Download Datasets - Revision history

Mmaciejewski at 17:06, 10 June 2025

2025-06-10T17:06:19Z

← Older revision		Revision as of 17:06, 10 June 2025
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	~~<span style="display:inline-block; margin-bottom:1em;">[[~~Datasets~~#Actions\|← Back to Dataset Browser --> Actions]]</span>~~		{{Datasets}}

	== Overview ==		== Overview ==

Mmaciejewski: /* Example Layout */

2025-05-28T13:42:09Z

Example Layout

← Older revision		Revision as of 13:42, 28 May 2025
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	├── experiment.csv		├── experiment.csv
	├── identity.xml		├── identity.xml
			├── supplemental_data.csv
	├── supplemental_data/		├── supplemental_data/
	└── post_acquisition/		└── post_acquisition/
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	│ ├── experiment.csv		│ ├── experiment.csv
	│ ├── identity.xml		│ ├── identity.xml
			\| ├── supplemental_data.csv
	\| ├── supplemental_data/		\| ├── supplemental_data/
	\| └── post_acquisition/		\| └── post_acquisition/
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	│ ├── experiment.csv		│ ├── experiment.csv
	│ ├── identity.xml		│ ├── identity.xml
			\| ├── supplemental_data.csv
	\| ├── supplemental_data/		\| ├── supplemental_data/
	\| └── post_acquisition/		\| └── post_acquisition/
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	├── experiment.csv		├── experiment.csv
	├── identity.xml		├── identity.xml
			├── supplemental_data.csv
	├── supplemental_data/		├── supplemental_data/
	└── post_acquisition/		└── post_acquisition/

Apaterson: Typo fix

2025-05-27T20:22:47Z

Typo fix

← Older revision		Revision as of 20:22, 27 May 2025
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	The <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, <code>supplemental_data.csv</code>, and <code>identity.xml</code> files as well as directories for <code>supplemental_data</code> and <code>post_acquisition</code>are placed inside the experiment number (EXPNO) directory alongside the standard TopSpin files.		The <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, <code>supplemental_data.csv</code>, and <code>identity.xml</code> files as well as directories for <code>supplemental_data</code> and <code>post_acquisition</code>are placed inside the experiment number (EXPNO) directory alongside the standard TopSpin files.

	This format is ideal when multiple experiments would need to be opened in TopSpin as the ~~experiment_diretory~~/EXPNO format is strictly preserved with multiple EXPNO directories residing under the experiment_directory.		This format is ideal when multiple experiments would need to be opened in TopSpin as the experiment_directory/EXPNO format is strictly preserved with multiple EXPNO directories residing under the experiment_directory.

	=== Example Layout ===		=== Example Layout ===

Mmaciejewski: /* Organized by Experiment File Layout */

2025-05-27T19:00:47Z

Organized by Experiment File Layout

← Older revision		Revision as of 19:00, 27 May 2025
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	Each dataset resides in the experiment number (EXPNO) subdirectory under the experiment directory. If two datasets have the same experiment directory and experiment number, the older one will have a timestamp suffix to avoid overwriting (e.g., <code>9_20250224000647</code>).		Each dataset resides in the experiment number (EXPNO) subdirectory under the experiment directory. If two datasets have the same experiment directory and experiment number, the older one will have a timestamp suffix to avoid overwriting (e.g., <code>9_20250224000647</code>).

	The <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, and <code>identity.xml</code> files as well as directories for <code>supplemental_data</code> and <code>post_acquisition</code>are placed inside the experiment number (EXPNO) directory alongside the standard TopSpin files.		The <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, <code>supplemental_data.csv</code>, and <code>identity.xml</code> files as well as directories for <code>supplemental_data</code> and <code>post_acquisition</code>are placed inside the experiment number (EXPNO) directory alongside the standard TopSpin files.

	This format is ideal when multiple experiments would need to be opened in TopSpin as the experiment_diretory/EXPNO format is strictly preserved with multiple EXPNO directories residing under the experiment_directory.		This format is ideal when multiple experiments would need to be opened in TopSpin as the experiment_diretory/EXPNO format is strictly preserved with multiple EXPNO directories residing under the experiment_directory.
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	* That folder contains the experiment number as a subfolder (e.g., <code>5</code>, <code>9</code>, <code>10</code>)		* That folder contains the experiment number as a subfolder (e.g., <code>5</code>, <code>9</code>, <code>10</code>)
	* The experiment directory contains the standard TopSpin file layout		* The experiment directory contains the standard TopSpin file layout
	* The dataset-specific <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, and <code>identity.xml</code> files are placed in the top-level timestamped directory		* The dataset-specific <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, <code>supplemental_data.csv</code>, and <code>identity.xml</code> files are placed in the top-level timestamped directory. The supplemental_data and post_acquisition directories are located within the experiment number directory

	=== Example Layout ===		=== Example Layout ===

Mmaciejewski: /* Organized for TopSpin File Layout */

2025-05-27T18:54:11Z

Organized for TopSpin File Layout

← Older revision		Revision as of 18:54, 27 May 2025
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	When '''Organized for TopSpin''' is selected, the download is structured to match the standard Bruker TopSpin format. Datasets are grouped under directories named for the spectrometer used for acquisition (e.g., <code>NMR800-NEO</code>, <code>NMR600-NEO</code>).		When '''Organized for TopSpin''' is selected, the download is structured to match the standard Bruker TopSpin format. Datasets are grouped under directories named for the spectrometer used for acquisition (e.g., <code>NMR800-NEO</code>, <code>NMR600-NEO</code>).

	Each dataset resides in ~~a subdirectory under the dataset name, with an additional level for~~ the experiment number (EXPNO). If two datasets have the same ~~dataset name~~ and experiment number, the older one will have a timestamp suffix to avoid overwriting (e.g., <code>9_20250224000647</code>).		Each dataset resides in the experiment number (EXPNO) subdirectory under the experiment directory. If two datasets have the same experiment directory and experiment number, the older one will have a timestamp suffix to avoid overwriting (e.g., <code>9_20250224000647</code>).

	The <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, and <code>identity.xml</code> files are placed inside the experiment number (EXPNO) directory alongside the standard TopSpin files.		The <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, and <code>identity.xml</code> files as well as directories for <code>supplemental_data</code> and <code>post_acquisition</code>are placed inside the experiment number (EXPNO) directory alongside the standard TopSpin files.

	This format is ideal when multiple experiments would need to be opened in TopSpin as the experiment_diretory/EXPNO format is strictly preserved with multiple EXPNO directories residing under the experiment_directory.		This format is ideal when multiple experiments would need to be opened in TopSpin as the experiment_diretory/EXPNO format is strictly preserved with multiple EXPNO directories residing under the experiment_directory.

Mmaciejewski: /* Overview */

2025-05-27T18:23:48Z

Overview

← Older revision		Revision as of 18:23, 27 May 2025
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	\|fb5323d6-fcae-4328-a908-9f6ff1d8854		\|fb5323d6-fcae-4328-a908-9f6ff1d8854
	\|}		\|}
	''Note that the column names used in this table have been shortened versus the actual experiment.csv file to make viewing the table on the Wiki page easier''		''Note that the column names used in this table have been shortened versus the actual experiment.csv file to make viewing the table on the Wiki page easier and the data is not real.''

	== Dataset Metadata Files added by NAN ==		== Dataset Metadata Files added by NAN ==

Mmaciejewski at 18:22, 27 May 2025

2025-05-27T18:22:42Z

← Older revision		Revision as of 18:22, 27 May 2025
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	<span style="display:inline-block; margin-bottom:1em;">[[Datasets#Actions\|← Back to Actions]]</span>		<span style="display:inline-block; margin-bottom:1em;">[[Datasets#Actions\|← Back to Dataset Browser --> Actions]]</span>

	== Overview ==		== Overview ==

Mmaciejewski at 18:21, 27 May 2025

2025-05-27T18:21:11Z

← Older revision		Revision as of 18:21, 27 May 2025
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			<span style="display:inline-block; margin-bottom:1em;">[[Datasets#Actions\|← Back to Actions]]</span>

	== Overview ==		== Overview ==
	Datasets may be downloaded by selecting the '''Download''' action from the context menu, which is accessed from the context menu by right-clicking on a selected dataset (or set of datasets).		Datasets may be downloaded by selecting the '''Download''' action from the context menu, which is accessed from the context menu by right-clicking on a selected dataset (or set of datasets).

Mmaciejewski: /* Overview */

2025-05-27T18:16:03Z

Overview

← Older revision		Revision as of 18:16, 27 May 2025
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	\|fb5323d6-fcae-4328-a908-9f6ff1d8854		\|fb5323d6-fcae-4328-a908-9f6ff1d8854
	\|}		\|}
			''Note that the column names used in this table have been shortened versus the actual experiment.csv file to make viewing the table on the Wiki page easier''

	== Dataset Metadata Files added by NAN ==		== Dataset Metadata Files added by NAN ==

Mmaciejewski: /* Download */

2025-05-27T18:13:45Z

Download

← Older revision		Revision as of 18:13, 27 May 2025
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	== ~~Download~~ ==		== Overview ==
	Datasets may be downloaded by selecting the '''Download''' action from the context menu, which is accessed from the context menu by right-clicking on a selected dataset (or set of datasets).		Datasets may be downloaded by selecting the '''Download''' action from the context menu, which is accessed from the context menu by right-clicking on a selected dataset (or set of datasets).

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	The selected datasets are packaged into a zip file and downloaded through your browser to the local Downloads folder.		The selected datasets are packaged into a zip file and downloaded through your browser to the local Downloads folder.

	All files are included, including supplemental data ~~and~~ any contents from the post-acquisition directory.		All files are included, including supplemental data, any contents from the post-acquisition directory, and a series of metadata files added by NAN described below.

	An `experiments.csv` file is placed in the root of the zip archive. It lists the downloaded experiments in the following format:		An `experiments.csv` file is placed in the root of the zip archive. It lists the downloaded experiments in the following format:
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	\|}		\|}

	== Dataset Metadata Files ==		== Dataset Metadata Files added by NAN ==
	Each individual dataset directory includes several additional files or directories		Each individual dataset directory includes several additional files or directories
	* <code>provenance.prov</code> – a W3C PROV file describing the complete provenance of the dataset		* <code>provenance.prov</code> – a W3C PROV file describing the complete provenance of the dataset
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	The location of these files / directories differs slightly depending on the organization format.		The location of these files / directories differs slightly depending on the organization format.

	== Organized for TopSpin ==		== Organized for TopSpin File Layout ==
	When '''Organized for TopSpin''' is selected, the download is structured to match the standard Bruker TopSpin format. Datasets are grouped under directories named for the spectrometer used for acquisition (e.g., <code>NMR800-NEO</code>, <code>NMR600-NEO</code>).		When '''Organized for TopSpin''' is selected, the download is structured to match the standard Bruker TopSpin format. Datasets are grouped under directories named for the spectrometer used for acquisition (e.g., <code>NMR800-NEO</code>, <code>NMR600-NEO</code>).

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	experiments.csv</pre>		experiments.csv</pre>

	== Organized by Experiment ==		== Organized by Experiment File Layout ==
	When '''Organized by Experiment''' is selected, the download is structured so that each dataset resides in its own top-level directory named using the format:		When '''Organized by Experiment''' is selected, the download is structured so that each dataset resides in its own top-level directory named using the format: