From 1e2d04921a3c0c9d5fbf55eb80546dfc1b60aaee Mon Sep 17 00:00:00 2001
From: "anastasiya.boersch@unibas.ch" <anastasiya.boersch@unibas.ch>
Date: Fri, 24 Jan 2020 14:09:57 +0100
Subject: [PATCH] Update README
---
scripts/README.md | 23 +++++++++++++++++++++++
scripts/labkey_api.py | 6 +++---
2 files changed, 26 insertions(+), 3 deletions(-)
create mode 100644 scripts/README.md
diff --git a/scripts/README.md b/scripts/README.md
new file mode 100644
index 0000000..5c32ea2
--- /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 b9f24e8..759acb4 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)
--
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