Connection Objects #1
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| #' @title Return type of PHG connection | ||
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How are phgType and httProtocol different? If phgType is a connection type, does that mean http vs https?
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phgType is something from v1 since I needed to differentiate between local Postgress/Sqlite connections and the BrAPI connections it returns either local or server depending on the object created. httProtocol simply returns if the server has only http or https encryption. I was thinking maybe further down the road to implement something like this with a direct interface to TileDB.
| "SERVER_INFO" = "serverinfo", | ||
| "VARIANT_TABLES" = "variantTables", | ||
| "VARIANTS" = "variants" | ||
| ) |
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Does this list imply that all of these endpoints are supported? What are your allelematrix vs variantTables endpoints? Are these old endpoints from v1? We currently only support sample, serverinfo, variants, and soon variantSets (the latter gives you a link to a multi-sample vcf file)
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This is another copy from v1. I made this because I (1) wanted a simple data structure to point to all possible BrAPI connections since a lot of these are used in other downstream functions. I can probably remove a majority of these at a later date once we finalize v2 endpoints.
| @@ -1,4 +1,4 @@ | |||
| Package: rphg2 | |||
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Since we are going with phg, should this be rphg?
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This will have to be rPHG2 to avoid package collisions with the already existing rPHG.
| exportMethods(phgType) | ||
| exportMethods(port) | ||
| exportMethods(readSamples) | ||
| exportMethods(serverInfo) |
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Yes - export() is for exporting function calls into the R namespace and exportMethods() is for exporting any package defined generics that are not in the base libraries.
| "METHOD_TABLE" = "allelematrix", | ||
| "SAMPLES" = "samples", | ||
| "SERVER_INFO" = "serverinfo", | ||
| "VARIANT_TABLES" = "variantTables", |
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Should variantTables have a capital T?
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This is something that was transferred over from the v1 ktor service. I will keep it in for now until the v2 service matures.
This PR adds the initial class objects, utilities, and unit tests used to set up connections to BrAPI-compliant PHGv2 endpoints for data retrieval.