diff --git a/scripts/README.md b/scripts/README.md new file mode 100644 index 0000000000000000000000000000000000000000..5c32ea2a2ab6a445208fe0d91e0adef91d055b49 --- /dev/null +++ b/scripts/README.md @@ -0,0 +1,23 @@ +This is the description how to connect to the LabKey through API: +1. Create a file named ".netrc" in your home directory. This file must include the following three lines: +machine <remote-instance-of-labkey-server> +login <user-email> +password <user-password> + +E.g.: + +machine labkey.scicore.unibas.ch +login eva.pujadas@unibas.ch +password xxxxx + +To secure the file, set permissions in a way that only you can see the content of the file +$ chmod 400 .netrc + +2. For running the script labkey_api.py libraries "labkey" and "pandas" are required. Either you install them and run the script with the standard python or you use the module "labkey-api-python/1.1.0-foss-2018b-Python-3.6.6" provided by SciCore. Execute the following command: +python labkey_api.py arg1 arg2 +Here, arg1 stands for the project name, arg2 stands for the name of the LabKey table. + +E.g.: +python labkey_api.py TEST_ABOERSCH RNA_Seq_data_template + +The script outputs the complete LabKey table in the form of pandas data frame. diff --git a/scripts/labkey_api.py b/scripts/labkey_api.py index b9f24e80d5f94e42758f6e23ad192acc5a83dc81..759acb4a90bd3ed933eca74dcd32fede71a6ef83 100644 --- a/scripts/labkey_api.py +++ b/scripts/labkey_api.py @@ -14,14 +14,14 @@ import sys from labkey.query import QueryFilter if __name__ == "__main__": - #project_name = "TEST_ABOERSCH" - #query_name = "RNA_Seq_data_template" + # These are values of variables for which the script works + # project_name = "TEST_ABOERSCH" + # query_name = "RNA_Seq_data_template" project_name = sys.argv[1] query_name = sys.argv[2] server_context = labkey.utils.create_server_context('labkey.scicore.unibas.ch', '/Zavolan Group/'+project_name, 'labkey', use_ssl=True) schema_name = "lists" results = labkey.query.select_rows(server_context,schema_name,query_name) - print(results) table_of_data = pd.DataFrame(results["rows"]) print(table_of_data)