Batch processing in cypher Or upload multiple files from Neo4j browser - command-line

I am loading data from csv to Neo4j using the following query:
CREATE CONSTRAINT ON (e:Entity) ASSERT e.entity IS UNIQUE;
USING PERIODIC COMMIT 1000
LOAD CSV WITH HEADERS FROM 'file:/file1.csv' AS line FIELDTERMINATOR '|'
WITH line
MERGE (e0:Entity {entity: line.entities_0_entity})
ON CREATE SET e0.confidence = toFloat(line.entities_0_confidence)
MERGE (e1:Entity {entity: line.entities_1_entity})
ON CREATE SET e1.confidence = toFloat(line.entities_1_confidence)
MERGE (e0)-[r:REL {name: line.relation_relation, confidence: toFloat(line.relation_confidence)}]->(e1)
RETURN *
Could anyone tell the equivalent query to load data from Neo4j command line or a way to change the file name dynamically in browser or pass it like "file:/file*"...??

If you want to process the same Cypher statement multiple times, adjusting one or more values each time, the APOC procedure apoc.periodic.iterate can be used.
In your example, you'd want to perform the CREATE CONSTRAINT statement beforehand (and just once).
For example:
CALL apoc.periodic.iterate(
"
WITH ['file1', 'x', 'y'] AS filenames,
UNWIND filenames AS name
RETURN name;
",
"
USING PERIODIC COMMIT 1000
LOAD CSV WITH HEADERS FROM 'file:/' + {name} + '.csv' AS line FIELDTERMINATOR '|'
WITH line
MERGE (e0:Entity {entity: line.entities_0_entity})
ON CREATE SET e0.confidence = toFloat(line.entities_0_confidence)
MERGE (e1:Entity {entity: line.entities_1_entity})
ON CREATE SET e1.confidence = toFloat(line.entities_1_confidence)
MERGE (e0)-[r:REL {name: line.relation_relation, confidence: toFloat(line.relation_confidence)}]->(e1);
",
{});
This query will execute the LOAD CSV statement 3 times (sequentially, since the parallel option of the procedure is false by default), passing one of the strings ("file1", "y", and "z") each time as the name parameter.

You can simply put all your files in the neo4j's import directory and then use a bash script to load them all :
#!bin/sh
for file in /Users/ikwattro/dev/_graphs/310/import/*
do
curl -H "Content-Type: application/json" \
-d '{"statements": [{"statement": "LOAD CSV WITH HEADERS FROM file:///$file AS row ..."}]' \
http://localhost:7474/db/data/transaction/commit
done
There is no standard way in Neo4j itself to specify multiple files to be imported.

Related

Write Extracted values to csv or text Gatling

I am trying to write extracted values from session to the csv file in a scala gatling script , I am extracting multiple fields and need to write data to multiple columns in csv . Can someone please suggest how to implement this.
You can use session to first save all the required values and later save it to the file via exec call:
exec(
...
.check(regex("data(.*?)\"").findAll.saveAs("userIds")))
)
.exec( session => {
scala.reflect.io.File("data.csv").appendAll(session("userIds").as[Seq[String]].mkString(",")+"\n")
session
})
in example above I assume you get a list of userId and you write it in a single line.
You can check more advanced example for writing headers & rows here

Splayed table upsert leading to error: `cast

I built a data loader prototype that saves CSV into splayed tables. The workflow is as follows:
Create schema the first time e.g. volatilitysurface table:
volatilitysurface::([date:`datetime$(); ccypair:`symbol$()] atm_convention:`symbol$(); premium_included:`boolean$(); smile_type:`symbol$(); vs_type:`symbol$(); delta_ratio:`float$(); delta_setting:`float$(); wing_extrapolation:`float$(); spread_type:`symbol$());
For every file in the rawdata folder import it:
myfiles:#[system;"dir /b /o:gn ",string `$getenv[`KDBRAWDATA],"*.volatilitysurface.csv 2> nul";()];
if[myfiles~();.lg.o[`load;"no volatilitysurface files found!"];:0N];
.lg.o[`load;"loading data files ..."];
/ load each file
{
mypath:"" sv (string `$getenv[`KDBRAWDATA];x);
.lg.o[`load;"loading file name '",mypath,"' ..."];
myfile:hsym`$mypath;
tmp1:select date,ccypair,atm_convention,premium_included,smile_type,vs_type,delta_ratio,delta_setting,wing_extrapolation,spread_type from update date:x, premium_included:?[premium_included = `$"true";1b;0b] from ("ZSSSSSFFFS";enlist ",")0:myfile;
`volatilitysurface upsert tmp1;
} #/: myfiles;
delete tmp1 from `.;
.Q.gc[];
.lg.o[`done;"loading volatilitysurface data done"];
.lg.o[`save;"saving volatilitysurface schema to ",string afolder];
volatilitysurface::0!volatilitysurface;
.Q.dpft[afolder;`;`ccypair;`volatilitysurface];
.lg.o[`cleanup;"removing volatilitysurface from memory"];
delete volatilitysurface from `.;
.Q.gc[];
.lg.o[`done;"saving volatilitysurface schema done"];
This works perfectly. I use .Q.gc[]; frequently to avoid hitting the wsfull. When new CSV files are available I open the existing schema, upsert into it and save it again effectively overwriting the existing HDB file system.
Open schema:
.lg.o[`open;"tables already exists, opening the schema ..."];
#[system;"l ",(string afolder) _ 0;{.lg.e[`open;"failed to load hdb directory: ", x]; 'x}];
/ Re-create table index
volatilitysurface::`date`ccypair xkey select from volatilitysurface;
Re-run step #2 to append new CSV files into the existing volatilitysurfacetable, it upserts the first CSV perfectly but the second CSV fails with:
error: `cast
I debug to the point of the error and to double-check I see that the metadata of tmp1 and volatilitysurface are perfectly the same. Any ideas why this is happening? I get the same issue with any other table. I have tried cleaning the keys from the table after every upsert but doesn't help i.e.
volatilitysurface::0!volatilitysurface;
volatilitysurface::`date`ccypair xkey volatilitysurface;
And the metadata comparison at the point of the cast error:
meta tmp1
c | t f a
------------------| -----
date | z
ccypair | s
atm_convention | s
premium_included | b
smile_type | s
vs_type | s
delta_ratio | f
delta_setting | f
wing_extrapolation| f
spread_type | s
meta volatilitysurface
c | t f a
------------------| -----
date | z
ccypair | s p
atm_convention | s
premium_included | b
smile_type | s
vs_type | s
delta_ratio | f
delta_setting | f
wing_extrapolation| f
spread_type | s
UPDATE Using the input of the answer below I tried using Torq's .loader.loadallfiles function like this (it doesn't fail but nothing happens either, the table is not created in memory and the data is not written to the database):
.loader.loadallfiles[`headers`types`separator`tablename`dbdir`dataprocessfunc!(`x`ccypair`atm_convention`premium_included`smile_type`vs_type`delta_ratio`delta_setting`wing_extrapolation`spread_type;"ZSSSSSFFFS";enlist ",";`volatilitysurface;`:hdb; {[p;t] select date,ccypair,atm_convention,premium_included,smile_type,vs_type,delta_ratio,delta_setting,wing_extrapolation,spread_type from update date:x, premium_included:?[premium_included = `$"true";1b;0b] from t}); `:rawdata]
UDPATE2 This is the output I get from TorQ:
2017.11.20D08:46:12.550618000|wsp18497wn|dataloader|dataloader1|INF|dataloader|**** LOADING :rawdata/20171102_113420.disccurve.csv ****
2017.11.20D08:46:12.550618000|wsp18497wn|dataloader|dataloader1|INF|dataloader|reading in data chunk
2017.11.20D08:46:12.566218000|wsp18497wn|dataloader|dataloader1|INF|dataloader|Read 10000 rows
2017.11.20D08:46:12.566218000|wsp18497wn|dataloader|dataloader1|INF|dataloader|processing data
2017.11.20D08:46:12.566218000|wsp18497wn|dataloader|dataloader1|INF|dataloader|Enumerating
2017.11.20D08:46:12.566218000|wsp18497wn|dataloader|dataloader1|INF|dataloader|writing 4525 rows to :hdb/2017.09.12/volatilitysurface/
2017.11.20D08:46:12.581819000|wsp18497wn|dataloader|dataloader1|INF|dataloader|writing 4744 rows to :hdb/2017.09.13/volatilitysurface/
2017.11.20D08:46:12.659823000|wsp18497wn|dataloader|dataloader1|INF|dataloader|writing 731 rows to :hdb/2017.09.14/volatilitysurface/
2017.11.20D08:46:12.737827000|wsp18497wn|dataloader|dataloader1|INF|init|retrieving sort settings from :C:/Dev/torq//config/sort.csv
2017.11.20D08:46:12.737827000|wsp18497wn|dataloader|dataloader1|INF|sort|sorting the volatilitysurface table
2017.11.20D08:46:12.737827000|wsp18497wn|dataloader|dataloader1|INF|sorttab|No sort parameters have been specified for : volatilitysurface. Using default parameters
2017.11.20D08:46:12.737827000|wsp18497wn|dataloader|dataloader1|INF|sortfunction|sorting :hdb/2017.09.05/volatilitysurface/ by these columns : sym, time
2017.11.20D08:46:12.753428000|wsp18497wn|dataloader|dataloader1|ERR|sortfunction|failed to sort :hdb/2017.09.05/volatilitysurface/ by these columns : sym, time. The error was: hdb/2017.09.
I get the following error sorttab|No sort parameters have been specified for : volatilitysurface. Using default parameters where is this sorttab documented? does it use the table PK by default?
UPDATE3 Ok fixed UPDATE2 out by providing a non-default sort.csv under my config folder:
tabname,att,column,sort
default,p,sym,1
default,,time,1
volatilitysurface,,date,1
volatilitysurface,,ccypair,1
But now I see that if I call the function multiple times on the same files, it simply appends duplicated data instead of upserting it.
UPDATE4 Still not there yet ... assuming I can check to make sure that no duplicate file is used. When I load and then start the database I get some structure back that ressembles some sort of dictionary and not a table.
2017.10.31| (,`volatilitysurface)!,+`date`ccypair`atm_convention`premium_incl..
2017.11.01| (,`volatilitysurface)!,+`date`ccypair`atm_convention`premium_incl..
2017.11.02| (,`volatilitysurface)!,+`date`ccypair`atm_convention`premium_incl..
2017.11.03| (,`volatilitysurface)!,+`date`ccypair`atm_convention`premium_incl..
sym | `AUDNOK`AUDCNH`AUDJPY`AUDHKD`AUDCHF`AUDSGD`AUDCAD`AUDDKK`CADSGD`C..
Note that date is actually datetime Z and not just date. My full and latest version of the function invocation is:
target:hsym `$("" sv ("./";getenv[`KDBHDB];"/volatilitysurface"));
rawdatadir:hsym `$getenv[`KDBRAWDATA];
.loader.loadallfiles[`headers`types`separator`tablename`dbdir`partitioncol`dataprocessfunc!(`x`ccypair`atm_convention`premium_included`smile_type`vs_type`delta_ratio`delta_setting`wing_extrapolation`spread_type;"ZSSSSSFFFS";enlist ",";`volatilitysurface;target;`date;{[p;t] select date,ccypair,atm_convention,premium_included,smile_type,vs_type,delta_ratio,delta_setting,wing_extrapolation,spread_type from update date:x, premium_included:?[premium_included = `$"true";1b;0b] from t}); rawdatadir];
I'm going to add a second answer here to try and tackle the question about using TorQ's data loader.
I'd like to clarify what output you are getting after running this function? There should be some logging messages output, can you post these? For example when I run the function:
jmcmurray#homer ~/deploy/TorQ (master) $ q torq.q -procname loader -proctype loader -debug
<torq startup messages removed>
q).loader.loadallfiles[`headers`types`separator`tablename`dbdir`partitioncol`dataprocessfunc!(c;"TSSFJFFJJBS";enlist",";`quotes;`:testdb;`date;{[p;t] select date:.z.d,time:TIME,sym:INSTRUMENT,BID,ASK from t});`:csvtest]
2017.11.17D15:03:20.312336000|homer.aquaq.co.uk|loader|loader|INF|dataloader|**** LOADING :csvtest/tradesandquotes20140421.csv ****
2017.11.17D15:03:20.319110000|homer.aquaq.co.uk|loader|loader|INF|dataloader|reading in data chunk
2017.11.17D15:03:20.339414000|homer.aquaq.co.uk|loader|loader|INF|dataloader|Read 11000 rows
2017.11.17D15:03:20.339463000|homer.aquaq.co.uk|loader|loader|INF|dataloader|processing data
2017.11.17D15:03:20.339519000|homer.aquaq.co.uk|loader|loader|INF|dataloader|Enumerating
2017.11.17D15:03:20.340061000|homer.aquaq.co.uk|loader|loader|INF|dataloader|writing 11000 rows to :testdb/2017.11.17/quotes/
2017.11.17D15:03:20.341669000|homer.aquaq.co.uk|loader|loader|INF|dataloader|**** LOADING :csvtest/tradesandquotes20140422.csv ****
2017.11.17D15:03:20.349606000|homer.aquaq.co.uk|loader|loader|INF|dataloader|reading in data chunk
2017.11.17D15:03:20.370793000|homer.aquaq.co.uk|loader|loader|INF|dataloader|Read 11000 rows
2017.11.17D15:03:20.370858000|homer.aquaq.co.uk|loader|loader|INF|dataloader|processing data
2017.11.17D15:03:20.370911000|homer.aquaq.co.uk|loader|loader|INF|dataloader|Enumerating
2017.11.17D15:03:20.371441000|homer.aquaq.co.uk|loader|loader|INF|dataloader|writing 11000 rows to :testdb/2017.11.17/quotes/
2017.11.17D15:03:20.460118000|homer.aquaq.co.uk|loader|loader|INF|init|retrieving sort settings from :/home/jmcmurray/deploy/TorQ/config/sort.csv
2017.11.17D15:03:20.466690000|homer.aquaq.co.uk|loader|loader|INF|sort|sorting the quotes table
2017.11.17D15:03:20.466763000|homer.aquaq.co.uk|loader|loader|INF|sorttab|No sort parameters have been specified for : quotes. Using default parameters
2017.11.17D15:03:20.466820000|homer.aquaq.co.uk|loader|loader|INF|sortfunction|sorting :testdb/2017.11.17/quotes/ by these columns : sym, time
2017.11.17D15:03:20.527216000|homer.aquaq.co.uk|loader|loader|INF|applyattr|applying p attr to the sym column in :testdb/2017.11.17/quotes/
2017.11.17D15:03:20.535095000|homer.aquaq.co.uk|loader|loader|INF|sort|finished sorting the quotes table
After all this, I can run \l testdb and there is a table called "quotes" containing my loaded data
If you can post logging messages like these, it could be helpful to see what's going on.
UPDATE
"But now I see that if I call the function multiple times on the same files, it simply appends duplicated data instead of upserting it."
If I'm understanding the problem correctly, it sounds like you likely shouldn't call the function multiple times on the same files. Another process within TorQ could be useful here, the "file alerter". This process will monitor a directory for new & updated files, and can call a function on any that appear (so you can have it call the loader function with every new file automatically). It has a number of options such as moving files after processing (so you can "archive" loaded CSVs)
Note that the file alerter requires that a function take exactly two parameters - the directory & the file name. This effectively means you will need a "wrapper" function around the loader function, which takes a dictionary & a directory. I don't think TorQ includes a function similar to .loader.loadallfiles for a single file, so it might be necessary to copy the target file to a temporary directory, run loadallfiles on that directory and then delete the file from there before loading the next.
`cast error refers to a value not being enumerated
I can't see any enumeration going on here, splayed tables on disk need to have symbol columns enumerated. For example, this can be done with the following line, before calling .Q.dpft
volatilitysurface:.Q.en[afolder;volatilitysurface];
You may like to consider using an example CSV loader for loading your data. One such example is included in TorQ, the KDB framework developed by AquaQ Analytics (as a disclaimer, I work for AquaQ)
The framework is available (free of charge) here: https://github.com/AquaQAnalytics/TorQ
The specific component you will likely be interested in is dataloader.q and is documented here: http://aquaqanalytics.github.io/TorQ/utilities/#dataloaderq
This script will handle everything necessary, loading all files, enumerating, sorting on disk, applying attributes etc. as well as using .Q.fsn to prevent running out of memory

Is there a way to use User Activity Variables to store SQL in Datastage

I am considering using RCP to run a generic datastage job, but the initial SQL changes each time it's called. Is there a process in which I can use a User Activity Variable to inject SQL from a text file or something so I can use the same datastage?
I know this Routine can read a file to look up parameters:
Routine = ‘ReadFile’
vFileName = Arg1
vArray = ”
vCounter = 0
OPENSEQ vFileName to vFileHandle
Else Call DSLogFatal(“Error opening file list: “:vFileName,Routine)
Loop
While READSEQ vLine FROM vFileHandle
vCounter = vCounter + 1
vArray = Fields(vLine,’,’,1)
vArray = Fields(vLine,’,’,2)
vArray = Fields(vLine,’,’,3)
Repeat
CLOSESEQ vFileHandle
Ans = vArray
Return Ans
But does that mean I just store the SQL in one Single line, even if it's long?
Thanks.
Why not just have the SQL within the routine itself and propagate parameters?
I have multiple queries within a single routine that does just that (one for source and one for AfterSQL statement)
This is an example and apologies I'm answering this on my mobile!
InputCol=Trim(pTableName)
If InputCol='Table1' then column='Day'
If InputCol='Table2' then column='Quarter, Day'
SQLCode = ' Select Year, Month, '
SQLCode := column:", Time, "
SQLCode := " to_date(current_timestamp, 'YYYY-MM-DD HH24:MI:SS'), "
SQLCode := \ "This is example text as output" \
SQLCode := "From DATE_TABLE"
crt SQLCode
I've used the multiple encapsulations in the example above, when passing out to a parameter make sure you check the ', " have either been escaped or are displaying correctly
Again, apologies for the quality but I hope it gives you some ideas!
You can give this a try
As you mentioned ,maintain the SQL in a file ( again , if the SQL keeps changing , you need to build a logic to automate populating the new SQL)
In the Datastage Sequencer , use a Execute Command Activity to open the SQL file
eg : cat /home/bk/query.sql
In the job activity which calls your generic job . you should map the command output of your EC activity to a job parameter
so if EC activity name is exec_query , then the job parameter will be
exec_query.$CommandOuput
When you run the sequence , your query will flow from
SQL file --> EC activity-->Parameter in Job activity-->DB stage( query parameterised)
Has you thinked to invoke a shellscript who connect to database and execute the SQL script from the sequential job? You could use sqlplus to connect in the shellscript and read the file with the SQL and use it. To execute the shellscript from the sequential job use a ExecCommand Stage (sh, ./, ...), it depends from the interpreter.
Other way to solve this, depends of the modification degree of your SQL; you could invoke a routine base who handle the parameters and invokes your parallel job.
The principal problem that I think you could have, is the limit of the long of the variable where you could store the parameter.
Tell me what option you choose and I could help you more.

SQLAlchemy, Psycopg2 and Postgresql COPY

It looks like Psycopg has a custom command for executing a COPY:
psycopg2 COPY using cursor.copy_from() freezes with large inputs
Is there a way to access this functionality from with SQLAlchemy?
accepted answer is correct but if you want more than just the EoghanM's comment to go on the following worked for me in COPYing a table out to CSV...
from sqlalchemy import sessionmaker, create_engine
eng = create_engine("postgresql://user:pwd#host:5432/db")
ses = sessionmaker(bind=engine)
dbcopy_f = open('/tmp/some_table_copy.csv','wb')
copy_sql = 'COPY some_table TO STDOUT WITH CSV HEADER'
fake_conn = eng.raw_connection()
fake_cur = fake_conn.cursor()
fake_cur.copy_expert(copy_sql, dbcopy_f)
The sessionmaker isn't necessary but if you're in the habit of creating the engine and the session at the same time to use raw_connection you'll need separate them (unless there is some way to access the engine through the session object that I don't know). The sql string provided to copy_expert is also not the only way to it, there is a basic copy_to function that you can use with subset of the parameters that you could past to a normal COPY TO query. Overall performance of the command seems fast for me, copying out a table of ~20000 rows.
http://initd.org/psycopg/docs/cursor.html#cursor.copy_to
http://docs.sqlalchemy.org/en/latest/core/connections.html#sqlalchemy.engine.Engine.raw_connection
If your engine is configured with a psycopg2 connection string (which is the default, so either "postgresql://..." or "postgresql+psycopg2://..."), you can create a psycopg2 cursor from an SQL Alchemy session using
cursor = session.connection().connection.cursor()
which you can use to execute
cursor.copy_from(...)
The cursor will be active in the same transaction as your session currently is. If a commit or rollback happens, any further use of the cursor with throw a psycopg2.InterfaceError, you would have to create a new one.
You can use:
def to_sql(engine, df, table, if_exists='fail', sep='\t', encoding='utf8'):
# Create Table
df[:0].to_sql(table, engine, if_exists=if_exists)
# Prepare data
output = cStringIO.StringIO()
df.to_csv(output, sep=sep, header=False, encoding=encoding)
output.seek(0)
# Insert data
connection = engine.raw_connection()
cursor = connection.cursor()
cursor.copy_from(output, table, sep=sep, null='')
connection.commit()
cursor.close()
I insert 200000 lines in 5 seconds instead of 4 minutes
It doesn't look like it.
You may have to just use psycopg2 to expose this functionality and forego the ORM capabilities. I guess I don't really see the benefit of ORM in such an operation anyway since it's a straight bulk insert and dealing with individual objects a la an ORM would not really make a whole lot of sense.
If you're starting from SQLAlchemy, you need to first get to the connection engine (also known by the property name bind on some SQLAlchemy objects):
engine = create_engine('postgresql+psycopg2://myuser:password#localhost/mydb')
# or
engine = session.engine
# or any other way you know to get to the engine
From the engine you can isolate a psycopg2 connection:
# get a psycopg2 connection
connection = engine.connect().connection
# get a cursor on that connection
cursor = connection.cursor()
Here are some templates for the COPY statement to use with cursor.copy_expert(), a more complete and flexible option than copy_from() or copy_to() as it is indicated here: https://www.psycopg.org/docs/cursor.html#cursor.copy_expert.
# to dump to a file
dump_to = """
COPY mytable
TO STDOUT
WITH (
FORMAT CSV,
DELIMITER ',',
HEADER
);
"""
# to copy from a file:
copy_from = """
COPY mytable
FROM STDIN
WITH (
FORMAT CSV,
DELIMITER ',',
HEADER
);
"""
Check out what the options above mean and others that may be of interest to your specific situation https://www.postgresql.org/docs/current/static/sql-copy.html.
IMPORTANT NOTE: The link to the documentation of cursor.copy_expert() indicates to use STDOUT to write out to a file and STDIN to copy from a file. But if you look at the syntax on the PostgreSQL manual, you'll notice that you can also specify the file to write to or from directly in the COPY statement. Don't do that, you're likely just wasting your time if you're not running as root (who runs Python as root during development?) Just do what's indicated in the psycopg2's docs and specify STDIN or STDOUT in your statement with cursor.copy_expert(), it should be fine.
# running the copy statement
with open('/path/to/your/data/file.csv') as f:
cursor.copy_expert(copy_from, file=f)
# don't forget to commit the changes.
connection.commit()
You don't need to drop down to psycopg2, use raw_connection nor a cursor.
Just execute the sql as usual, you can even use bind parameters with text():
engine.execute(text('''copy some_table from :csv
delimiter ',' csv'''
).execution_options(autocommit=True),
csv='/tmp/a.csv')
You can drop the execution_options(autocommit=True) if this PR will be accepted

Replacing contents of xml attribute in xml column in DB2

I have an xml document saved in a DB2 Table with XML datatype and I want to update the value of a node. I tried this:
XQUERY replace value of node db2-fn:sqlquery('select my_xml_column from myTable where someId = someValue)/some/xpath/with/#attribute with "foobar"
(and I tried several variants, everything that google hinted that it could do the job).
But unfortunatelly I am just getting error messages. Here:
SQL16002N An XQuery expression has an unexpected token "value" following "replace ". Expected tokens may include: "
What am I doing wrong?
update myTable SET myXmlColumn = XMLQUERY('
transform copy $copy := $original
modify do replace value of $copy/some/xpath/with/#attribute with "FOOBAR"
return $copy
'
PASSING myXmlColumn AS "original"
) WHERE someId = someValue
This works and has the desired effect. It hoped for somebody to come up with a pure XQuery solution, but the problem is solved...