I am new in rmongodb. I would like to make a query in one collection in MongoDB using the value of a variable. It goes like this:
OBS_ID<-"20150510120000"
QUERY_DATA<-mongo.find.all(MONGO, "prod.CUSTDATA", query='{"Obs_ID" :
OBS_ID}')
This code doesn't work. I can not find any related documentation in rmongodb on how to deal with this.
Looking forward for your answers! Thank you!
I think you should try dbGetQuery as below :
library('RMongo')
dbName <- mongoDbConnect('dbname')
query <- dbGetQuery(dbName,'collectionName',"{'Obs_ID' : '20150510120000'}")
I have already found the solution to this problem. I need to create a mongo.bson.buffer object.
Set up the query
OBS_ID<-"20150510120000"
buf <- mongo.bson.buffer.create()
mongo.bson.buffer.start.object(buf,"Obs_ID")
mongo.bson.buffer.append(buf,"$eq",OBS_ID)
criteria <- mongo.bson.from.buffer(buf)
Query from MongoDB using the criteria
QUERY<-mongo.find.all(MONGO, "prod.CUSTDATA", query=criteria)
Related
I can retrieve EPPO DB info from GET requests.
I am looking for help to retrieve the info from POST requests.
Example code and other info in the linked Rmarkdown HTMP output
As suggested, I have gone trough the https://httr.r-lib.org/ site.
Interesting. I followed the links to https://httr.r-lib.org/articles/api-packages.html and then to https://cdn.zapier.com/storage/learn_ebooks/e06a35cfcf092ec6dd22670383d9fd12.pdf.
I suppose that the arguments for the POST() function should be (more or less) as follows, but yet the response is always 404
url = "https://data.eppo.int/api/rest/1.0/"
config = list(authtoken=my_authtoken)
body = list(intext = "Fraxinus anomala|Tobacco ringspot virus|invalide name|Sequoiadendron giganteum")
encode = "json"
#handle = ???
Created on 2021-04-26 by the reprex package (v0.3.0)
How do I find the missing pieces?
It is a little bit tricky:
You need to use correct url with name of the service from https://data.eppo.int/documentation/rest, e.g. to use Search preferred names from EPPOCodes list:
url = "https://data.eppo.int/api/rest/1.0/tools/codes2prefnames"
Authorization should be passed to body:
body = list(authtoken = "yourtoken", intext = "BEMITA")
So, if you want to check names for two eppocodes: XYLEFA and BEMITA the code should look like:
httr::POST(
url = "https://data.eppo.int/api/rest/1.0/tools/codes2prefnames",
body = list(authtoken = "yourtoken", intext = "BEMITA|XYLEFA")
)
Nonetheless, I would also recommend you to just use the pestr package. However, to find eppocodes it uses SQLite database under the hood instead of EPPO REST API. Since the db is not big itself (circa 40MB) this shouldn't be an issue.
I found the easy way following a suggestion in the DataCamp course:
"To find an R client for an API service search 'CRAN '"
I found the 'pestr' package that gives great access to EPPO database.
I still do not know how to use the POST() function myself. Any hint on that side is warmly welcome.
Here is a solution to loop over names to get EPPO-codes. Whit minor adjustments this also works for distribution and other information in the EPPO DB
# vector of species names
host_name <- c("Fraxinus anomala", "Tobacco ringspot virus", "invalide name",
"Sequoiadendron giganteum")
EPPO_key <- "enter personal key"
# EPPO url
path_eppo_code <- "https://data.eppo.int/api/rest/1.0/tools/names2codes"
# epty list
my_list <- list()
for (i in host_name) {
# POST request on eppo database
response <- httr::POST(path_eppo_code, body=list(authtoken=EPPO_key,
intext=i))
# get EPPO code
pest_eppo_code <- strsplit(httr::content(response)[[1]], ";")[[1]][2]
# add to list
my_list[[i]] <- pest_eppo_code
}
# list to data frame
data <- plyr::ldply(my_list)
I have a JanusGraph database with a graph structure as follows:
(Paper)<-[AuthorOf]-(Author)
I'm want to use Gremlin's match clause to query the data and assign the results to a subgraph. This is what I have so far:
g.V().match(
__.as('a').has('Paper','paperTitle', 'The name of my paper'),
__.as('a').in('AuthorOf').outV().as('b')).
select('b').values()
This query returns what I want, the Authors of the paper I'm for which I'm searching. However, I want to assign the results to a subgraph so I can export it using:
sg.io(IoCore.graphml()).writeGraph("/home/ubuntu/myresults.graphml")
Previously, I've achieved this with a different query structure like this:
sg = g.V().has('paperTitle', 'The name of my paper').
inE('AuthorOf').subgraph('sg1').
outV().
cap('sg1').
next()
Is there away to achieve the same results using the 'match()' statement?
After a little trial and error I was able to create a working solution:
sg = g.V().match(
__.as('a').has('Paper','paperTitle', 'ladle pouring guide'),
__.as('a').inE('AuthorOf').subgraph('sg').outV().as('b')).
cap('sg').next()
At first, I was trying to use the 'select' statement to isolate the subgraph. After reviewing the documentation on 'subgraph' and learning more about side-effects in gremlin I realized it wasn't necessary.
Need a little help with the following R code. I’ve got quite a number of data to load from a Microsoft sql database. I tried to do a few things to make the sql queries manageable.
1) Stored the query as object names with unique prefix
2) Using search to return a vector of the object names with unique prefix
3) using for loop to loop through the vector to load data <- this part didn’t work.
Library(odbc)
Library(tidyverse)
Library(stringer)
#setting up dB connection, odbc pkg
db<- DBI::dbConnect(odbc::odbc(),Driver =‘SQL Server’, Server=‘Server_name’, Database=‘Datbase name’, UID=‘User ID’, trusted_connection=‘yes’)
#defining the sql query
Sql_query1<-“select * from db1”
Sql_query2<-“select top 100 * from db2”
#the following is to store the sql query object name in a vector by searching for object names with prefix sql_
Sql_list <- ls()[str_detect(ls(),regex(“sql_”,ignore_case=TRUE))]
#This is the part where the code didn’t work
For (i in Sql_list){ i <- dbGetQuery(db, i)}
The error I’ve got is “Error: ‘Sql_query1’ nanodb.cpp:1587: 42000: [Microsoft][ODBC SQL Server Driver][SQL Server]Could not find stored procedure ‘Sql_query1’
However, if i don’t use the loop, no error occurred! It may be feasible if I’ve only got 2 -3 queries to manage... unfortunately I’ve 20 of them!
dbGetquery(db,Sql_query1)
Can anyone help? Thank you!
#Rohits solution written down:
first part from your side is fine
#setting up dB connection, odbc pkg
db<- DBI::dbConnect(odbc::odbc(),Driver =‘SQL Server’, Server=‘Server_name’, Database=‘Datbase name’, UID=‘User ID’, trusted_connection=‘yes’)
But then it would be more convenient to do something like this:
A more verbose version:
sqlqry_lst <- vector(mode = 'list', length = 2)#create a list to hold queries the in real life length = 20
names(sqlqry_lst) <- paste0('Sql_query', 1:2)#assign names to your list again jut use 1:20 here in your real life example
#put the SQL code into the list elements
sqlqry_lst['Sql_query1'] <- "select * from db1"
sqlqry_lst['Sql_query2'] <- "select top 100 * from db2"
#if you really want to use for loops
res <- vector(mode = 'list', length(sqlqry_lst))#result list
for (i in length(sqlqry_lst)) res[[i]] <- dbGetquery(db,sqlqry_lst[[i]])
Or as a two liner, a bit more R stylish and imho elegant:
sqlqry_lst <- list(Sql_query1="select * from db1", Sql_query2="select top 100 * from db2")
res <- lapply(sqlqry_lst, FUN = dbGetQuery, conn=db)
I suggest you mix and mingle the verbose eg for creating or more precisely for naming the query list and the short version for running the queries against the database as it suits u best.
This is similar to the question here:
MongoDB password with "#" in it
However, I'm using the R package mongolite to connect so I can't apply that solution. Any recommendations on how to modify it so that it still works for the mongolite package
For example if my username is: user1, and my password is: p#ssword, how would I write:
mongodb://user1:p#ssword#myip
Thank you!
I used this structure and worked for me
newdb <- mongo(collection= "name_collection",
db = "name_db",
url = "mongodb://user:password#your_ip:port_number/name_db",
verbose = TRUE)
I just ran into this problem and solved it by escaping the # in the password by using its corresponding percent-encoding, e.g. use%40 to ecape it. So in your case:
mongodb://user1:p%40ssword#myip
should work.
Edit: I did not see you already had the answer in a comment :) The escape worked in my case so I assume you may have a mistake in either your username or password.
In your p#ssword # character is creating problem so replace it by %40 as suggested by https://stackoverflow.com/users/4455096/rapture
I am using hazelcast3.3.3 for cache.When I use IMap.values(Predicate) querying data,I find a problem.When I use this query,I can find the data.The query is
the data is
but when I use this query,I can't find the data.I can make sure the nextExecuteTime is also meet the conditions.Is it a bug of hazelcast?Do you meet such environment?
It should work both ways. Could you try:
Predicates.and(
Predicates.lessThan("nextExecuteTime", 1463975296703), Predicates.regex("autoIncrementId", ".*[5,6,7,8,9]$")
)