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--- eln-guide-basic-data-dryad [2026/04/06 20:35] – kalbanese
+++ eln-guide-basic-data-dryad [2026/08/12 23:30] (current) – csdunham
@@ Line 11: / Line 11: @@
 The Data Dryad workflow is described in the following sections.
-===== Step 1: API token =====
+===== Step 1: Dryad API Credentials =====
-In order to submit data to Data Dryad, you must first obtain an API token from your Data Dryad account page. Upon activating the API account, you will see the ability to generate an API token at the bottom of the page, as shown in Fig 2. Upon generating a token, it will remain active/usable for 10 hours. After 10 hours, the user will need to get a new token.
+In order to submit data to Data Dryad, you must first obtain API credentials from your Data Dryad account page. Upon activating the API account, you will see two fields: client ID and secret, as shown in Fig 2. Once you have these values, go to the Data Dryad Launchpad in the ELN, where you will be prompted to enter your client ID and secret (Fig 3). These values are subsequently encrypted and stored in the Portal, and are used to generate the API tokens necessary to transmit information to Data Dryad.
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-{{:dryad-token.png?600|}}
+{{:datadryad-user-creds.png?600|}}
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-//Fig 2. Data dryad token generator. Clicking the button to get a new token will provide the user with an API token. This token lasts for 10 hours, after which a new token must be generated.//
+//Fig 2. Data Dryad API account credentials.//
+\\
+\\
+{{:datadryad-cred-request.png?600|}}
+\\
+//Fig 3. ELN Dryad Launchpad Request for Dryad Credentials.//
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 ===== Step 2: Create a Dataset =====
-Data Dryad datasets are created using the form shown in Fig 3. Many of the fields are required by default from Dryad, including: a title, author information, funder information, keywords, field of science, and so on. The first two fields -- Pages Relevant to Dataset and DataDryad API token -- are not part of the standard Data Dryad dataset creation process, but are necessary for the Launchpad. Why?
+Data Dryad datasets are created using the form shown in Fig 4. Many of the fields are required by default from Dryad, including: a title, author information, funder information, keywords, field of science, and so on. The first field, Pages Relevant to Dataset, is not part of the standard Data Dryad dataset creation process, but is necessary for the Launchpad. Why?
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-Well, the first part (Pages Relevant to Dataset) is used to designate which ELN pages are part of the dataset. This process then turns attached ELN files into available files for sending to Data Dryad (discussed further in the next section). The second part (API token) is necessary in order to carry out Data Dryad operations, or at least, it is as of April 6 2026.
+Well, the Pages Relevant to Dataset field is used to designate which ELN pages are part of the dataset. This process then turns attached ELN files into available files for sending to Data Dryad (discussed further in the next section).
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 {{:dryad-create-dataset.png?600|}}
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-//Fig 3. Dryad dataset creation form. Contains all the standard fields you would find on the Data Dryad website, plus two others: relevant page selection and Dryad API token.//
+//Fig 4. Dryad dataset creation form. Contains all the standard fields you would find on the Data Dryad website, plus relevant page selection.//
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-It is worth noting that Data Dryad datasets are account-wide for the first author, i.e., the user who is signed in is able to see all of their created Dryad datasets, which are displayed as cards (Fig 4).
+It is worth noting that Data Dryad datasets are account-wide for the first author, i.e., the user who is signed in is able to see all of their created Dryad datasets, which are displayed as cards (Fig 5).
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 {{:dryad-dataset-card.png?300|}}
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-//Fig 4. Example Data Dryad dataset card.//
+//Fig 5. Example Data Dryad dataset card.//
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-The card provides a direct link to the web-editable Dataset, as well as a View button to make further edits to the dataset in the ELN (Fig 5). It is from this View window that you can update dataset metadata, upload files directly to Dryad (Step 3), generate a README file (Step 4), and lock and export the README to Data Dryad (Step 5).
+The card provides a direct link to the web-editable Dataset, as well as a View button to make further edits to the dataset in the ELN (Fig 6). It is from this View window that you can update dataset metadata, upload files directly to Dryad (Step 3), generate a README file (Step 4), and lock and export the README to Data Dryad (Step 5).
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 {{:dryad-dataset-view.png?600|}}
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-//Fig 5. Landing page when Viewing a Dataset. Shows the dataset editing form, available and uploaded-to-Dryad files, and README editor.//
+//Fig 6. Landing page when Viewing a Dataset. Shows the dataset editing form, available and uploaded-to-Dryad files, and README editor.//
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 ===== Step 3: Sending Files to Dryad =====
-As you link ELN pages to your Dataset, any and all attached files that are available to the ELN page become available to direct upload to Data Dryad. Fig 6 shows this window in more detail. Clicking 'Add to Dryad' expands the file card to display a form with fields for your API token and a file description. Successful submission of this form will move the file from the 'Available for Upload' column to the 'Uploaded to Dryad' column, and the button text will change to 'In Dryad'.
+As you link ELN pages to your Dataset, any and all attached files that are available to the ELN page become available to direct upload to Data Dryad. Fig 7 shows this window in more detail. Clicking 'Add to Dryad' expands the file card to display a form with a field for a file description. Successful submission of this form will move the file from the 'Available for Upload' column to the 'Uploaded to Dryad' column, and the button text will change to 'In Dryad'.
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 {{:dryad-send-files.png?600|}}
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-//Fig 6. Dryad file management window. This window shows two panels, or columns, one for Available for Upload and another for Upload to Dryad.//
+//Fig 7. Dryad file management window. This window shows two panels, or columns, one for Available for Upload and another for Upload to Dryad.//
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 ===== Step 4: README File Editor =====
-All Data Dryad submissions require a README file. Details of the README file can, and should, be viewed at the Data Dryad website. Data Dryad README files are written in the Markdown language, and in order to help you write your READMEs for Dryad, we've produced a rich text-to-Markdown editor (Fig 7) that looks and works exactly like the ELN's text editor you're familiar with, except it outputs Markdown content! It also has had some features removed that are not Markdown-compatible.
+All Data Dryad submissions require a README file. Details of the README file can, and should, be viewed at the Data Dryad website. Data Dryad README files are written in the Markdown language, and in order to help you write your READMEs for Dryad, we've produced a rich text-to-Markdown editor (Fig 8) that looks and works exactly like the ELN's text editor you're familiar with, except it outputs Markdown content! It also has had some features removed that are not Markdown-compatible.
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 {{:dryad-readme-editor.png?600|}}
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-//Fig 7. Rich text-to-Markdown editor. The editor content is always loaded with the default Markdown template provided by Data Dryad to get you started with your README file.//
+//Fig 8. Rich text-to-Markdown editor. The editor content is always loaded with the default Markdown template provided by Data Dryad to get you started with your README file.//
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 ===== Step 5: Lock & Export =====
-Once you've finished sending files to Dryad, editing your Dataset's metadata, and formatting your README file, the time will come to close up shop for this Dataset and lock and export your README file to Data Dryad. This is where the Lock & Export feature is used. Clicking this button reveals a form field for your Dryad API token. Upon providing the token and clicking Confirm Export, another dialog box will pop up to reminder you of the consequences of this action: the editor will become locked, editing the Dataset metadata in the Launchpad utility will be disabled, and files will no longer be available to upload to Dryad from this dataset. In short, it deactivates all mechanisms to send data from the Launchpad Dataset to Dryad. Please make sure this is the action you want and are ready for!
+Once you've finished sending files to Dryad, editing your Dataset's metadata, and formatting your README file, the time will come to close up shop for this Dataset and lock and export your README file to Data Dryad. This is where the Lock & Export feature is used. Clicking this button reveals a form field. Upon clicking Confirm Export, another dialog box will pop up to remind you of the consequences of this action: the editor will become locked, editing the Dataset metadata in the Launchpad utility will be disabled, and files will no longer be available to upload to Dryad from this dataset. In short, it deactivates all mechanisms to send data from the Launchpad Dataset to Dryad. Please make sure this is the action you want and are ready for!
 ====== Launchpad Caveats ======