sbtools get #272
sbtools get #272
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Still working on |
| credList <- readRDS(sbCreds) | ||
| un <- rawToChar(credList$username) | ||
| pw <- rawToChar(credList$password) | ||
| sbtools::authenticate_sb(un, pw) |
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this looks like a good solution already, but is secrets the way of the future? you mentioned that you and JW got it working for you...are you ready to switch over here?
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I don't think it's ready thanks to the windows complications. I'll make an issue for later
| is_logged_in() | ||
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| Each user has a specific ScienceBase id associated with their account. The user ids can be used to inspect what top-level items saved under your account (discussed in next section). To determine your user id, use the function `user_id` in an authenticated session. No arguments are necessary. |
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i know the function is user_id, but it bothers me to call a user's top level item an id. what about home item?
Each user has a home ScienceBase item associated with their account. You can inspect the items and
files attached to your home item (discussed in next section) and even add new items and files
(discussed in next lesson). To determine the ScienceBase ID of your home item, use the function
`user_id` in an authenticated session. No arguments are necessary.
or maybe personal if you don't like home?
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I think home item works, and that really helps clear up some of the initial confusion I had with working on this function. I like it 👍
| user_id() | ||
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| When you're done with your session, you can actively logout using the `session_logout`. No arguments are required. If you do not do this, you will be automatically logged out after a certain amount of time or when you close R. |
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"the session_logout" -> "session_logout" or "the session_logout function"
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| ## Inspect and download items | ||
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| The first inspection step for ScienceBase items is to determine if the item even exists. To do this, use the function `identifier_exists`. The only required argument is `sb_id` which can be either a character string of the item id or an `sbitem`. It will return a logical to indicate if the item exists or not. |
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based on http://www.quickanddirtytips.com/education/grammar/if-versus-whether, i'd recommend "It will return a logical to indicate whether the item exists or not."
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📖 learning so much!
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| ScienceBase items can be described by alternative identifiers, e.g. digital object identifiers, IPDS codes, etc. They are defined on ScienceBase with a scheme, type, and key. For examples of identifiers, see the "Additional Information | Identifiers" section of [Differential Heating](https://www.sciencebase.gov/catalog/item/580587a2e4b0824b2d1c1f23). | ||
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| You can use the function `item_exists` to check whether or not a scheme-type-key tuple already exists. The function has three required arguments - `scheme`, `type`, and `key`. Note that the table of alternative identifiers on ScienceBase is in a different order than this function accepts. On ScienceBase: type, scheme, key. For `item_exists`: scheme, type, key. |
| item_exists(scheme = "State Inventory", type = "UniqueKey", key = "1234") | ||
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| You can create sbitems from just the ScienceBase id. To do this use `as.sbitem`. *why you would use it* |
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i think you could safely leave out as.sbitem entirely and just show item_get here instead. see comment on item_get below.
| ex_id_parent$title | ||
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| Now, let's see if this item has any children by using the `item_list_children` function. Notice that this function says "list" and not "get" as the previous one did. Functions with "list" only return a few fields associated with each item. Functions with "get" are pulling down all available information, including files, associated with an item. |
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i really like that you've attempted a high-level explanation here. that said, i don't think item_get_parent and item_get_fields actually pull down files, do they? maybe only item_get_wfs (if and when we get that one to work).
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Oh hmmm good point. I think I was going for the fact that there is more info. What's your take? Any higher-level difference here worth noting?
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well...hmm...no, i'm not seeing any consistent patterns here...
- item_list_children returns a list of sbitems
- item_list_files returns a data.frame
- item_get_parent returns a single sbitem
- item_get_fields returns a list of info or drops from list to vector
- item_get_wfs returns an sp object, e.g., SpatialPolygonsDataFrame
- item_get returns a single sbitem
you could almost claim that item_get* expects one of each of whatever it's looking for, except that item_get_fields(x, 'identifiers') can return more than one set of identifiers, so...still nope.
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Ok, I'll just leave this out completely.
| xml2::read_xml(ex_id_files$url[1]) | ||
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| You can also inspect specific metadata fields of ScienceBase items. To do this, use the `item_get_fields` function. This function requires a second argument to the item id called `fields` that is a character vector of the fields you want to retrieve. See the [developer documentation for a SB item model](https://my.usgs.gov/confluence/display/sciencebase/ScienceBase+Item+Core+Model) for a list of potential fields. You can also use the argument `drop` to indicate that if only one field is requested, the object returned remains a list (`drop=FALSE`) or becomes a vector (`drop=TRUE`). The default is `drop=TRUE`. |
| If a field is empty, it will return `NULL`. | ||
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| ```{r sbtools-fields-empty} | ||
| # request a nonexistent fields |
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"request a nonexistent fields" -> "request nonexistent fields"
| names(ex_id_item) | ||
| ``` | ||
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| ## Web feature services to visualize spatial data??? |
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yeah...i'll work on this next
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ok, @lindsaycarr, my training-oriented notes are at #276 and i made a new sbtools issue at DOI-USGS/sbtools#244. it won't be super impressive, but I did identify three sb_ids whose WFSes can be retrieved.
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per luke's comments on DOI-USGS/sbtools#244, you could introduce item_get_wfs sorta like this: "the developers thought this could be a cool feature. here's what it might look like. the developers didn't want to invest too much if there wouldn't be demand, but if you'd use it a lot, submit or thumbs-up a GitHub issue"
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@aappling-usgs could you just take a quick look at my stab for content on item_get_wfs. I think that's good enough for now, and we can update later with #276 |
| ## Web feature services to visualize spatial data??? | ||
| ## Web feature services to visualize spatial data | ||
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| This function allows you to pull down web feature services (WFS) data from ScienceBase. Note that this is not the most robust function. The developers thought this could be a cool feature, but didn't want to invest too much time if there wouldn't be demand. If you'd use it a lot, visit the [`sbtools` GitHub page](https://github.com/USGS-R/sbtools/issues) and let the developers know through a new issue or "thumbs-up" an existing, related issue. |
Fixes for #114.