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‎CONTRIBUTING.md‎

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# How to contribute
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We would love to get contributions from you! To keep the process manageable we please ask you to follow the workflow
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below. By participating in this project, you agree to abide by the [code of conduct](https://clowder.ncsa.illinois.edu/docs/Clowder-CoC.pdf).
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Before your code can be accepted, you will have to sign a [CLA](https://clowder.ncsa.illinois.edu/docs/Clowder-CLA.pdf)
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below. By participating in this project, you agree to abide by the [code of conduct](https://clowderframework.org/docs/Clowder-CoC.pdf).
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Before your code can be accepted, you will have to sign a [CLA](https://clowderframework.org/docs/Clowder-CLA.pdf)
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and mail it to [email protected].
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Most of the core development happens on [NCSA Bitbucket][bitbucket]. The `master` and `develop` branches are pushed to
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[wiki]: https://opensource.ncsa.illinois.edu/confluence/display/CATS
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[bitbucket]: https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS
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[bamboo]: https://opensource.ncsa.illinois.edu/bamboo/browse/CATS
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[userdocs]: https://clowder.ncsa.illinois.edu/docs/
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[userdocs]: https://clowderframework.org/docs/
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[confluence]: https://opensource.ncsa.illinois.edu/confluence/display/CATS/Home

‎README.md‎

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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1196568.svg)](https://doi.org/10.5281/zenodo.1196568)
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A customizable and scalable data management system you can install in the cloud or on your own hardware.
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More information is available at [https://clowder.ncsa.illinois.edu/](https://clowder.ncsa.illinois.edu/).
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More information is available at [https://clowderframework.org/](https://clowderframework.org/).
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## Installation
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‎app/views/main.scala.html‎

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<li class="dropdown">
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<a href="#" class="dropdown-toggle nav-icon" data-toggle="dropdown" title="Help">Help<b class="caret"></b></a>
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<ul class="dropdown-menu" role="menu">
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<li><a href="https://clowder.ncsa.illinois.edu/" target="_blank">About Clowder</a></li>
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<li><a href="https://clowderframework.org/" target="_blank">About Clowder</a></li>
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<li><a href="@routes.Application.about">About this instance</a></li>
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@if(user.isDefined) {
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<li><a href="@routes.Application.email("")">Contact server admins</a></li>

‎app/views/metadatald/addMetadata.scala.html‎

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@@ -153,7 +153,7 @@ <h5 class="pull-left">Add metadata</h5>
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if (field_value != "") {
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// define contexts
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var contexts = [];
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contexts.push("https://clowder.ncsa.illinois.edu/contexts/metadata.jsonld");
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contexts.push("https://clowderframework.org/contexts/metadata.jsonld");
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var context = {};
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context[field_label] = field_id;
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contexts.push(context);
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if (field_value != "") {
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// define contexts
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var contexts = [];
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contexts.push("https://clowder.ncsa.illinois.edu/contexts/metadata.jsonld");
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contexts.push("https://clowderframework.org/contexts/metadata.jsonld");
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var context = {};
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context[field_label] = field_id;
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contexts.push(context);

‎doc/src/sphinx/api.rst‎

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The RESTful application programming interface is the best way to interact with Clowder programmatically. Much of the web
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frontend and the extractors use this same API to interact with the system. For a full list of available endpoints please
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see the `Swagger documentation <https://clowder.ncsa.illinois.edu/swagger/?url=https://clowder.ncsa.illinois.edu/clowder/swagger>`_.
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see the `Swagger documentation <https://clowderframework.org/swagger/?url=https://clowderframework.org/clowder/swagger>`_.
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Depending on the privacy settings of a specific Clowder instance, a user API key might be required. Users can create
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API keys through the web UI on their profile page (upper right user icon on any page). API Keys can be provided in the
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.. code-block:: bash
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curl -X GET "https://clowder.ncsa.illinois.edu/clowder/api/datasets/5cd47b055e0e57385688f788/metadata.jsonld?key=*yourapikey*"
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curl -X GET "https://clowderframework.org/clowder/api/datasets/5cd47b055e0e57385688f788/metadata.jsonld?key=*yourapikey*"
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Here is an example of requesting the metadata attached to a *file* and providing the API key as the HTTP header *X-API-Key*:
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.. code-block:: bash
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curl -X GET -H "X-API-Key: *yourapikey*" "https://clowder.ncsa.illinois.edu/clowder/api/files/5d07b5fe5e0ec351d75ff064/metadata.jsonld"
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curl -X GET -H "X-API-Key: *yourapikey*" "https://clowderframework.org/clowder/api/files/5d07b5fe5e0ec351d75ff064/metadata.jsonld"

‎doc/src/sphinx/index.rst‎

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.. note::
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* For a high level overview of the project please visit `https://clowder.ncsa.illinois.edu <https://clowder.ncsa.illinois.edu/>`_.
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* For a high level overview of the project please visit `https://clowderframework.org <https://clowderframework.org/>`_.
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* If you have questions for the Clowder you can chat with the developers on
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`Slack <https://join.slack.com/t/clowder-software/shared_invite/enQtMzQzOTg0Nzk3OTUzLTUxYzVhMzZlZDlhMTc0NzNiZTBiNjcyMTEzNjdmMjc5MTA2MTAzMDQwNmUzYTdmNDQyNGMwOWM1Y2YxMzdhNGM>`_

‎doc/src/sphinx/userguide/ug_signingup.rst‎

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The first one is to use a third-party network, like google, crowd, facebook, twitter, linkedin. They are enabled in
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some instances on Clowder, and you can ask your Clowder administrator to enable them if they are not.
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Each Clowder instance manages its own user database, for example: https://clowder.ncsa.illinois.edu/clowder/.
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Each Clowder instance manages its own user database, for example: https://clowderframework.org/clowder/.
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If you want to login using this method, you can click on the Login button in the top-right corner as marked by a blue
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square on Figure 1.
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Signing up through a Local Account
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==================================
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Click on the highlighted link in blue in your Clowder instance (https://clowder.ncsa.illinois.edu/clowder/r)
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Click on the highlighted link in blue in your Clowder instance (https://clowderframework.org/clowder/r)
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.. image:: /_static/ug-signingup-6.png
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:width: 80%

‎public/swagger.yml‎

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{
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"@context":
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[
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"https://clowder.ncsa.illinois.edu/contexts/metadata.jsonld",
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"https://clowderframework.org/contexts/metadata.jsonld",
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{
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"csv_headers": "http://clowder.ncsa.illinois.edu/metadata/ncsa.csvheaders"
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}
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],
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"attached_to":
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{
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"resource_type": "cat:file",
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"url": "https://clowder.ncsa.illinois.edu/clowder/files/5b2a836d5e0e8956ed865b29"
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"url": "https://clowderframework.org/clowder/files/5b2a836d5e0e8956ed865b29"
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},
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"created_at": "Wed Jun 20 11:40:25 CDT 2018",
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"agent":
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{
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"@type": "cat:extractor",
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"name": "https://clowder.ncsa.illinois.edu/clowder/extractors/ncsa.csvheaders/1.0",
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"extractor_id": "https://clowder.ncsa.illinois.edu/clowder/extractors/ncsa.csvheaders/1.0"
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"name": "https://clowderframework.org/clowder/extractors/ncsa.csvheaders/1.0",
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"extractor_id": "https://clowderframework.org/clowder/extractors/ncsa.csvheaders/1.0"
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},
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"content":
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{

‎scripts/jupyter-notebook/collections.ipynb‎

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" 'description': description,\n",
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" 'space': space_id\n",
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" })\n",
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" r = requests.post('https://clowder.ncsa.illinois.edu/clowder/api/collections',\n",
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" r = requests.post('https://clowderframework.org/clowder/api/collections',\n",
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" data=payload,\n",
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" headers=headers,\n",
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" auth=auth)\n",
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"outputs": [],
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"source": [
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"def list_collections():\n",
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" r = requests.get('https://clowder.ncsa.illinois.edu/clowder/api/collections/allCollections', \n",
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" r = requests.get('https://clowderframework.org/clowder/api/collections/allCollections', \n",
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" auth=auth)\n",
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" print(r.status_code)\n",
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" print(r.text)"
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" ''' parameters: collection id; dataset id\n",
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" '''\n",
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" empty_payload = json.dumps({})\n",
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" r = requests.post('https://clowder.ncsa.illinois.edu/clowder/api/collections/'\n",
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" r = requests.post('https://clowderframework.org/clowder/api/collections/'\n",
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" + collection_id +'/datasets/' + dataset_id,\n",
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" data=empty_payload,\n",
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" headers=headers,\n",

‎scripts/jupyter-notebook/dataset_files.ipynb‎

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"outputs": [],
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"source": [
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"def list_datasets():\n",
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" r = requests.get('https://clowder.ncsa.illinois.edu/clowder/api/datasets', \n",
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" r = requests.get('https://clowderframework.org/clowder/api/datasets', \n",
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" auth=auth)\n",
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" print(r.status_code)\n",
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" print(r.text)"
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" 'space':space,\n",
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" 'collection':collection}) \n",
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"\n",
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" r = requests.post('https://clowder.ncsa.illinois.edu/clowder/api/datasets/createempty',\n",
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" r = requests.post('https://clowderframework.org/clowder/api/datasets/createempty',\n",
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" data=payload,\n",
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" headers=headers,\n",
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" auth=auth)\n",
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"\n",
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" payload = json.dumps({'description':description})\n",
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" \n",
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" r = requests.put('https://clowder.ncsa.illinois.edu/clowder/api/datasets/'\n",
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" r = requests.put('https://clowderframework.org/clowder/api/datasets/'\n",
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" + dataset_id +'/description',\n",
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" data=payload,\n",
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" headers=headers,\n",
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"def edit_dataset_name(dataset_id, name):\n",
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"\n",
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" payload = json.dumps({'name': name})\n",
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" r = requests.put('https://clowder.ncsa.illinois.edu/clowder/api/datasets/' + dataset_id +'/title',\n",
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" r = requests.put('https://clowderframework.org/clowder/api/datasets/' + dataset_id +'/title',\n",
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" data=payload,\n",
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" headers=headers,\n",
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" auth=auth)\n",
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"def add_tags_to_dataset(dataset_id, tags):\n",
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" \n",
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" payload = json.dumps({'tags':tags})\n",
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" r = requests.post('https://clowder.ncsa.illinois.edu/clowder/api/datasets/' + dataset_id +'/tags',\n",
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" r = requests.post('https://clowderframework.org/clowder/api/datasets/' + dataset_id +'/tags',\n",
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" data=payload,\n",
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" headers=headers,\n",
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" auth=auth)\n",
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" '''\n",
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" \n",
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" payload = json.dumps(metadata)\n",
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" r = requests.post('https://clowder.ncsa.illinois.edu/clowder/api/datasets/' + dataset_id +'/metadata',\n",
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" r = requests.post('https://clowderframework.org/clowder/api/datasets/' + dataset_id +'/metadata',\n",
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" data=payload,\n",
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" headers=headers,\n",
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" auth=auth)\n",
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"outputs": [],
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"source": [
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"def delete_dtaset(dataset_id):\n",
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" r = requests.delete('https://clowder.ncsa.illinois.edu/clowder/api/datasets/'+ dataset_id,\n",
265+
" r = requests.delete('https://clowderframework.org/clowder/api/datasets/'+ dataset_id,\n",
266266
" auth=auth)\n",
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" print(r.status_code)\n",
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" print(r.text)"
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"source": [
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"def upload_files_to_dataset(dataset_id, url):\n",
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" payload = json.dumps({'url':url})\n",
302-
" r = requests.post('https://clowder.ncsa.illinois.edu/clowder/api/datasets/' + dataset_id + '/urls',\n",
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" r = requests.post('https://clowderframework.org/clowder/api/datasets/' + dataset_id + '/urls',\n",
303303
" data=payload,\n",
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" headers=headers,\n",
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" auth=auth)\n",
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" \n",
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" payload = json.dumps({'tags':tags})\n",
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" headers = {'Content-type': 'application/json', 'accept': 'application/json'}\n",
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" r = requests.post('https://clowder.ncsa.illinois.edu/clowder/api/files/' + file_id +'/tags',\n",
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" r = requests.post('https://clowderframework.org/clowder/api/files/' + file_id +'/tags',\n",
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" data=payload,\n",
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" headers=headers,\n",
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" auth=auth)\n",
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"def add_description_to_file(file_id, description):\n",
371371
"\n",
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" payload = json.dumps({'description':description})\n",
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" r = requests.put('https://clowder.ncsa.illinois.edu/clowder/api/files/' \n",
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" r = requests.put('https://clowderframework.org/clowder/api/files/' \n",
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" + file_id +'/updateDescription',\n",
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" data=payload,\n",
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" headers=headers,\n",
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" \n",
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" payload = json.dumps(metadata)\n",
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" headers = {'Content-type': 'application/json', 'accept': 'application/json'}\n",
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" r = requests.post('https://clowder.ncsa.illinois.edu/clowder/api/files/' + file_id +'/metadata',\n",
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" r = requests.post('https://clowderframework.org/clowder/api/files/' + file_id +'/metadata',\n",
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" data=payload,\n",
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" headers=headers,\n",
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" auth=auth)\n",
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"source": [
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"def delete_file(file_id):\n",
445445
" \n",
446-
" r = requests.delete('https://clowder.ncsa.illinois.edu/clowder/api/files/'+ file_id, auth=auth)\n",
446+
" r = requests.delete('https://clowderframework.org/clowder/api/files/'+ file_id, auth=auth)\n",
447447
" print(r.status_code)\n",
448448
" print(r.text)"
449449
]

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