Passing na.strings to dbWriteTable - database

I'm trying to run the following command in R in order to read a local tab-delimited file as a SQLite database:
library(RSQLite)
banco <- dbConnect(drv = "SQLite",
dbname = "data.sqlite")
dbWriteTable(conn = banco,
name = "Tarefas",
value = "data.tsv",
sep = "\t",
dec = ",",
na.strings = c("", NA),
row.names = FALSE,
header = TRUE)
However, the statements above yield the following error:
Error in read.table(fn, sep = sep, header = header, skip = skip, nrows
= nrows, : formal argument "na.strings" matched by multiple actual arguments
Which makes me think I'm not being able to pass na.strings explicitly as a read.delim argument. Running dbWriteTable without this argument gives me "RS-DBI driver: (RS_sqlite_import: ./data.tsv line 17696 expected 20 columns of data but found 18)". This is understandable, since I've checked line 17696 and it is almost completely blank.
Another test run using sqldf also gives me an error:
> read.csv2.sql(file = "data.tsv",
+ sql = "CREATE TABLE Tarefas AS SELECT * FROM FILE LIMIT 5",
+ dbname = "data.sqlite",
+ header = TRUE,
+ row.names = FALSE)
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: no such table: FILE)
Which I believe is an unrelated error, but still very confusing for someone who's pretty much an absolute SQL noob such as myself. Runnin read.csv.sql instead gives me this error:
Error in read.table(fn, sep = sep, header = header, skip = skip, nrows = nrows, :
more columns than column names
So is there a way to pass na.strings = c("", NA) at dbWriteTable? Is there a better way to read 10 GB tab-delimited files into R aside from sqldf and RSQLite? I've already tried data.table and ff.

Related

Lua Script error: bad argument #2 'to open' (invalid mode)

I am trying to create a file or read a already existing file but I keep getting the same error: bad argument #2 'to open' (invalid mode)
player_pos = player.pposition()
world_nam = server.worldName()
attribs = player.attributes()
xp = attribs.id(6).value
timesavename = world_nam .. player_pos .. xp
f = io.open(timesavename, ".txt", "r")
if f ~= nil then
io.input(f)
resultstart = f:read("*line")
resultstop = f:read("*line")
f:close()
end
Using , in a function will make it think its another argument, like in the comment you got you should concat the strings with ..

Snowflake Python Connector: Copy Command Status and Error Handling

According to the Snowflake docs, when a user executes a copy command it will return 1 of 3 status values:
loaded
load failed
partially loaded
My question is if I use the Python Snowflake Connector (see example code below) to execute a copy command is an exception raised if the status returned is load failed or partially loaded?
Thank you!
copy_dml = 'copy into database.schema.table ' \
'from #fully_qualified_stage pattern = \'.*'+ table_name +'.*[.]json\' ' \
'file_format = (format_name = fully_qualified_json_format) ' \
'force = true;'
try:
import snowflake.connector
#-------------------------------------------------------------------------------------------------------------------------------
#snowflake variables
snowflake_warehouse = credentials.iloc[0]['snowflake_warehouse']
snowflake_account = credentials.iloc[0]['snowflake_account']
snowflake_role = credentials.iloc[0]['snowflake_role']
snowflake_username = credentials.iloc[0]['Username']
snowflake_password = credentials.iloc[0]['Password']
snowflake_connection = ''
cs = ''#snowflake connection cursor
exec_copy_dml = ''
copy_result_field_metadata = ''
copy_result = ''
snowflake_copy_result_df = ''
#-------------------------------------------------------------------------------------------------------------------------------
# load JSON file(s) into Snowflake
snowflake_connection = snowflake.connector.connect(
user = snowflake_username,
password = snowflake_password,
account = snowflake_account,
warehouse = snowflake_warehouse,
role = snowflake_role)
cs = snowflake_connection.cursor()
exec_copy_dml = cs.execute(copy_dml)
copy_result = exec_copy_dml.fetchall()
copy_result_field_metadata = cs.description
snowflake_copy_result_df = snowflake_results_df(copy_result_field_metadata,copy_result)
except snowflake.connector.errors.ProgrammingError as copy_error:
copy_exception_message = "There was a problem loading JSON files to Snowflake," + \
"a snowflake.connector.errors.ProgrammingError exception was raised."
print(copy_exception_message)
raise
except Exception as error_message:
raise
finally:
snowflake_connection.close()
I believe it won't raise exception for load status, you have to check the load status and take necessary action if required.
After you issue your COPY INTO dml, you can run the following query -
SELECT * FROM TABLE(VALIDATE(TABLE_NAME, job_id => '_last'))
This will give you details on the files that you were trying to load. It will normally return empty, unless you encountered issues upload.
You can save this save results in an object and make necessary control adjustments.

Writing a single column of R object into pre-existing postgres db table

I have a working knowledge of R but I haven't used it in conjunction with databases too much. My question seems very similar to this question:
update table in postgresql database through r
But I can't get that code to work and the doMC package is not available for recent versions of R.
I'm able to connect to the geodatabase, read in data and manipulate it. I can also write an R object into the geodatabase as an entire table. I'm having trouble though, appending an existing geodatabase table with an R object. Unfortunately it's a secure database, so I can't give my connection information out.
-"wearing", "weekday", and "days" are blank columns in a pre-existing table in the geodatabase
-"participant_id", "date_id" and "gps_time" are populated columns in the pre-existing table that I would like to merge on.
-ucsd is the schema name and sage_choi is the existing table name
choifnl <- structure(list(wearing = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("nw",
"w"), class = "factor"), weekday = c("Saturday", "Saturday",
"Saturday", "Saturday", "Saturday", "Saturday"), days = c(1,
1, 1, 1, 1, 1), participant_id = c("0adf37c4-f950-40ad-9370-6bee2f93e935",
"0adf37c4-f950-40ad-9370-6bee2f93e935", "0adf37c4-f950-40ad-9370-6bee2f93e935",
"0adf37c4-f950-40ad-9370-6bee2f93e935", "0adf37c4-f950-40ad-9370-6bee2f93e935",
"0adf37c4-f950-40ad-9370-6bee2f93e935"), date = c("20130202",
"20130202", "20130202", "20130202", "20130202", "20130202"),
time = structure(1:6, .Label = c("00:00:00", "00:01:00",
"00:02:00", "00:03:00", "00:04:00", "00:05:00", "00:06:00",
"00:07:00", "00:08:00", "00:09:00", "00:10:00", "00:11:00",
"00:12:00", "00:13:00", "00:14:00", "00:15:00", "00:16:00",
"00:17:00", "00:18:00", "00:19:00", "00:20:00", "00:21:00",
"00:22:00", "00:23:00", "00:24:00", "00:25:00", "00:26:00",
"00:27:00", "00:28:00", "00:29:00", "00:30:00", "00:31:00",
"00:32:00", "00:33:00", "00:34:00", "00:35:00", "00:36:00",
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"00:57:00", "00:58:00", "00:59:00", "01:00:00", "01:01:00",
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"01:57:00", "01:58:00", "01:59:00", "02:00:00", "02:01:00",
"02:02:00", "02:03:00", "02:04:00", "02:05:00", "02:06:00",
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"02:27:00", "02:28:00", "02:29:00", "02:30:00", "02:31:00",
"02:32:00", "02:33:00", "02:34:00", "02:35:00", "02:36:00",
"02:37:00", "02:38:00", "02:39:00", "02:40:00", "02:41:00",
"02:42:00", "02:43:00", "02:44:00", "02:45:00", "02:46:00",
"02:47:00", "02:48:00", "02:49:00", "02:50:00", "02:51:00",
"02:52:00", "02:53:00", "02:54:00", "02:55:00", "02:56:00",
"02:57:00", "02:58:00", "02:59:00", "03:00:00", "03:01:00",
"03:02:00", "03:03:00", "03:04:00", "03:05:00", "03:06:00",
"03:07:00", "03:08:00", "03:09:00", "03:10:00", "03:11:00",
"03:12:00", "03:13:00", "03:14:00", "03:15:00", "03:16:00",
"03:17:00", "03:18:00", "03:19:00", "03:20:00", "03:21:00",
"03:22:00", "03:23:00", "03:24:00", "03:25:00", "03:26:00",
"03:27:00", "03:28:00", "03:29:00", "03:30:00", "03:31:00",
"03:32:00", "03:33:00", "03:34:00", "03:35:00", "03:36:00",
"03:37:00", "03:38:00", "03:39:00", "03:40:00", "03:41:00",
"03:42:00", "03:43:00", "03:44:00", "03:45:00", "03:46:00",
"03:47:00", "03:48:00", "03:49:00", "03:50:00", "03:51:00",
"03:52:00", "03:53:00", "03:54:00", "03:55:00", "03:56:00",
"03:57:00", "03:58:00", "03:59:00", "04:00:00", "04:01:00",
"04:02:00", "04:03:00", "04:04:00", "04:05:00", "04:06:00",
"04:07:00", "04:08:00", "04:09:00", "04:10:00", "04:11:00",
"04:12:00", "04:13:00", "04:14:00", "04:15:00", "04:16:00",
"04:17:00", "04:18:00", "04:19:00", "04:20:00", "04:21:00",
"04:22:00", "04:23:00", "04:24:00", "04:25:00", "04:26:00",
"04:27:00", "04:28:00", "04:29:00", "04:30:00", "04:31:00",
"04:32:00", "04:33:00", "04:34:00", "04:35:00", "04:36:00",
"04:37:00", "04:38:00", "04:39:00", "04:40:00", "04:41:00",
"04:42:00", "04:43:00", "04:44:00", "04:45:00", "04:46:00",
"04:47:00", "04:48:00", "04:49:00", "04:50:00", "04:51:00",
"04:52:00", "04:53:00", "04:54:00", "04:55:00", "04:56:00",
"04:57:00", "04:58:00", "04:59:00", "05:00:00", "05:01:00",
"05:02:00", "05:03:00", "05:04:00", "05:05:00", "05:06:00",
"05:07:00", "05:08:00", "05:09:00", "05:10:00", "05:11:00",
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"05:22:00", "05:23:00", "05:24:00", "05:25:00", "05:26:00",
"05:27:00", "05:28:00", "05:29:00", "05:30:00", "05:31:00",
"05:32:00", "05:33:00", "05:34:00", "05:35:00", "05:36:00",
"05:37:00", "05:38:00", "05:39:00", "05:40:00", "05:41:00",
"05:42:00", "05:43:00", "05:44:00", "05:45:00", "05:46:00",
"05:47:00", "05:48:00", "05:49:00", "05:50:00", "05:51:00",
"05:52:00", "05:53:00", "05:54:00", "05:55:00", "05:56:00",
"05:57:00", "05:58:00", "05:59:00", "06:00:00", "06:01:00",
"06:02:00", "06:03:00", "06:04:00", "06:05:00", "06:06:00",
"06:07:00", "06:08:00", "06:09:00", "06:10:00", "06:11:00",
"06:12:00", "06:13:00", "06:14:00", "06:15:00", "06:16:00",
"06:17:00", "06:18:00", "06:19:00", "06:20:00", "06:21:00",
"06:22:00", "06:23:00", "06:24:00", "06:25:00", "06:26:00",
"06:27:00", "06:28:00", "06:29:00", "06:30:00", "06:31:00",
"06:32:00", "06:33:00", "06:34:00", "06:35:00", "06:36:00",
"06:37:00", "06:38:00", "06:39:00", "06:40:00", "06:41:00",
"06:42:00", "06:43:00", "06:44:00", "06:45:00", "06:46:00",
"06:47:00", "06:48:00", "06:49:00", "06:50:00", "06:51:00",
"06:52:00", "06:53:00", "06:54:00", "06:55:00", "06:56:00",
"06:57:00", "06:58:00", "06:59:00", "07:00:00", "07:01:00",
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"07:17:00", "07:18:00", "07:19:00", "07:20:00", "07:21:00",
"07:22:00", "07:23:00", "07:24:00", "07:25:00", "07:26:00",
"07:27:00", "07:28:00", "07:29:00", "07:30:00", "07:31:00",
"07:32:00", "07:33:00", "07:34:00", "07:35:00", "07:36:00",
"07:37:00", "07:38:00", "07:39:00", "07:40:00", "07:41:00",
"07:42:00", "07:43:00", "07:44:00", "07:45:00", "07:46:00",
"07:47:00", "07:48:00", "07:49:00", "07:50:00", "07:51:00",
"07:52:00", "07:53:00", "07:54:00", "07:55:00", "07:56:00",
"07:57:00", "07:58:00", "07:59:00", "08:00:00", "08:01:00",
"08:02:00", "08:03:00", "08:04:00", "08:05:00", "08:06:00",
"08:07:00", "08:08:00", "08:09:00", "08:10:00", "08:11:00",
"08:12:00", "08:13:00", "08:14:00", "08:15:00", "08:16:00",
"08:17:00", "08:18:00", "08:19:00", "08:20:00", "08:21:00",
"08:22:00", "08:23:00", "08:24:00", "08:25:00", "08:26:00",
"08:27:00", "08:28:00", "08:29:00", "08:30:00", "08:31:00",
"08:32:00", "08:33:00", "08:34:00", "08:35:00", "08:36:00",
"08:37:00", "08:38:00", "08:39:00", "08:40:00", "08:41:00",
"08:42:00", "08:43:00", "08:44:00", "08:45:00", "08:46:00",
"08:47:00", "08:48:00", "08:49:00", "08:50:00", "08:51:00",
"08:52:00", "08:53:00", "08:54:00", "08:55:00", "08:56:00",
"08:57:00", "08:58:00", "08:59:00", "09:00:00", "09:01:00",
"09:02:00", "09:03:00", "09:04:00", "09:05:00", "09:06:00",
"09:07:00", "09:08:00", "09:09:00", "09:10:00", "09:11:00",
"09:12:00", "09:13:00", "09:14:00", "09:15:00", "09:16:00",
"09:17:00", "09:18:00", "09:19:00", "09:20:00", "09:21:00",
"09:22:00", "09:23:00", "09:24:00", "09:25:00", "09:26:00",
"09:27:00", "09:28:00", "09:29:00", "09:30:00", "09:31:00",
"09:32:00", "09:33:00", "09:34:00", "09:35:00", "09:36:00",
"09:37:00", "09:38:00", "09:39:00", "09:40:00", "09:41:00",
"09:42:00", "09:43:00", "09:44:00", "09:45:00", "09:46:00",
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"10:22:00", "10:23:00", "10:24:00", "10:25:00", "10:26:00",
"10:27:00", "10:28:00", "10:29:00", "10:30:00", "10:31:00",
"10:32:00", "10:33:00", "10:34:00", "10:35:00", "10:36:00",
"10:37:00", "10:38:00", "10:39:00", "10:40:00", "10:41:00",
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"10:57:00", "10:58:00", "10:59:00", "11:00:00", "11:01:00",
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"11:27:00", "11:28:00", "11:29:00", "11:30:00", "11:31:00",
"11:32:00", "11:33:00", "11:34:00", "11:35:00", "11:36:00",
"11:37:00", "11:38:00", "11:39:00", "11:40:00", "11:41:00",
"11:42:00", "11:43:00", "11:44:00", "11:45:00", "11:46:00",
"11:47:00", "11:48:00", "11:49:00", "11:50:00", "11:51:00",
"11:52:00", "11:53:00", "11:54:00", "11:55:00", "11:56:00",
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"12:22:00", "12:23:00", "12:24:00", "12:25:00", "12:26:00",
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"12:32:00", "12:33:00", "12:34:00", "12:35:00", "12:36:00",
"12:37:00", "12:38:00", "12:39:00", "12:40:00", "12:41:00",
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"13:32:00", "13:33:00", "13:34:00", "13:35:00", "13:36:00",
"13:37:00", "13:38:00", "13:39:00", "13:40:00", "13:41:00",
"13:42:00", "13:43:00", "13:44:00", "13:45:00", "13:46:00",
"13:47:00", "13:48:00", "13:49:00", "13:50:00", "13:51:00",
"13:52:00", "13:53:00", "13:54:00", "13:55:00", "13:56:00",
"13:57:00", "13:58:00", "13:59:00", "14:00:00", "14:01:00",
"14:02:00", "14:03:00", "14:04:00", "14:05:00", "14:06:00",
"14:07:00", "14:08:00", "14:09:00", "14:10:00", "14:11:00",
"14:12:00", "14:13:00", "14:14:00", "14:15:00", "14:16:00",
"14:17:00", "14:18:00", "14:19:00", "14:20:00", "14:21:00",
"14:22:00", "14:23:00", "14:24:00", "14:25:00", "14:26:00",
"14:27:00", "14:28:00", "14:29:00", "14:30:00", "14:31:00",
"14:32:00", "14:33:00", "14:34:00", "14:35:00", "14:36:00",
"14:37:00", "14:38:00", "14:39:00", "14:40:00", "14:41:00",
"14:42:00", "14:43:00", "14:44:00", "14:45:00", "14:46:00",
"14:47:00", "14:48:00", "14:49:00", "14:50:00", "14:51:00",
"14:52:00", "14:53:00", "14:54:00", "14:55:00", "14:56:00",
"14:57:00", "14:58:00", "14:59:00", "15:00:00", "15:01:00",
"15:02:00", "15:03:00", "15:04:00", "15:05:00", "15:06:00",
"15:07:00", "15:08:00", "15:09:00", "15:10:00", "15:11:00",
"15:12:00", "15:13:00", "15:14:00", "15:15:00", "15:16:00",
"15:17:00", "15:18:00", "15:19:00", "15:20:00", "15:21:00",
"15:22:00", "15:23:00", "15:24:00", "15:25:00", "15:26:00",
"15:27:00", "15:28:00", "15:29:00", "15:30:00", "15:31:00",
"15:32:00", "15:33:00", "15:34:00", "15:35:00", "15:36:00",
"15:37:00", "15:38:00", "15:39:00", "15:40:00", "15:41:00",
"15:42:00", "15:43:00", "15:44:00", "15:45:00", "15:46:00",
"15:47:00", "15:48:00", "15:49:00", "15:50:00", "15:51:00",
"15:52:00", "15:53:00", "15:54:00", "15:55:00", "15:56:00",
"15:57:00", "15:58:00", "15:59:00", "16:00:00", "16:01:00",
"16:02:00", "16:03:00", "16:04:00", "16:05:00", "16:06:00",
"16:07:00", "16:08:00", "16:09:00", "16:10:00", "16:11:00",
"16:12:00", "16:13:00", "16:14:00", "16:15:00", "16:16:00",
"16:17:00", "16:18:00", "16:19:00", "16:20:00", "16:21:00",
"16:22:00", "16:23:00", "16:24:00", "16:25:00", "16:26:00",
"16:27:00", "16:28:00", "16:29:00", "16:30:00", "16:31:00",
"16:32:00", "16:33:00", "16:34:00", "16:35:00", "16:36:00",
"16:37:00", "16:38:00", "16:39:00", "16:40:00", "16:41:00",
"16:42:00", "16:43:00", "16:44:00", "16:45:00", "16:46:00",
"16:47:00", "16:48:00", "16:49:00", "16:50:00", "16:51:00",
"16:52:00", "16:53:00", "16:54:00", "16:55:00", "16:56:00",
"16:57:00", "16:58:00", "16:59:00", "17:00:00", "17:01:00",
"17:02:00", "17:03:00", "17:04:00", "17:05:00", "17:06:00",
"17:07:00", "17:08:00", "17:09:00", "17:10:00", "17:11:00",
"17:12:00", "17:13:00", "17:14:00", "17:15:00", "17:16:00",
"17:17:00", "17:18:00", "17:19:00", "17:20:00", "17:21:00",
"17:22:00", "17:23:00", "17:24:00", "17:25:00", "17:26:00",
"17:27:00", "17:28:00", "17:29:00", "17:30:00", "17:31:00",
"17:32:00", "17:33:00", "17:34:00", "17:35:00", "17:36:00",
"17:37:00", "17:38:00", "17:39:00", "17:40:00", "17:41:00",
"17:42:00", "17:43:00", "17:44:00", "17:45:00", "17:46:00",
"17:47:00", "17:48:00", "17:49:00", "17:50:00", "17:51:00",
"17:52:00", "17:53:00", "17:54:00", "17:55:00", "17:56:00",
"17:57:00", "17:58:00", "17:59:00", "18:00:00", "18:01:00",
"18:02:00", "18:03:00", "18:04:00", "18:05:00", "18:06:00",
"18:07:00", "18:08:00", "18:09:00", "18:10:00", "18:11:00",
"18:12:00", "18:13:00", "18:14:00", "18:15:00", "18:16:00",
"18:17:00", "18:18:00", "18:19:00", "18:20:00", "18:21:00",
"18:22:00", "18:23:00", "18:24:00", "18:25:00", "18:26:00",
"18:27:00", "18:28:00", "18:29:00", "18:30:00", "18:31:00",
"18:32:00", "18:33:00", "18:34:00", "18:35:00", "18:36:00",
"18:37:00", "18:38:00", "18:39:00", "18:40:00", "18:41:00",
"18:42:00", "18:43:00", "18:44:00", "18:45:00", "18:46:00",
"18:47:00", "18:48:00", "18:49:00", "18:50:00", "18:51:00",
"18:52:00", "18:53:00", "18:54:00", "18:55:00", "18:56:00",
"18:57:00", "18:58:00", "18:59:00", "19:00:00", "19:01:00",
"19:02:00", "19:03:00", "19:04:00", "19:05:00", "19:06:00",
"19:07:00", "19:08:00", "19:09:00", "19:10:00", "19:11:00",
"19:12:00", "19:13:00", "19:14:00", "19:15:00", "19:16:00",
"19:17:00", "19:18:00", "19:19:00", "19:20:00", "19:21:00",
"19:22:00", "19:23:00", "19:24:00", "19:25:00", "19:26:00",
"19:27:00", "19:28:00", "19:29:00", "19:30:00", "19:31:00",
"19:32:00", "19:33:00", "19:34:00", "19:35:00", "19:36:00",
"19:37:00", "19:38:00", "19:39:00", "19:40:00", "19:41:00",
"19:42:00", "19:43:00", "19:44:00", "19:45:00", "19:46:00",
"19:47:00", "19:48:00", "19:49:00", "19:50:00", "19:51:00",
"19:52:00", "19:53:00", "19:54:00", "19:55:00", "19:56:00",
"19:57:00", "19:58:00", "19:59:00", "20:00:00", "20:01:00",
"20:02:00", "20:03:00", "20:04:00", "20:05:00", "20:06:00",
"20:07:00", "20:08:00", "20:09:00", "20:10:00", "20:11:00",
"20:12:00", "20:13:00", "20:14:00", "20:15:00", "20:16:00",
"20:17:00", "20:18:00", "20:19:00", "20:20:00", "20:21:00",
"20:22:00", "20:23:00", "20:24:00", "20:25:00", "20:26:00",
"20:27:00", "20:28:00", "20:29:00", "20:30:00", "20:31:00",
"20:32:00", "20:33:00", "20:34:00", "20:35:00", "20:36:00",
"20:37:00", "20:38:00", "20:39:00", "20:40:00", "20:41:00",
"20:42:00", "20:43:00", "20:44:00", "20:45:00", "20:46:00",
"20:47:00", "20:48:00", "20:49:00", "20:50:00", "20:51:00",
"20:52:00", "20:53:00", "20:54:00", "20:55:00", "20:56:00",
"20:57:00", "20:58:00", "20:59:00", "21:00:00", "21:01:00",
"21:02:00", "21:03:00", "21:04:00", "21:05:00", "21:06:00",
"21:07:00", "21:08:00", "21:09:00", "21:10:00", "21:11:00",
"21:12:00", "21:13:00", "21:14:00", "21:15:00", "21:16:00",
"21:17:00", "21:18:00", "21:19:00", "21:20:00", "21:21:00",
"21:22:00", "21:23:00", "21:24:00", "21:25:00", "21:26:00",
"21:27:00", "21:28:00", "21:29:00", "21:30:00", "21:31:00",
"21:32:00", "21:33:00", "21:34:00", "21:35:00", "21:36:00",
"21:37:00", "21:38:00", "21:39:00", "21:40:00", "21:41:00",
"21:42:00", "21:43:00", "21:44:00", "21:45:00", "21:46:00",
"21:47:00", "21:48:00", "21:49:00", "21:50:00", "21:51:00",
"21:52:00", "21:53:00", "21:54:00", "21:55:00", "21:56:00",
"21:57:00", "21:58:00", "21:59:00", "22:00:00", "22:01:00",
"22:02:00", "22:03:00", "22:04:00", "22:05:00", "22:06:00",
"22:07:00", "22:08:00", "22:09:00", "22:10:00", "22:11:00",
"22:12:00", "22:13:00", "22:14:00", "22:15:00", "22:16:00",
"22:17:00", "22:18:00", "22:19:00", "22:20:00", "22:21:00",
"22:22:00", "22:23:00", "22:24:00", "22:25:00", "22:26:00",
"22:27:00", "22:28:00", "22:29:00", "22:30:00", "22:31:00",
"22:32:00", "22:33:00", "22:34:00", "22:35:00", "22:36:00",
"22:37:00", "22:38:00", "22:39:00", "22:40:00", "22:41:00",
"22:42:00", "22:43:00", "22:44:00", "22:45:00", "22:46:00",
"22:47:00", "22:48:00", "22:49:00", "22:50:00", "22:51:00",
"22:52:00", "22:53:00", "22:54:00", "22:55:00", "22:56:00",
"22:57:00", "22:58:00", "22:59:00", "23:00:00", "23:01:00",
"23:02:00", "23:03:00", "23:04:00", "23:05:00", "23:06:00",
"23:07:00", "23:08:00", "23:09:00", "23:10:00", "23:11:00",
"23:12:00", "23:13:00", "23:14:00", "23:15:00", "23:16:00",
"23:17:00", "23:18:00", "23:19:00", "23:20:00", "23:21:00",
"23:22:00", "23:23:00", "23:24:00", "23:25:00", "23:26:00",
"23:27:00", "23:28:00", "23:29:00", "23:30:00", "23:31:00",
"23:32:00", "23:33:00", "23:34:00", "23:35:00", "23:36:00",
"23:37:00", "23:38:00", "23:39:00", "23:40:00", "23:41:00",
"23:42:00", "23:43:00", "23:44:00", "23:45:00", "23:46:00",
"23:47:00", "23:48:00", "23:49:00", "23:50:00", "23:51:00",
"23:52:00", "23:53:00", "23:54:00", "23:55:00", "23:56:00",
"23:57:00", "23:58:00", "23:59:00"), class = "factor")), .Names = c("wearing",
"weekday", "days", "participant_id", "date", "time"), row.names = c(NA,
6L), class = "data.frame")
update <- function(i) {
drv <- dbDriver("PostgreSQL")
con <- dbConnect(drv, dbname = "", host = "",port <- , user = "", password = "") ##connect w/username and password
txt <- paste("UPDATE ucsd.sage_choi SET wearing=",choifnl$wearing[i],",weekday=",
choifnl$weekday[i],",days=",choifnl$days[i],",where participant_id=",
choifnl$participant_id[i],",AND date_id=", choifnl$date[i],
"AND gps_time=", choifnl$time[i])
dbGetQuery(con, txt)
dbDisconnect(con)
}
library("foreach")
registerDoMC()
foreach(i = 1:length(choifnl$wearing), .inorder=FALSE,.packages="RPostgreSQL")%dopar%{
update(i)
}
####EDIT
This is the final solution (connection info omitted) that works well. I had some issues with encoding and also including the right kinds of quotes (single).
update <- function(con,i) {
txt <- paste("UPDATE ucsd.sage_final_choi SET wearing=", paste("'",choifnl$wearing[i],"'",sep=""),
", weekday=", paste("'",choifnl$weekday[i],"'",sep=""),
", days=", choifnl$days[i],
"WHERE participant_id=",paste("'",choifnl$participant_id[i],"'",sep=""),
"AND date_id=", paste("'",choifnl$date[i],"'",sep=""),
"AND gps_time=", paste("'",choifnl$time[i],"'",sep=""), ";")
dbSendQuery(con, txt) # edit 2
}
drv <- dbDriver("PostgreSQL")
con <- dbConnect(drv, dbname = "", host = "",
port <- 5432, user = "", password = "",options="-c search_path= schemaName") ##connect w/username and password
foreach(i = 1:length(choifnl$wearing), .inorder=FALSE,.packages="RPostgreSQL")%do%{
update(con,i) # passing in the open connection as an argument
}
I'm assuming here you are using the CRAN library RPostgreSQL and that your question is,
"How can I update an existing postgresql record using R?"
If I interpreted your question correctly, I have good news and I'll make minor mods to your existing code to get it working below. Now, the good news:
The error is in your SQL and
You do not need doMC (nor foreach, for that matter).
You're already connected to your database--that's usually the more onerous part!
If you really need parallelism you can see the basic format for initializing multiple workers with doSNOW. Either way, it is much easier to debug a single-threaded application so you should just straight up change your loop to a single-threaded loop by changing the %dopar% argument at the end of your foreach statement to %do% and then register your parallel backend AFTER you get the SQL working.
foreach(i = 1:length(choifnl$wearing),.inorder=FALSE,.packages="RPostgreSQL") %do% {
update(i)
}
Then you might see that your SQL has a syntax error, notably in that "where" and your first "and" erroneously follow commas. I typically break large statements into more human readable form like below so it is easier to spot inconsistencies in form. I removed the inadvertent commas in this snippet below:
### SQL error resolved
update <- function(i) {
drv <- dbDriver("PostgreSQL")
con <- dbConnect(drv, dbname = "", host = "",port <- , user = "", password = "") ##connect w/username and password
txt <- paste("UPDATE ucsd.sage_choi SET wearing=", choifnl$wearing[i],
", weekday=", choifnl$weekday[i],
", days=", choifnl$days[i],
"where participant_id=",choifnl$participant_id[i],
"AND date_id=", choifnl$date[i],
"AND gps_time=", choifnl$time[i])
dbGetQuery(con, txt)
dbDisconnect(con)
}
From a performance standpoint, you are going to do much better if you initialize your connection outside the for loop because you do not need to sink the time and cost to re-establish the connection for each record.
### SQL error resolved, connection made outside loop
update <- function(con,i) {
txt <- paste("UPDATE ucsd.sage_choi SET wearing=", choifnl$wearing[i],
", weekday=", choifnl$weekday[i],
", days=", choifnl$days[i],
"where participant_id=",choifnl$participant_id[i],
"AND date_id=", choifnl$date[i],
"AND gps_time=", choifnl$time[i])
dbSendQuery(con, txt) # edit 2
}
drv <- dbDriver("PostgreSQL")
con <- dbConnect(drv, dbname = "", host = "",port <- , user = "", password = "") ##connect w/username and password
foreach(i = 1:length(choifnl$wearing), .inorder=FALSE,.packages="RPostgreSQL")%dopar%{
update(con,i) # passing in the open connection as an argument
}
dbDisconnect(con)
If I understood the question correctly, this is fairly easy using dplyr's ability to connect to databases
library(dplyr)
library(RPostgreSQL)
my_db <- src_postgres(host="<HOST>",
user="<USER>",
password="<PASS>",
db = "ucsd")
sage_choi <- tbl(my_db,"sage_choi")
sage_choi %>%
select( participant_id, date_id, gps_time) %>%
left_join( choifnl, copy=TRUE, by=c("participant_id"="participant_id",
"date_id"="date",
"gps_time"="time")) %>%
compute(name="sage_choi2", temporary=FALSE)
Once you run the code, table sage_choi2 would contain the populated columns.

ValueError: could not convert string to float: E-3 [duplicate]

This question already has answers here:
Issue querying from Access database: "could not convert string to float: E+6"
(3 answers)
Closed 7 years ago.
I am trying to access some of the columns in a Microsoft Access database table which contains numbers of type double but I am getting the error mentioned in the title.The code used for querying the database is as below, the error is occurring in the line where cur.execute(....) command is executed. Basically I am trying filter out data captured in a particular time interval. If I exclude the columns CM3_Up, CG3_Up, CM3_Down, CG3_Down which contains double data type in the cur.execute(....) command I wont get the error. Same logic was used to access double data type from other tables and it worked fine, I am not sure what is going wrong.
Code:
start =datetime.datetime(2015,03,28,00,00)
a=start
b=start+datetime.timedelta(0,240)
r=7
while a < (start+datetime.timedelta(1)):
params = (a,b)
sql = "SELECT Date_Time, CM3_Up, CG3_Up, CM3_Down, CG3_Down FROM
Lysimeter_Facility_Data_5 WHERE Date_Time >= ? AND Date_Time <= ?"
for row in cur.execute(sql,params):
if row is None:
continue
r = r+1
ws.cell(row = r,column=12).value = row.get('CM3_Up')
ws.cell(row = r,column=13).value = row.get('CG3_Up')
ws.cell(row = r,column=14).value = row.get('CM3_Down')
ws.cell(row = r,column=15).value = row.get('CG3_Down')
a = a+five_min
b = b+five_min
wb.save('..\SE_SW_Lysimeters_Weather_Mass_Experiment-02_03_26_2015.xlsx')
Complete error report:
Traceback (most recent call last):
File "C:\DB_PY\access_mdb\db_to_xl.py", line 318, in <module>
for row in cur.execute(sql,params):
File "build\bdist.win32\egg\pypyodbc.py", line 1920, in next
row = self.fetchone()
File "build\bdist.win32\egg\pypyodbc.py", line 1871, in fetchone
value_list.append(buf_cvt_func(alloc_buffer.value))
ValueError: could not convert string to float: E-3
As to this discussion:
Python: trouble reading number format
the trouble could be that e should be d, like:
float(row.get('CM3_Up').replace('E', 'D'))
Sounds weird to me though, but I know only little of Python.
It sounds like you receive strings like '2.34E-3', so try with a conversion. Don't know Python, but in C# it could be like:
ws.cell(row = r,column=12).value = Convert.ToDouble(row.get('CM3_Up'))
ws.cell(row = r,column=13).value = Convert.ToDouble(row.get('CG3_Up'))
ws.cell(row = r,column=14).value = Convert.ToDouble(row.get('CM3_Down'))
ws.cell(row = r,column=15).value = Convert.ToDouble(row.get('CG3_Down'))

dbWriteTable in RMySQL error in name pasting

i have many data.frames() that i am trying to send to MySQL database via RMySQL().
# Sends data frame to database without a problem
dbWriteTable(con3, name="SPY", value=SPY , append=T)
# stock1 contains a character vector of stock names...
stock1 <- c("SPY.A")
But when I try to loop it:
i= 1
while(i <= length(stock1)){
# converts "SPY.A" into SPY
name <- print(paste0(str_sub(stock1, start = 1, end = -3))[i], quote=F)
# sends data.frame to database
dbWriteTable(con3,paste0(str_sub(stock1, start = 1, end = -3))[i], value=name, append=T)
i <- 1+i
}
The following warning is returned & nothing was sent to database
In addition: Warning message:
In file(fn, open = "r") :
cannot open file './SPY': No such file or directory
However, I believe that the problem is with pasting value onto dbWriteTable() since writing dbWriteTable(con3, "SPY", SPY, append=T) works but dbWriteTable(con3, "SPY", name, append=T) will not...
You are probably using a non-base package for str_sub and I'm guessing you get the same behavior with substr. Does this succeed?
dbWriteTable(con3, substr( stock1, 1,3) , get(stock1), append=T)

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