From 5f8e6b50e4a6b532820a76b0897f180998cb2ee5 Mon Sep 17 00:00:00 2001 From: Marc van Dijk Date: Thu, 14 Jun 2018 08:38:08 +0200 Subject: [PATCH] Move microservice WAMP test from MDStudio/tests to package --- tests/wamp_test/files/structure.mol2 | 50 ++++++++++++++++++++++ tests/wamp_test/settings.dev.yml | 5 +++ tests/wamp_test/test_lie_atb.py | 62 ++++++++++++++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 tests/wamp_test/files/structure.mol2 create mode 100644 tests/wamp_test/settings.dev.yml create mode 100644 tests/wamp_test/test_lie_atb.py diff --git a/tests/wamp_test/files/structure.mol2 b/tests/wamp_test/files/structure.mol2 new file mode 100644 index 0000000..3b5a5df --- /dev/null +++ b/tests/wamp_test/files/structure.mol2 @@ -0,0 +1,50 @@ +@MOLECULE +ligand + 21 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 O -0.5471 -1.0180 0.3433 O.3 1 LIG11 -0.4613 + 2 C 0.8785 -1.0224 0.2270 C.3 1 LIG11 0.1036 + 3 H 1.2914 -1.5214 1.1112 H 1 LIG11 0.0734 + 4 C 1.2911 0.4358 0.2226 C.3 1 LIG11 -0.0056 + 5 C 0.0674 1.1651 -0.2725 C.3 1 LIG11 0.0483 + 6 C -1.0428 0.2213 0.0666 C.2 1 LIG11 0.3075 + 7 O -2.2294 0.5000 0.0615 O.2 1 LIG11 -0.2508 + 8 C 1.3167 -1.7790 -1.0313 C.3 1 LIG11 -0.0159 + 9 C 0.8755 -3.2458 -0.9950 C.3 1 LIG11 -0.0526 + 10 C 1.5208 -4.0539 -2.1102 C.3 1 LIG11 -0.0652 + 11 H 2.1837 0.6440 -0.3752 H 1 LIG11 0.0306 + 12 H 1.5085 0.7543 1.2497 H 1 LIG11 0.0306 + 13 H 0.0921 1.3157 -1.3549 H 1 LIG11 0.0379 + 14 H -0.0623 2.1187 0.2457 H 1 LIG11 0.0379 + 15 H 2.4088 -1.7257 -1.1182 H 1 LIG11 0.0301 + 16 H 0.8915 -1.3085 -1.9265 H 1 LIG11 0.0301 + 17 H -0.2148 -3.3087 -1.0892 H 1 LIG11 0.0264 + 18 H 1.1445 -3.6961 -0.0325 H 1 LIG11 0.0264 + 19 H 1.2769 -3.6384 -3.0927 H 1 LIG11 0.0230 + 20 H 1.1684 -5.0899 -2.0799 H 1 LIG11 0.0230 + 21 H 2.6104 -4.0662 -2.0021 H 1 LIG11 0.0230 +@BOND + 1 1 2 1 + 2 2 3 1 + 3 2 4 1 + 4 4 5 1 + 5 5 6 1 + 6 1 6 1 + 7 6 7 2 + 8 2 8 1 + 9 8 9 1 + 10 9 10 1 + 11 4 11 1 + 12 4 12 1 + 13 5 13 1 + 14 5 14 1 + 15 8 15 1 + 16 8 16 1 + 17 9 17 1 + 18 9 18 1 + 19 10 19 1 + 20 10 20 1 + 21 10 21 1 diff --git a/tests/wamp_test/settings.dev.yml b/tests/wamp_test/settings.dev.yml new file mode 100644 index 0000000..02c4108 --- /dev/null +++ b/tests/wamp_test/settings.dev.yml @@ -0,0 +1,5 @@ +session: + username: mdadmin + password: this_should_be_replaced_for_production!@#$%^&*()_+1234567890-= +settings: + printInEndpoint: false \ No newline at end of file diff --git a/tests/wamp_test/test_lie_atb.py b/tests/wamp_test/test_lie_atb.py new file mode 100644 index 0000000..560c1c6 --- /dev/null +++ b/tests/wamp_test/test_lie_atb.py @@ -0,0 +1,62 @@ +from mdstudio.deferred.chainable import chainable +from mdstudio.component.session import ComponentSession +from mdstudio.runner import main +from os.path import join +import os +import shutil + +file_path = os.path.realpath(__file__) +root = os.path.split(file_path)[0] + + +def create_workdir(name, path="/tmp/mdstudio/lie_atb"): + """Create temporal workdir dir""" + workdir = join(path, name) + if not os.path.isdir(workdir): + os.makedirs(workdir) + return workdir + + +def copy_to_workdir(file_path, workdir): + shutil.copy(file_path, workdir) + base = os.path.basename(file_path) + return join(workdir, base) + + +workdir = create_workdir("lie_atb") +path_mol = copy_to_workdir( + join(root, "files/structure.mol2"), workdir) + +dict_query = { + "netcharge": 0, + "dim": 3, + "exactmass": 128.083729624, + "title": "ligand", + "PartialCharges": "GASTEIGER", + "energy": 0.0, + "molwt": 128.16898000000003, + "structure_format": "mol2", + "mol": path_mol, + "formula": "C7H12O2", + "isfile": True, + "workdir": workdir +} + + +class Run_atb(ComponentSession): + + def authorize_request(self, uri, claims): + return True + + @chainable + def on_run(self): + with self.group_context('mdgroup'): + + result_collect = yield self.call( + "mdgroup.lie_atb.endpoint.structure_query", + dict_query) + print(result_collect) + + +if __name__ == "__main__": + main(Run_atb)