From 7104eb959cb1e5a9e961bfdefebc5e0909098136 Mon Sep 17 00:00:00 2001
From: Lauri Himanen <lauri.himanen@gmail.com>
Date: Tue, 13 Feb 2024 11:45:23 +0000
Subject: [PATCH] Fixed broken links and typos.
---
examples/data/cow_tutorial/Tutorial.ipynb | 25 +++++++++++------------
1 file changed, 12 insertions(+), 13 deletions(-)
diff --git a/examples/data/cow_tutorial/Tutorial.ipynb b/examples/data/cow_tutorial/Tutorial.ipynb
index 733817c62f..d5f211f365 100644
--- a/examples/data/cow_tutorial/Tutorial.ipynb
+++ b/examples/data/cow_tutorial/Tutorial.ipynb
@@ -48,7 +48,7 @@
},
"outputs": [],
"source": [
- "# This is necessary is some development environments. You can ignore this!\n",
+ "# This is necessary in some development environments. You can ignore this!\n",
"from nomad.config import client\n",
"client.url = client.url.replace('://localhost', '://host.docker.internal')\n",
"# A utility to show structured data in cell outputs.\n",
@@ -87,7 +87,7 @@
"Ideally you are here, because you created the example upload *NOMAD as a Data Management Framework Tutorial* and you started the `Tutorial.ipynb` notebook. *No other preparation is required.*\n",
"\n",
"Alternatively, you can download the [necessary files from gitlab](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/tree/develop/examples/data/cow_tutorial).\n",
- "From the downloaded directory, you can run the `Tutotial.ipynb` using our Jupyterlab docker image:\n",
+ "From the downloaded directory, you can run the `Tutorial.ipynb` using our Jupyterlab docker image:\n",
"\n",
"```\n",
"docker run --rm -p 8888:8888 -v `pwd`:/home/jovyan/work \\\n",
@@ -170,13 +170,13 @@
"\n",
"## Schema\n",
"\n",
- "You might also read [How to write a schema](https://nomad-lab.eu/prod/v1/staging/docs/schemas/basics.html)\n",
+ "You might also read [How to write a schema](https://nomad-lab.eu/prod/v1/staging/docs/howto/customization/basics.html)\n",
"or [Structured data](https://nomad-lab.eu/prod/v1/staging/docs/explanation/data.html) from the NOMAD\n",
"documentation. \n",
"\n",
"With a first impression on the data, we start to design a schema. \n",
"\n",
- "The basic building blocks of schemas are: *sections*, *quantities*, and *sub-sections*. We can define *sections* as Python classes. The NOMAD Python package provides a base class `MSection` to required for all section classes. The property `Quantity` can be used to define *quantities* as attributes:"
+ "The basic building blocks of schemas are: *sections*, *quantities*, and *sub-sections*. We can define *sections* as Python classes. The NOMAD Python package provides a base class `MSection` which is required for all section classes. The property `Quantity` can be used to define *quantities* as attributes:"
]
},
{
@@ -448,7 +448,7 @@
"id": "f21e73fe-054e-4326-9526-97b648f793a1",
"metadata": {},
"source": [
- "This is an extremely simple example, but `normalize` functions can be incredible powerful as they allow to incorporate custom Python code into NOMAD's data processing. This can be used for exmaple to fit your data on the fly, to add derived quantities, or even retrieve data drom external APIs."
+ "This is an extremely simple example, but `normalize` functions can be incredible powerful as they allow to incorporate custom Python code into NOMAD's data processing. This can be used for example to fit your data on the fly, to add derived quantities, or even retrieve data drom external APIs."
]
},
{
@@ -461,10 +461,10 @@
"## Parsing\n",
"\n",
"You might also read [From file to data](https://nomad-lab.eu/prod/v1/staging/docs/explanation/basics.html)\n",
- "or [How to write a parser](https://nomad-lab.eu/prod/v1/staging/docs/develop/parsers.html) from the NOMAD\n",
+ "or [How to write a parser](https://nomad-lab.eu/prod/v1/staging/docs/howto/customization/parsers.html) from the NOMAD\n",
"documentation. \n",
"\n",
- "We don't want to always create schema instances by hand, we want to automatize and write a parser that populates the schema with data from a file as soon as it gets detected by a NOMAD instalation (for example, via drag'n dropping or uploading it via the NOMAD API).\n",
+ "We don't want to always create schema instances by hand, we want to automatize and write a parser that populates the schema with data from a file as soon as it gets detected by a NOMAD installation (for example, via drag'n dropping or uploading it via the NOMAD API).\n",
"\n",
"A parser *reads* the contents from a file and *writes* the data in the NOMAD format based on a schema into an *archive*. The signature for a `parse` function, i.e. within a NOMAD plugin, is this:"
]
@@ -610,7 +610,7 @@
"\n",
"## Plugins\n",
"\n",
- "You might also read [How to develop, publish, and install plugins](https://nomad-lab.eu/prod/v1/staging/docs/plugins/plugins.html)\n",
+ "You might also read [How to develop and publish plugins](https://nomad-lab.eu/prod/v1/staging/docs/howto/customization/plugins_dev.html)\n",
"from the NOMAD documentation. \n",
"\n",
"Above, we showed how to write a simple `parse` function. To add a parser to a NOMAD instalation, i.e. as a plugin, we need to do a little more:\n",
@@ -683,7 +683,7 @@
"tags": []
},
"source": [
- "Once we added the parser as a plugin to the NOMAD configuration, we can use the [parsing programming interface described in the documentation](https://nomad-lab.eu/docs/apis/local_parsers.html#from-a-python-program)."
+ "Once we added the parser as a plugin to the NOMAD configuration, we can use the [parsing programming interface described in the documentation](https://nomad-lab.eu/prod/v1/staging/docs/howto/programmatic/local_parsers.html#from-a-python-program)."
]
},
{
@@ -803,7 +803,7 @@
"\n",
"## Analysis\n",
"\n",
- "You might also read [How to use the API](https://nomad-lab.eu/prod/v1/staging/docs/apis/api.html) or [How to access processed data](https://nomad-lab.eu/prod/v1/staging/docs/apis/archive_query.html).\n",
+ "You might also read [How to use the API](https://nomad-lab.eu/prod/v1/staging/docs/howto/programmatic/api.html) or [How to access processed data](https://nomad-lab.eu/prod/v1/staging/docs/howto/programmatic/archive_query.html).\n",
"from the NOMAD documentation. \n",
"\n",
"<div class=\"alert alert-block alert-warning\">\n",
@@ -955,7 +955,7 @@
"id": "e61f9efa-40fd-4bc6-bd18-eeec346f0100",
"metadata": {},
"source": [
- "We can also put visualizations into the schema, allowing the NOMAD UI to show them. We can either add a schema *annotation* that informs the UI how to do the visualzation, or we can add a Plotly figure to our data and let the UI simply show it."
+ "We can also put visualizations into the schema, allowing the NOMAD UI to show them. We can either add a schema *annotation* that informs the UI how to do the visualization, or we can add a Plotly figure to our data and let the UI simply show it."
]
},
{
@@ -1063,7 +1063,7 @@
"id": "1a9253eb-185b-4c25-b5a8-09c4f7c3aad1",
"metadata": {},
"source": [
- "### Ploting during processing"
+ "### Creating custom plots programmatically"
]
},
{
@@ -1102,7 +1102,6 @@
"\n",
" def normalize(self, archive, logger):\n",
" super(Country, self).normalize(archive, logger)\n",
- " raise\n",
" self.population_density = self.population / self.area\n",
"\n",
" self.figures.append(PlotlyFigure(\n",
--
GitLab