From 4c21fc8f978716ec6d0fb22ca278f33d5aca6455 Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@unibas.ch>
Date: Fri, 24 Jan 2020 15:29:10 +0100
Subject: [PATCH] Update labkey_api.md
---
scripts/labkey_api.md | 20 +++++++++++++-------
1 file changed, 13 insertions(+), 7 deletions(-)
diff --git a/scripts/labkey_api.md b/scripts/labkey_api.md
index 04e3ec0..5846e03 100644
--- a/scripts/labkey_api.md
+++ b/scripts/labkey_api.md
@@ -1,7 +1,9 @@
-> **NOTE**: Include this info in the main doc in the root directory once available
+> **NOTE**: Include this info in the main doc in the root directory once
+> available; add information on how to get credentials for the LabKey server
+> (i.e., how to obatain a password for the `.netrc` file)
-In order to connect to the LabKey through API, you will first need to create a file `.netrc` in your
-home directory:
+In order to connect to the LabKey through API, you will first need to create a
+file `.netrc` in your home directory:
```bash
touch ${HOME}/.netrc
@@ -15,13 +17,15 @@ login <user-email>
password <user-password>
```
-To secure the file, set permissions in a way that only you can see the content of the file:
+To secure the file, set permissions in a way that only you can see the content
+of the file:
```bash
chmod 400 .netrc
```
-Install the `labkey` and `pandas` packages, ideally from a virtual environment (e.g., `virtualenv` or `conda`):
+Install the `labkey` and `pandas` packages, ideally from a virtual environment
+(e.g., `virtualenv` or `conda`):
```bash
pip install labkey pandas
@@ -39,5 +43,7 @@ Example:
python labkey_api.py TEST_ABOERSCH RNA_Seq_data_template
```
-Right now the script prints a representation of a `pandas` data frame containing the requested LabKey table the the screen.
-For further processing the current script could be included in another script, or it could be modified to write out the data in a desired file format (e.g., TSV).
+Right now the script prints a representation of a `pandas` data frame
+containing the requested LabKey table the the screen. For further processing
+the current script could be included in another script, or it could be modified
+to write out the data in a desired file format (e.g., TSV).
--
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