "as.dto.{}.id.{}Identifier".format(
- entity.lower(), entity_capitalize
- ),
+ "@type": f"as.dto.{entity.lower()}.id.{entity_capitalize}Identifier",
}
else:
search_request = {
"permId": ident,
- "@type": "as.dto.{}.id.{}PermId".format(entity.lower(), entity_capitalize),
+ "@type": f"as.dto.{entity.lower()}.id.{entity_capitalize}PermId",
}
return search_request
@@ -253,9 +251,7 @@ def _tagIds_for_tags(tags=None, action="Add"):
"actions": [
{
"items": items,
- "@type": "as.dto.common.update.ListUpdateAction{}".format(
- action.capitalize()
- ),
+ "@type": f"as.dto.common.update.ListUpdateAction{action.capitalize()}",
}
],
"@type": "as.dto.common.update.IdListUpdateValue",
@@ -274,7 +270,7 @@ def _list_update(ids=None, entity=None, action="Add"):
map(
lambda id: {
"code": id,
- "@type": "as.dto.{}.id.{}Code".format(entity.lower(), entity),
+ "@type": f"as.dto.{entity.lower()}.id.{entity}Code",
},
ids,
)
@@ -284,9 +280,7 @@ def _list_update(ids=None, entity=None, action="Add"):
"actions": [
{
"items": items,
- "@type": "as.dto.common.update.ListUpdateAction{}".format(
- action.capitalize()
- ),
+ "@type": f"as.dto.common.update.ListUpdateAction{action.capitalize()}",
}
],
"@type": "as.dto.common.update.IdListUpdateValue",
@@ -295,7 +289,7 @@ def _list_update(ids=None, entity=None, action="Add"):
def get_field_value_search(field, value, comparison="StringEqualToValue"):
- return {"value": value, "@type": "as.dto.common.search.{}".format(comparison)}
+ return {"value": value, "@type": f"as.dto.common.search.{comparison}"}
def _common_search(search_type, value, comparison="StringEqualToValue"):
@@ -303,7 +297,7 @@ def _common_search(search_type, value, comparison="StringEqualToValue"):
"@type": search_type,
"fieldValue": {
"value": value,
- "@type": "as.dto.common.search.{}".format(comparison),
+ "@type": f"as.dto.common.search.{comparison}",
},
}
return sreq
@@ -351,7 +345,7 @@ def _subcriteria_for_userId(userId):
def _subcriteria_for_type(code, entity):
return {
- "@type": "as.dto.{}.search.{}TypeSearchCriteria".format(entity.lower(), entity),
+ "@type": f"as.dto.{entity.lower()}.search.{entity}TypeSearchCriteria",
"criteria": [
{
"@type": "as.dto.common.search.CodeSearchCriteria",
@@ -431,7 +425,7 @@ def _gen_search_criteria(req):
elif key == "operator":
sreq["operator"] = val.upper()
else:
- sreq["@type"] = "as.dto.{}.search.{}SearchCriteria".format(key, val)
+ sreq["@type"] = f"as.dto.{key}.search.{val}SearchCriteria"
return sreq
@@ -1087,9 +1081,7 @@ class Openbis:
"token",
]
for attr in attrs:
- html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
- attr, getattr(self, attr, "")
- )
+ html += f"<tr> <td>{attr}</td> <td>{getattr(self, attr, '')}</td> </tr>"
html += """
</tbody>
@@ -1259,9 +1251,7 @@ class Openbis:
return pstore.get("password")
else:
raise Exception(
- "This method can only be called from these internal methods: {}".format(
- allowed_methods
- )
+ f"This method can only be called from these internal methods: {allowed_methods}"
)
def unmount(self, mountpoint=None):
@@ -1285,21 +1275,19 @@ class Openbis:
if not os.path.ismount(full_mountpoint_path):
return
- status = subprocess.call("umount {}".format(full_mountpoint_path), shell=True)
+ status = subprocess.call(f"umount {full_mountpoint_path}", shell=True)
if status == 1:
status = subprocess.call(
- 'pkill -9 sshfs && umount "{}"'.format(full_mountpoint_path), shell=True
+ f'pkill -9 sshfs && umount "{full_mountpoint_path}"', shell=True
)
if status == 1:
raise OSError(
- "could not unmount mountpoint: {} Please try to unmount manually".format(
- full_mountpoint_path
- )
+ f"could not unmount mountpoint: {full_mountpoint_path} Please try to unmount manually"
)
else:
if VERBOSE:
- print("Successfully unmounted {}".format(full_mountpoint_path))
+ print(f"Successfully unmounted {full_mountpoint_path}")
self.mountpoint = None
def is_mounted(self, mountpoint=None):
@@ -1388,9 +1376,7 @@ class Openbis:
"""
if self.is_mounted():
if VERBOSE:
- print(
- "openBIS dataStore is already mounted on {}".format(self.mountpoint)
- )
+ print(f"openBIS dataStore is already mounted on {self.mountpoint}")
return
def check_sshfs_is_installed():
@@ -1437,13 +1423,11 @@ class Openbis:
supported_platforms = ["darwin", "linux"]
if platform not in supported_platforms:
raise ValueError(
- "This method is not yet supported on {} plattform".format(platform)
+ f"This method is not yet supported on {platform} plattform"
)
os_options = {
- "darwin": "-oauto_cache,reconnect,defer_permissions,noappledouble,negative_vncache,volname={} -oStrictHostKeyChecking=no ".format(
- hostname
- ),
+ "darwin": f"-oauto_cache,reconnect,defer_permissions,noappledouble,negative_vncache,volname={hostname} -oStrictHostKeyChecking=no ",
"linux": "-oauto_cache,reconnect -oStrictHostKeyChecking=no",
}
@@ -1475,7 +1459,7 @@ class Openbis:
if status == 0:
if VERBOSE:
- print("Mounted successfully to {}".format(full_mountpoint_path))
+ print(f"Mounted successfully to {full_mountpoint_path}")
self.mountpoint = full_mountpoint_path
return self.mountpoint
else:
@@ -1581,7 +1565,7 @@ class Openbis:
try:
return self._post_request(self.as_v1, request)
except Exception as e:
- raise ValueError("Could not generate a code for {}: {}".format(entity, e))
+ raise ValueError(f"Could not generate a code for {entity}: {e}")
def gen_permId(self, count=1):
"""Generate a permId (or many permIds) for a dataSet"""
@@ -1590,7 +1574,7 @@ class Openbis:
try:
return self._post_request(self.as_v3, request)
except Exception as exc:
- raise ValueError("Could not generate a code: {}".format(exc))
+ raise ValueError(f"Could not generate a code: {exc}")
def new_person(self, userId, space=None):
"""creates an openBIS person or returns the existing person"""
@@ -1681,7 +1665,7 @@ class Openbis:
else:
pass
else:
- raise ValueError("unknown search argument {}".format(attr))
+ raise ValueError(f"unknown search argument {attr}")
search_criteria["criteria"] = sub_crit
@@ -1748,7 +1732,7 @@ class Openbis:
resp = self._post_request(self.as_v3, request)
if len(resp) == 0:
- raise ValueError("No assigned role found for techId={}".format(techId))
+ raise ValueError(f"No assigned role found for techId={techId}")
for permid in resp:
data = resp[permid]
@@ -1771,7 +1755,7 @@ class Openbis:
role = role.upper()
defs = get_definition_for_entity("roleAssignment")
if role not in defs["role"]:
- raise ValueError("Role should be one of these: {}".format(defs["role"]))
+ raise ValueError(f"Role should be one of these: {defs['role']}")
userId = None
groupId = None
spaceId = None
@@ -2738,9 +2722,7 @@ class Openbis:
kind = kind.upper()
if kind not in ["PHYSICAL", "CONTAINER", "LINK"]:
raise ValueError(
- "unknown dataSet kind: {}. It should be one of the following: PHYSICAL, CONTAINER or LINK".format(
- kind
- )
+ f"unknown dataSet kind: {kind}. It should be one of the following: PHYSICAL, CONTAINER or LINK"
)
fetchopts["kind"] = kind
raise NotImplementedError("you cannot search for dataSet kinds yet")
@@ -3072,7 +3054,7 @@ class Openbis:
if not isinstance(permids, list):
permids = [permids]
- type = "as.dto.{}.id.{}".format(entity.lower(), entity.capitalize())
+ type = f"as.dto.{entity.lower()}.id.{entity.capitalize()}"
search_params = []
for permid in permids:
# decide if we got a permId or an identifier
@@ -3224,9 +3206,7 @@ class Openbis:
if resp is None or len(resp) == 0:
raise ValueError(
- "no VocabularyTerm found with code='{}' and vocabularyCode='{}'".format(
- code, vocabularyCode
- )
+ f"no VocabularyTerm found with code='{code}' and vocabularyCode='{vocabularyCode}'"
)
else:
parse_jackson(resp)
@@ -3313,7 +3293,7 @@ class Openbis:
resp = self._post_request(self.as_v3, request)
if len(resp) == 0:
- raise ValueError("no {} found with identifier: {}".format(entity, code))
+ raise ValueError(f"no {entity} found with identifier: {code}")
else:
parse_jackson(resp)
for ident in resp:
@@ -3384,7 +3364,7 @@ class Openbis:
if just_one:
if len(resp) == 0:
- raise ValueError("no such tag found: {}".format(permId))
+ raise ValueError(f"no such tag found: {permId}")
parse_jackson(resp)
for permId in resp:
@@ -3817,7 +3797,7 @@ class Openbis:
if only_one:
if len(resp) == 0:
- raise ValueError("no such propertyType: {}".format(code))
+ raise ValueError(f"no such propertyType: {code}")
for ident in resp:
if only_data:
return resp[ident]
@@ -4078,7 +4058,7 @@ class Openbis:
parse_jackson(resp)
if len(identifiers) == 1:
if len(resp) == 0:
- raise ValueError("no such {}: {}".format(entity, identifier[0]))
+ raise ValueError(f"no such {entity}: {identifier[0]}")
for ident in resp:
if only_data:
return resp[ident]
@@ -4112,14 +4092,10 @@ class Openbis:
optional_attributes = []
search_request = {
- "@type": "as.dto.{}.search.{}TypeSearchCriteria".format(
- entity.lower(), entity
- )
+ "@type": f"as.dto.{entity.lower()}.search.{entity}TypeSearchCriteria"
}
fetch_options = {
- "@type": "as.dto.{}.fetchoptions.{}TypeFetchOptions".format(
- entity.lower(), entity
- )
+ "@type": f"as.dto.{entity.lower()}.fetchoptions.{entity}TypeFetchOptions"
}
fetch_options["from"] = start_with
fetch_options["count"] = count
@@ -4147,12 +4123,10 @@ class Openbis:
if len(response["objects"]) == 1:
return EntityType(openbis_obj=self, data=response["objects"][0])
elif len(response["objects"]) == 0:
- raise ValueError("No such {} type: {}".format(entity, type_name))
+ raise ValueError(f"No such {entity} type: {type_name}")
else:
raise ValueError(
- "There is more than one entry for entity={} and type={}".format(
- entity, type_name
- )
+ f"There is more than one entry for entity={entity} and type={type_name}"
)
types = []
@@ -4280,7 +4254,7 @@ class Openbis:
resp = self._post_request(self.as_v3, request)
if just_one:
if len(resp) == 0:
- raise ValueError("no such dataset found: {}".format(permIds))
+ raise ValueError(f"no such dataset found: {permIds}")
parse_jackson(resp)
@@ -4518,7 +4492,7 @@ class Openbis:
if only_one:
if len(resp) == 0:
- raise ValueError("no such sample found: {}".format(sample_ident))
+ raise ValueError(f"no such sample found: {sample_ident}")
parse_jackson(resp)
for sample_ident in resp:
@@ -5212,9 +5186,7 @@ class ServerInformation:
"""
for attr in self.attrs:
- html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
- attr, getattr(self, attr, "")
- )
+ html += f"<tr> <td>{attr}</td> <td>{getattr(self, attr, '')}</td> </tr>"
html += """
</tbody>
diff --git a/pybis/src/python/pybis/role_assignment.py b/pybis/src/python/pybis/role_assignment.py
index f2fa0dbc5d3fa8c880b94d4d6bacbdc6ad189bb8..521eb495ff72aea8dff553cfc233b033f1a1264a 100644
--- a/pybis/src/python/pybis/role_assignment.py
+++ b/pybis/src/python/pybis/role_assignment.py
@@ -25,7 +25,7 @@ class RoleAssignment(OpenBisObject):
return ["id", "role", "roleLevel", "space", "project", "group"]
def __str__(self):
- return "{}".format(self.get("role"))
+ return f"{self.get('role')}"
def delete(self, reason="no reason specified"):
self.openbis.delete_openbis_entity(
@@ -33,7 +33,5 @@ class RoleAssignment(OpenBisObject):
)
if VERBOSE:
print(
- "RoleAssignment role={}, roleLevel={} successfully deleted.".format(
- self.role, self.roleLevel
- )
+ f"RoleAssignment role={self.role}, roleLevel={self.roleLevel} successfully deleted."
)
diff --git a/pybis/src/python/pybis/sample.py b/pybis/src/python/pybis/sample.py
index df1d7b0828e63a8ce73379397a65fb06a2efcc59..790e9681c4b42677720edde08a05a22de6b87f94 100644
--- a/pybis/src/python/pybis/sample.py
+++ b/pybis/src/python/pybis/sample.py
@@ -211,9 +211,7 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
or getattr(self.props, prop_name) == ""
):
raise ValueError(
- "Property '{}' is mandatory and must not be None".format(
- prop_name
- )
+ f"Property '{prop_name}' is mandatory and must not be None"
)
sampleProject = self.project.code if self.project else None
@@ -248,7 +246,7 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
if resp["rows"][0][0]["value"] != "OK":
raise ValueError("Status is not OK")
if VERBOSE:
- print("{} successfully created.".format(self.entity))
+ print(f"{self.entity} successfully created.")
permId = permid = resp["rows"][0][2]["value"]
new_entity_data = self.openbis.get_sample(permId, only_data=True)
self._set_data(new_entity_data)
diff --git a/pybis/src/python/pybis/semantic_annotation.py b/pybis/src/python/pybis/semantic_annotation.py
index 7c4aae67c38dd17f9a6dcee2157532c853163acf..af4e5fbb87c3953e92508408e3ba9f47d1f7aab3 100644
--- a/pybis/src/python/pybis/semantic_annotation.py
+++ b/pybis/src/python/pybis/semantic_annotation.py
@@ -161,9 +161,7 @@ class SemanticAnnotation:
"""
for attr in attrs:
- html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
- attr, getattr(self, attr, "")
- )
+ html += f"<tr> <td>{attr}</td> <td>{getattr(self, attr, '')}</td> </tr>"
html += """
</tbody>
diff --git a/pybis/src/python/pybis/space.py b/pybis/src/python/pybis/space.py
index 47fc3c07ddcb0f98dc283675f9dd1f4a78608b79..3a708a94a8f67a91b88aa437dbb169a2f5e60bdb 100644
--- a/pybis/src/python/pybis/space.py
+++ b/pybis/src/python/pybis/space.py
@@ -47,10 +47,10 @@ class Space(OpenBisObject, entity="space", single_item_method_name="get_space"):
return self.openbis.get_sample(sample_code)
else:
if project_code is None:
- return self.openbis.get_sample("/{}/{}".format(self.code, sample_code))
+ return self.openbis.get_sample(f"/{self.code}/{sample_code}")
else:
return self.openbis.get_sample(
- "/{}/{}/{}".format(self.code, project_code, sample_code)
+ f"/{self.code}/{project_code}/{sample_code}"
)
get_object = get_sample # Alias
diff --git a/pybis/src/python/pybis/things.py b/pybis/src/python/pybis/things.py
index 68c4acbfe37f128ea4736af4203022b4f2ddc54f..1bf370c2826a4f2cd838b532210d8d14b5cb4966 100644
--- a/pybis/src/python/pybis/things.py
+++ b/pybis/src/python/pybis/things.py
@@ -93,7 +93,7 @@ class Things:
def get_parents(self, **kwargs):
if self.entity not in ["sample", "dataset"]:
- raise ValueError("{}s do not have parents".format(self.entity))
+ raise ValueError(f"{self.entity}s do not have parents")
if self.df is not None and len(self.df) > 0:
dfs = []
@@ -116,7 +116,7 @@ class Things:
def get_children(self, **kwargs):
if self.entity not in ["sample", "dataset"]:
- raise ValueError("{}s do not have children".format(self.entity))
+ raise ValueError(f"{self.entity}s do not have children")
if self.df is not None and len(self.df) > 0:
dfs = []
@@ -140,7 +140,7 @@ class Things:
def get_samples(self, **kwargs):
if self.entity not in ["space", "project", "experiment"]:
- raise ValueError("{}s do not have samples".format(self.entity))
+ raise ValueError(f"{self.entity}s do not have samples")
if self.df is not None and len(self.df) > 0:
dfs = []
@@ -165,7 +165,7 @@ class Things:
def get_datasets(self, **kwargs):
if self.entity not in ["sample", "experiment"]:
- raise ValueError("{}s do not have datasets".format(self.entity))
+ raise ValueError(f"{self.entity}s do not have datasets")
if self.df is not None and len(self.df) > 0:
dfs = []
diff --git a/pybis/src/python/pybis/utils.py b/pybis/src/python/pybis/utils.py
index b8453c4fe2c16e5ff6c61ee1622fe8e1b856d9c3..bc5329fa73ce676682a9fef36c35abf183923a33 100644
--- a/pybis/src/python/pybis/utils.py
+++ b/pybis/src/python/pybis/utils.py
@@ -285,7 +285,7 @@ def extract_person(person):
def extract_person_details(person):
if not isinstance(person, dict):
return str(person)
- return "{} {} <{}>".format(person["firstName"], person["lastName"], person["email"])
+ return "{firstName} {lastName} <{email}>".format(**person)
def extract_id(id):
diff --git a/pybis/src/python/pybis/vocabulary.py b/pybis/src/python/pybis/vocabulary.py
index e2b09d707a6f18eca0347e71d633cdf45c67223d..76aa2d3a055204bc73d177ffd64f36bb22ebc935 100644
--- a/pybis/src/python/pybis/vocabulary.py
+++ b/pybis/src/python/pybis/vocabulary.py
@@ -25,9 +25,7 @@ class Vocabulary(
for key in kwargs:
if key not in allowed_attrs:
raise ValueError(
- "{} is an unknown Vocabulary attribute. Allowed attributes are: {}".format(
- key, ", ".join(allowed_attrs)
- )
+ f"{key} is an unknown Vocabulary attribute. Allowed attributes are: {', '.join(allowed_attrs)}"
)
if kwargs is not None:
@@ -77,7 +75,7 @@ class Vocabulary(
}
resp = self.openbis._post_request(self.openbis.as_v3, request)
if VERBOSE:
- print("{} {} successfully deleted.".format(self.entity, self.code))
+ print(f"{self.entity} {self.code} successfully deleted.")
def save(self):
terms = self._terms or []