From dd2f8728d5525fd9d07fe1769dc50ceaac71d22e Mon Sep 17 00:00:00 2001
From: Swen Vermeul <swen@ethz.ch>
Date: Tue, 24 May 2016 09:24:49 +0200
Subject: [PATCH] get_samples implemented, tests added
---
src/python/PyBis/pybis/__init__.py | 3 +-
src/python/PyBis/pybis/pybis.py | 139 ++++++++++++++++++++++---
src/python/PyBis/pybis/pybis_test.py | 22 ----
src/python/PyBis/pybis/scripts/cli.py | 46 +-------
src/python/PyBis/setup.py | 3 +-
src/python/pybis/tests/conftest.py | 12 +++
src/python/pybis/tests/test_imports.py | 4 +
src/python/pybis/tests/test_openbis.py | 25 +++++
8 files changed, 172 insertions(+), 82 deletions(-)
delete mode 100644 src/python/PyBis/pybis/pybis_test.py
create mode 100644 src/python/pybis/tests/conftest.py
create mode 100644 src/python/pybis/tests/test_imports.py
create mode 100644 src/python/pybis/tests/test_openbis.py
diff --git a/src/python/PyBis/pybis/__init__.py b/src/python/PyBis/pybis/__init__.py
index eea0a080777..52b99ce1741 100644
--- a/src/python/PyBis/pybis/__init__.py
+++ b/src/python/PyBis/pybis/__init__.py
@@ -1,4 +1,5 @@
__author__ = 'Chandrasekhar Ramakrishnan <chandrasekhar.ramakrishnan@id.ethz.ch>'
__version__ = '0.1.0'
-from . import pybis
\ No newline at end of file
+from . import pybis
+from .pybis import Openbis
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index b3a970a580b..ae5dc5a7c15 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -11,6 +11,9 @@ Copyright (c) 2016 ETH Zuerich. All rights reserved.
"""
import os
+import requests
+import json
+import re
class OpenbisCredentials:
@@ -79,23 +82,54 @@ class OpenbisCredentialStore:
class Openbis:
"""Interface for communicating with openBIS."""
- def __init__(self, url, credentials):
+ def __init__(self, host=None):
"""Initialize an interface to openBIS with information necessary to connect to the server.
- :param url:
- :param credentials:
+ :param host:
"""
- self.url = url
- self.credentials = credentials
+ self.host = host
+ self.token = None
- def login(self):
+ def token(self):
+ if self.token is None:
+ raise ValueError('no valid session available')
+
+ def logout(self):
+
+ logout_request = {
+ "method":"logout",
+ "params":[self.token],
+ "id":"1",
+ "jsonrpc":"2.0"
+ }
+ resp = requests.post(self.host, json.dumps(logout_request))
+ if resp.ok:
+ self.token = None
+
+
+ def login(self, username='openbis_test_js', password='password', store_credentials=False):
"""Log into openBIS.
- Expects credentials with username and password and updates the token on the credentials object.
+ Expects a username and a password and updates the token (session-ID).
+ The token is then used for every request.
Clients may want to store the credentials object in a credentials store after successful login.
Throw a ValueError with the error message if login failed.
"""
- if not self.credentials.has_username_and_password:
- raise ValueError('Cannot log into openBIS without a username and password')
- # TODO Implement the logic of this method.
+
+ login_request = {
+ "method":"login",
+ "params":[username, password],
+ "id":"1",
+ "jsonrpc":"2.0"
+ }
+ resp = requests.post(self.host, json.dumps(login_request))
+ if resp.ok:
+ self.token = resp.json()['result']
+
+ else:
+ raise ValueError(
+ 'Cannot log into openBIS. Got status code ' + resp.status_code
+ + ' with reason: ' + resp.reason
+ )
+
def is_token_valid(self):
"""Check if the connection to openBIS is valid.
@@ -103,9 +137,18 @@ class Openbis:
user to login again.
:return: Return True if the token is valid, False if it is not valid.
"""
- if not self.credentials.has_token():
+
+ if not self.token:
return False
- # TODO Implement the logic of this method.
+
+ def get_dataset(self, permid):
+
+ search = {
+ "permId": permid,
+ "@type": "as.dto.dataset.id.DataSetPermId"
+ }
+
+
def get_samples(self, sample_identifiers):
"""Retrieve metadata for the sample.
@@ -113,7 +156,77 @@ class Openbis:
to the same information visible in the ELN UI. The metadata will be on the file system.
:param sample_identifiers: A list of sample identifiers to retrieve.
"""
- pass
+
+ if not isinstance(sample_identifiers, list):
+ sample_identifiers = [sample_identifiers]
+
+
+ searches = []
+
+ for ident in sample_identifiers:
+
+ # assume we got a sample identifier e.g. /TEST/TEST-SAMPLE
+ match = re.match('/', ident)
+ if match:
+ searches.append({
+ "identifier": ident,
+ "@type": "as.dto.sample.id.SampleIdentifier"
+ })
+ continue
+
+ # look if we got a PermID eg. 234567654345-123
+ match = re.match('\d+\-\d+', ident)
+ if match:
+ searches.append({
+ "permId": ident,
+ "@type": "as.dto.sample.id.SamplePermId"
+ })
+ continue
+
+ raise ValueError(
+ '"' + ident + '" is neither a Sample Identifier nor a PermID'
+ )
+
+ sample_request = {
+ "method": "getSamples",
+ "params": [
+ self.token,
+ searches,
+ {
+ "type": {
+ "@type": "as.dto.sample.fetchoptions.SampleTypeFetchOptions"
+ },
+ "properties": {
+ "@type": "as.dto.property.fetchoptions.PropertyFetchOptions"
+ },
+ "parents": {
+ "@id": 20,
+ "@type": "as.dto.sample.fetchoptions.SampleFetchOptions",
+ "properties": {
+ "@type": "as.dto.property.fetchoptions.PropertyFetchOptions"
+ }
+ },
+ "dataSets": {
+ "@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions",
+ "properties": {
+ "@type": "as.dto.property.fetchoptions.PropertyFetchOptions"
+ }
+ }
+ }
+ ],
+ "id": "1",
+ "jsonrpc": "2.0"
+ }
+
+ resp = requests.post(self.host, json.dumps(sample_request))
+ if resp.ok:
+ data = resp.json()
+ if "error" in data:
+ raise ValueError("Request produced an error: " + data["message"])
+ else:
+ return data['result']
+
+
# TODO Implement the logic of this method
def get_samples_with_data(self, sample_identifiers):
diff --git a/src/python/PyBis/pybis/pybis_test.py b/src/python/PyBis/pybis/pybis_test.py
deleted file mode 100644
index 8f22386a658..00000000000
--- a/src/python/PyBis/pybis/pybis_test.py
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""
-pybis_test.py
-
-Tests for the pybis module. Written using pytest.
-
-Created by Chandrasekhar Ramakrishnan on 2016-05-10.
-Copyright (c) 2016 ETH Zuerich. All rights reserved.
-"""
-
-from .pybis import OpenbisCredentials, OpenbisCredentialStore
-
-
-def test_credentials_store(tmpdir):
- credentials = OpenbisCredentials("magic_token")
- store = OpenbisCredentialStore(str(tmpdir))
- store.write(credentials)
- disk_credentials = store.read()
- assert credentials.token == disk_credentials.token
- assert not disk_credentials.has_username_and_password()
diff --git a/src/python/PyBis/pybis/scripts/cli.py b/src/python/PyBis/pybis/scripts/cli.py
index 21e627ef723..5cdd73c2908 100644
--- a/src/python/PyBis/pybis/scripts/cli.py
+++ b/src/python/PyBis/pybis/scripts/cli.py
@@ -1,48 +1,4 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""
-cli.py
-
-Command-line interface to interact with openBIS.
-
-Created by Chandrasekhar Ramakrishnan on 2016-05-09.
-Copyright (c) 2016 ETH Zuerich. All rights reserved.
-"""
-
-from datetime import datetime
-
-import click
-
-
-def click_progress(progress_data):
- timestamp = datetime.now().strftime("%H:%M:%S")
- click.echo("{} {}".format(timestamp, progress_data['message']))
-
-
-def click_progress(progress_data):
- timestamp = datetime.now().strftime("%H:%M:%S")
- click.echo("{} {}".format(timestamp, progress_data['message']))
-
-
-@click.group()
-@click.option('-q', '--quiet', default=False, is_flag=True, help='Suppress status reporting.')
-@click.pass_context
-def cli(ctx, quiet):
- ctx.obj['quiet'] = quiet
-
-
-@cli.command()
-@click.pass_context
-@click.option('-u', '--username', prompt=True)
-@click.option('-p', '--password', prompt=True, hide_input=True, confirmation_prompt=False)
-def login(ctx, username, password):
- click.echo("login {}".format(username))
def main():
- cli(obj={})
-
-
-if __name__ == '__main__':
- main()
+ print("called")
diff --git a/src/python/PyBis/setup.py b/src/python/PyBis/setup.py
index 57008ab0cef..827a006e855 100644
--- a/src/python/PyBis/setup.py
+++ b/src/python/PyBis/setup.py
@@ -18,4 +18,5 @@ setup(name='pybis',
[console_scripts]
pybis=pybis.scripts.cli:main
''',
- zip_safe=False)
+ zip_safe=False
+)
diff --git a/src/python/pybis/tests/conftest.py b/src/python/pybis/tests/conftest.py
new file mode 100644
index 00000000000..e5e7d3b35b3
--- /dev/null
+++ b/src/python/pybis/tests/conftest.py
@@ -0,0 +1,12 @@
+import pytest
+
+from pybis import Openbis
+
+@pytest.yield_fixture(scope="module")
+def openbis_instance():
+ instance = Openbis("http://localhost:20000/openbis/openbis/rmi-application-server-v3.json")
+ print("\nLOGGING IN...")
+ instance.login()
+ yield instance
+ instance.logout()
+ print("LOGGED OUT...")
diff --git a/src/python/pybis/tests/test_imports.py b/src/python/pybis/tests/test_imports.py
new file mode 100644
index 00000000000..174a61ea0ce
--- /dev/null
+++ b/src/python/pybis/tests/test_imports.py
@@ -0,0 +1,4 @@
+
+
+def test_import():
+ from pybis import Openbis
diff --git a/src/python/pybis/tests/test_openbis.py b/src/python/pybis/tests/test_openbis.py
new file mode 100644
index 00000000000..ce5bd9cb802
--- /dev/null
+++ b/src/python/pybis/tests/test_openbis.py
@@ -0,0 +1,25 @@
+import json
+
+def test_token(openbis_instance):
+ assert openbis_instance.token is not None
+
+def test_get_samples_by_id(openbis_instance):
+ response = openbis_instance.get_samples('/TEST/TEST-SAMPLE-2-CHILD-1')
+ assert response is not None
+ assert response['/TEST/TEST-SAMPLE-2-CHILD-1'] is not None
+
+def test_get_samples_by_permid(openbis_instance):
+ response = openbis_instance.get_samples('20130415091923485-402')
+ assert response is not None
+ assert response['20130415091923485-402'] is not None
+
+def test_get_parents(openbis_instance):
+ id = '/TEST/TEST-SAMPLE-2'
+ response = openbis_instance.get_samples(id)
+ assert response is not None
+ #print(json.dumps(response))
+ assert 'parents' in response[id]
+ assert 'identifier' in response[id]['parents'][0]
+ assert response[id]['parents'][0]['identifier']['identifier'] == '/TEST/TEST-SAMPLE-2-PARENT'
+
+ response.parents[0].id
--
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