Merge pull request #30 from ncihtan/specific_assay_files

Caution re: Existing Manifests

data_submission/clin_biospec_assay.html

@@ -48,6 +48,7 @@
 <section id="submitting-assay-data-and-metadata" class="level1">
 <h1>Submitting Assay Data and Metadata</h1>
 <p>As stated in <a href="../data_submission/overview.md">Data Submission Overview</a>, data submission involves two key steps: 1. Uploading assay data files to Synapse; and 2. Completing and validating metadata using the Data Curator App (DCA).</p>
+<p>!!! Once assay data files are submitted to Synapse, the files will have entityIDs (e.g.&nbsp;syn12345670) assigned to them. These can then be prepopulated into the manifests on the DCA. For this reason, assay files should be submitted before generating the associated manifests. !!!</p>
 <p>This page provides details regarding those steps.</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
@@ -97,7 +98,8 @@ <h2 class="anchored" data-anchor-id="organize-and-upload-your-dataset-to-the-syn
 </section>
 <section id="validate-and-submit-metadata-using-synapses-data-curator-app-dca." class="level2">
 <h2 class="anchored" data-anchor-id="validate-and-submit-metadata-using-synapses-data-curator-app-dca.">Validate and submit metadata using Synapse’s Data Curator App (DCA).</h2>
-<p>The DCA contains HTAN-specific metadata templates which can be completed on the app or downloaded. Once these are completed by your center, they should then be validated and submitted via the DCA.</p>
+<p>The DCA contains HTAN-specific manifests (metadata templates) which can be 1) completed on the app, or 2) downloaded, completed and uploaded back to the DCA. Manifests for assay data will be pre-populated with assay file entityIDs once they are associated with a particular dataset folder. Once the metadata templates are completed by your center, they should then be validated and submitted via the DCA.</p>
+<p>!!! Please note: If you have added files where a pre-existing manifest exists, <strong>please add to data to the existing manifest on the DCA app or download the existing manifest from the DCA</strong> to make updates. <strong>Do not use a local copy of the manifest at your center</strong>. !!!</p>
 <p>Please see Synapse’s <a href="https://dca-docs.scrollhelp.site/DCA/Working-version/HTAN/validate-and-submit-your-metadata">Data Ingress Docs</a> for more details regarding the web app.</p>
 </section>
 </section>

data_submission/clin_biospec_assay.md

@@ -68,9 +68,16 @@ Data files can be transferred using the Synapse User Interface (Synapse UI) or p
 !!! If you upload files to Synapse programmatically, please use synapseclient version 3.0.0 or higher. 
 !!!
 
-
 ## Validate and submit metadata using Synapse's Data Curator App (DCA).
 
-The DCA contains HTAN-specific metadata templates which can be completed on the app or downloaded.  Once these are completed by your center, they should then be validated and submitted via the DCA.  
+The DCA contains HTAN-specific manifests (metadata templates) which can be 
+
+1. completed on the app, or 
+2. downloaded, completed and uploaded back to the DCA.  
+
+Manifests for assay data will be pre-populated with assay file entityIDs once they are associated with a particular Synapse dataset folder. Once the manifests are completed by your center, they should then be validated and submitted via the DCA. DCA validation checks for a subset of common errors. If any of these errors are found, you can edit the metadata and then revalidate and submit. 
+
+!!!  Please note: If you have added assay files to a Synapse folder where there is a pre-existing manifest or you are adding records to a pre-existing clinical data or biospecimen manifest, **please update the existing manifest on the DCA app or download the existing manifest from the DCA** to make updates. **Do not use a local copy of the manifest at your center to make updates**. Local copies may be out of sync with the data in Synapse. 
+!!!
 
 Please see Synapse's [Data Ingress Docs](https://dca-docs.scrollhelp.site/DCA/Working-version/HTAN/validate-and-submit-your-metadata) for more details regarding the web app.

data_submission/dates.md

@@ -4,7 +4,7 @@ order: 995
 
 # What is the index date?
 
-HTAN cannot accept dates because they are considered Protect Health Information (PHI). In order to obfuscate dates, they should be converted to days from an index date.  For most data case, the index date is the participant's date of birth.  For example, a participant's therapy start date would be recorded as 365 days if the therapy took place 365 days after a participant's date of birth. 
+HTAN cannot accept dates because they are considered Protect Health Information (PHI). In order to obfuscate dates, they should be converted to days from an index date.  For most data, the index date is the participant's date of birth.  For example, a participant's therapy start date would be recorded as 365 days if the therapy took place 365 days after a participant's date of birth. 
 
 !!!
 :warning: If your center has data indexed to enrollment date, the data needs to be converted to days from birth. 
@@ -26,4 +26,4 @@ The 'Diagnosis' manifest includes two attributes which are not indexed:
 - Days to Last Follow up; and
 - Days to Last Known Disease Status.
 
-Please provide these time intervals for these attributes as described in the data model.
+Please provide these time intervals as described in the data model.