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You may want to establish a SSH tunnel between your local workstation and the replica through the bastion. This is a common usage pattern, see your SSH client of choice documentation for instructions on how to configure this, see your SSH client of choice documentation for instructions on how to configure this.
Note that in typical usage with a SSH tunnel from a user's workstation to the bastion, the tunnel would use port forwarding. The SQL tool used on the user's desktop would actually connect using this local tunnel.
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The above approach is appropriate if only one or two trusted users will access the bastion. It is secure as long as the private keys are secured. Customers with more users will want to find more scalable ways to access the replica data. One could be a SSH persistent tunnel on the customer site, and used by other users at the site. AWS has a variety of options for this. See AWS VPNs and Direct Connect, which are two mechanisms to securely connect your sites to your own AWS account. From there a variety of options exist, including AWS PrivateLink to create secure connections between AWS accounts. It is the customer's responsibility to select and configure any options such as the above. Foundry Health will assist by suggesting approaches and making required configurations on our end. But the majority of the setup is in customer-owned infrastructure, and for this the customer is solely responsible. |
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An activity plan is a schedule of events for a given cohort. Activity Plans do not appear in CDSIC. In ODM, there is the notion of a FormRef. However, this design doesn't fit well with ph1 trials where forms are commonly repeated for a given study event (ie many PKs in a given day). As such, FormRef is implicitly available by way Scheduled Activities that are a part of a Segment / Activity Plan.
| Table | From CDISC? | Notes | |
|---|---|---|---|
| 1 | Study | Yes | This element collects static structural information about an individual study. A study is related to a given clinical trial protocol. |
| 2 | Activity Plan | No | A schedule of events for a given cohort. Plans can be assigned to multiple cohorts. A timed plan must have a reference time in order to properly provide UI feedback as segments and scheduled activities are set. Untimed Activity Plan:
Activity Plan fills the role of the FormRef in the ODM. |
| 3 | Segment | Partially | Holds a group of scheduled activities in an activity plan. The segment's offset seconds is essentially the time of the reference event, all scheduled activities are relative to this. Modeled somewhat of off CDISC SDM: "Segments are often seen as the basic building blocks of study design. A segment usually specifies a combination of planned observations and interventions, which may or may not involve treatment, during a period of time." |
| 4 | Scheduled Activity | No | Wraps a form, but adds metadata including timing. |
| 5 | Form | Yes | A form is basically a container for item groups. |
| 6 | Study Event | Yes | A study event represents a given 'visit'. In phase 1 trials this will commonly simply refer to a 'day'. When scheduling forms for a given schedule, the builder must associate the study event. Note: there are common study events that are typically reserved for special events: unscheduled, common (AE, CM), etc |
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| Data Definition Element | Data Capture Element | Notes |
|---|---|---|
| Item (ItemDef in CDISC) | ItemData | Represent the definition of a piece of data collected |
| ItemGroup (ItemGroupDef in CDISC) | ItemGroupData | Aggregates item data |
| Form (FormDef in CDISC) | FormData | Basically a container for item groups |
| StudyEvent (StudyEventDef in CDISC) | StudyEventData | Clinical data for a study event (visit) for a given subject |
With this in mind, below is a view of how these elements relate to each other.
this in mind, below is a view of how these elements relate to each other.
Note that form_data can have linkage to forms through scheduled activities or unscheduled.
ItemGroupData has an item_group_repeat_key which is used to track repeats.
| Table | From CDISC? | Notes | |
|---|---|---|---|
| 1 | form | Yes | Basically a container for item groups. |
| 2 | form_data | Yes | Form data represents data collected for a given subject. Instead of storing the scheduled time on this domain, we leverage the relationship to the encapsulated scheduledActivity domain and thus its relationship to the segment. We purposely don't set formRepeatKey in the domain. It is calculated later on when building ODM. |
| 3 | item_group | Yes | A collection of related items in a given form |
| 4 | item_group_ref | Yes | A given item group within a form definition. |
| 5 | item_group_data | Yes | Aggregates item data |
| 6 | item | Yes | Represents the definition of a piece of data collected. |
| 7 | item_ref | Yes | A given item within an item group definition. |
| 8 | item_data | Yes | A piece of collected data |
| 9 | study_event | Yes | A study event represents a given 'visit'. In phase 1 trials this will commonly simply refer to a 'day'. When scheduling forms for a given schedule, the builder must associate the study event. Note: there are common study events that are typically reserved for special events: unscheduled, common (AE, CM), etc |
| 10 | study_event_data | Yes | Clinical data for a study event (visit) for a given subject |
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As shown above, it is easy to connect to Read Replica data using Tableau using a SSH tunnel to a local workstation or gateway. The standard Tableau Desktop connection wizard will guide you through the steps to connect from there. Please contact a Tableau representative for more details. They provide consulting services and training.
Here is a presentation on using Tableau with the Read Replica from the 2017 ClinSpark User Group conference.
Tibco Spotfire
Tibco Spotfire can access the Read Replica in the same manner as Tableau.
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Crystal Reports or other similar products all can operate on MySQL databases. As such they can connect to and use the Read Replica. It is possible to create customer-specific reports using these tools.
SQL Examples
TODO: This part isn't started yet
Pick a few reports and show how SQL can produce similar results
Lab Data example
Item Data example