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--- eln-guide-basic-data-dryad [2026/04/06 16:43] – csdunham
+++ eln-guide-basic-data-dryad [2026/04/06 21:51] (current) – [Step 5: Lock & Export] saejinoh
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 //Fig 1. ELN navigation bar. Users can access the Data Dryad Launchpad from the navigation bar.//
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 ====== Dryad Dataset Workflow ======
 The Data Dryad workflow is described in the following sections.
 ===== Step 1: API token =====
-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 years. After 10 hours, the user will need to get a new token.
+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.
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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.//
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+----
 ===== Step 2: Create a Dataset =====
-TBD...
+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?
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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.
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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.//
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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).
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+{{:dryad-dataset-card.png?300|}}
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+//Fig 4. 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).
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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.//
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-===== Step 3: Attach Files =====
+----
-TBD...
-===== Step 4: README File =====
+===== Step 3: Sending Files to Dryad =====
-TBD...
+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'.
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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.//
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+Once a file has been uploaded to Dryad, it cannot be deleted from the Dataset without going directly to Data Dryad to do so. This is due to limitations in the Data Dryad API. A future update will permit file deletion from the LIMS in a manner similar to what exists for deleting a dataset from the LIMS (see the 'Launchpad Caveats' section).
-===== Step 5: Lock & Export =====
+----
-TBD...
+===== 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.
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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.//
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+The Markdown editor here has an autosave feature, and any content entered into the editor is automatically saved every 2 seconds. Successful saves display a timestamp for the last time they were saved. The Markdown editor supports standard Markdown features, such as: header levels, ordered and unordered lists, tables, and basic text formatting. These README files are not intended to hold image-based information, so image and video uploads are disabled.
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+**An important note:** Data Dryad has an expectation, really a requirement, that the README file contain at least a bit of information for every file that you've uploaded as part of your dataset. This information is often expected in the form of //**'[file_name]': description of file contents and how to use it correctly**//. However, Data Dryad's API does not communicate information about README file deficiencies like this, nor does it allow editing of an uploaded README over the API (or, at least, those methods aren't exposed; we will revise this section if that changes). A consequence of this is that we are not able to enforce some of Dryad's README conventions in the ELN's README editor, and so, you will need to reconcile discrepancies via the Data Dryad website (reminder: you can always access the Data Dryad website for your dataset by clicking the 'Link to Dryad' link on the dataset card).
+----
+===== 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 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 ======
-TBD...
+There are a select few operations that cannot be performed in the launchpad (deletion of files from Dryad, submitting a dataset to curation), or which have limitations (deleting a full Dryad dataset). These operations are discussed in more detail in the following sections.
 ===== Deleting Dryad Datasets =====
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 ===== Submitting Dryad Datasets for Peer Review =====
-TBD...
+The final step for any Data Dryad dataset is to submit it for curation/review. Although this step can be activated through their API, and thus could be engaged via the Launchpad, we made the decision to **not allow** this process for the following reason: there are some input fields that are only available through the Data Dryad website and cannot be accessed programmatically, including some important agreement documentation/terms of service acceptance, and some author settings. So, because of these limitations, the ability to submit your dataset to curation will only be available by accessing the Data Dryad site itself. If this becomes a sticking point for users, we may make changes.