processing time
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Joseph Montibello
Feb 2, 2021, 10:11:34 AM2/2/21
to OpenRefine
Hi,
I'm using openrefine to clean up some data. It's about 1.7 million rows, and maybe 20ish columns. Because doing operations against that whole dataset was going pretty slowly, I created a smaller set with only 10 lines of data in it, so I could figure out all the transforms I wanted to do.
Once I got the transforms set up the way I wanted, I extracted them from the smaller set, opened the bigger set, and applied the transforms to the bigger set. That was maybe an hour and a half ago, and it still says "Working..."
Is there any way to know if/when it will complete the transforms? I'm on a Mac, using OpenRefine 3.1. I already ensured that I was using Java 8 and I allocated 10 gigs of memory to OpenRefine.
I don't have a lot of experience with OpenRefine, so any thoughts you might have would be appreciated. Take care,
Joe Montibello
Joseph Montibello
Feb 2, 2021, 10:14:17 AM2/2/21
to OpenRefine
I forgot to mention that I put together a gist with the sample data and the transforms I'm doing:
https://gist.github.com/joemontibello/0b4f5f456da7cdc56651acf03af11fc5
Joe M.
https://gist.github.com/joemontibello/0b4f5f456da7cdc56651acf03af11fc5
Joe M.
Felix Lohmeier
Feb 2, 2021, 10:50:50 AM2/2/21
to OpenRefine
Hi Joe,
I would suggest to test with a larger sample (e.g. 100,000 rows) and apply the transformation steps one by one to find out which of the transformations takes so much time. To do this, you can disassemble the JSON and copy & paste with apply. The first step from the gist would be:
{
"op": "core/text-transform",
"description": "Text transform on cells in column TRANSACTION_GMT using expression grel:substring(cells['TRANSACTION_GMT'].value, 0, 10)",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "TRANSACTION_GMT",
"expression": "grel:substring(cells['TRANSACTION_GMT'].value, 0, 10)",
"onError": "keep-original",
"repeat": false,
"repeatCount": 10 }
Transformations where many new rows or columns are created (e.g. split) can take especially long. If the allocated memory is almost exhausted, then the JAVA garbage collector also takes a lot of time. It is best to observe the RAM consumption of the Java process during the transformations.
"op": "core/text-transform",
"description": "Text transform on cells in column TRANSACTION_GMT using expression grel:substring(cells['TRANSACTION_GMT'].value, 0, 10)",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "TRANSACTION_GMT",
"expression": "grel:substring(cells['TRANSACTION_GMT'].value, 0, 10)",
"onError": "keep-original",
"repeat": false,
"repeatCount": 10 }
Transformations where many new rows or columns are created (e.g. split) can take especially long. If the allocated memory is almost exhausted, then the JAVA garbage collector also takes a lot of time. It is best to observe the RAM consumption of the Java process during the transformations.
Best wishes,
Felix
Owen Stephens
Feb 2, 2021, 11:15:48 AM2/2/21
to OpenRefine
Hi Joseph,
General point - we generally recommend using the latest version of OpenRefine - so you might want to try updating to 3.4.1 which is the current release
When running OpenRefine on a Mac, the default option (just launching from the Applications folder by clicking the icon) doesn't output a visible log, so there isn't any information directly available to you about progress. However, it is possible to run with a visible log - you can following the Mac instructions https://docs.openrefine.org/manual/running#starting-and-exiting - look for the paragraph headed "To run OpenRefine using Terminal"
If you start OpenRefine on Mac this way then you'll see the application log in the terminal - which will give you a bit more information about what's happening. It won't necessarily tell you the whole story but you should at least see if there are any errors, which will point to issues with completing the full set of transformations.
Happy to give more guidance on starting OpenRefine on Mac this way and how to interpret the data in the log you can see
Best wishes
Owen
Antonin Delpeuch (lists)
Feb 2, 2021, 11:40:09 AM2/2/21
to openr...@googlegroups.com
Hi Joe,
In addition to Felix and Owen's comments, that sounds like a good test
case for the new architecture I have been working on. This is exactly
the sort of workflow that the new architecture is supposed to ease, so I
would be very interested to see how that works for you.
In which format is your original dataset?
If you feel adventurous, you could try this new version, which is still
very experimental:
http://pintoch.ulminfo.fr/e020603eea/openrefine-mac-spark.dmg
Do not try to open existing projects (created with OpenRefine 3) with
this new version - it will only work with projects created from this
version. To be on the safe side, it would be good to back up your
workspace first:
https://docs.openrefine.org/manual/installing/#back-up-your-data
If you don't feel that adventurous but could share your dataset, I would
be very interested to compare the performance on the previous and new
architectures.
Best,
Antonin
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In addition to Felix and Owen's comments, that sounds like a good test
case for the new architecture I have been working on. This is exactly
the sort of workflow that the new architecture is supposed to ease, so I
would be very interested to see how that works for you.
In which format is your original dataset?
If you feel adventurous, you could try this new version, which is still
very experimental:
http://pintoch.ulminfo.fr/e020603eea/openrefine-mac-spark.dmg
Do not try to open existing projects (created with OpenRefine 3) with
this new version - it will only work with projects created from this
version. To be on the safe side, it would be good to back up your
workspace first:
https://docs.openrefine.org/manual/installing/#back-up-your-data
If you don't feel that adventurous but could share your dataset, I would
be very interested to compare the performance on the previous and new
architectures.
Best,
Antonin
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Joseph Montibello
Feb 2, 2021, 12:49:21 PM2/2/21
to OpenRefine
Hi,
I thought I'd try the experimental version. I downloaded it, unzipped, moved it to Applications, and then went to
I thought I'd try the experimental version. I downloaded it, unzipped, moved it to Applications, and then went to
/Applications/OpenRefine.app/Contents/MacOS and ran ./JavaAppLauncher.
All I got back was "Error: Could not find or load main class com.google.refine.Refine"
...I'm not sure if that means I installed it incorrectly, or if there's something leftover on my machine from other installs that might be causing problems?
(I did also move the data directory out of the way, so I don't lose it. The original dataset is a csv file.)
Take care,
Joe M.
Tom Morris
Feb 2, 2021, 3:38:10 PM2/2/21
to openr...@googlegroups.com
Did you load the source CSV? It looks like it might be the processed version.
1. It died and didn't tell you (the error handling for the "Apply Operations" function is very minimal)
2. It ran out of memory and is spending 99% of its time garbage collecting the heap, but not giving up even though it's got little chance of making forward progress
3. It's still processing and will finish eventually.
Rather than jumping from 10 rows to 1.7M, perhaps try 10,000 or 100,000 rows to get a sense of the timing, memory usage, etc. It'll also be more likely to show up any problems in your code from data it isn't expecting. If 100K works, try 500K to get a sense for how the timing scales.
At a glance, your operation list doesn't look particularly troublesome. I'd suggest turning off "Guess Cell Types" when splitting columns. It's slow and often doesn't do what you want. Any of the multicase if() that can be converted to table lookups would probably help performance.
Tom
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Joseph Montibello
Feb 2, 2021, 4:50:08 PM2/2/21
to OpenRefine
Hi,
After a couple of attempts, I was able to install openrefine-mac-spark successfully. I opened my large dataset in that version, copied in my transformations, and it worked!
On the older version (3.1), doing all those transforms never completed, and I finally force quit OpenRefine after several hours of it "working". With the new version, it completed all the transforms in somewhere between 20 and 30 minutes! (I was outside with my dogs when it finished so I don't have the exact time.)
Some of my transforms were long lists of if statements, and those seemed to be the ones that took the longest when I walked through them step by step. (I'll have to read up about table lookups, that sounds better than the crazy-long 'if' statements I had.)
Many thanks to Felix, Owen, Antonin and Tom! I really appreciate all the help I got in such a short time.
Take care,
Joe Montibello
Antonin Delpeuch (lists)
Feb 3, 2021, 3:27:32 AM2/3/21
to openr...@googlegroups.com
Hi Joe,
Fantastic that you made it work! The error you got earlier was obviously
because I forgot to update the Mac bundle after the change of namespace,
but I assume you figured that out yourself then!
Thank you so much for giving the new architecture a try - I was lucky
that your workflow did not rely on one of the features that are still
not migrated (such as the extensions).
Antonin
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Fantastic that you made it work! The error you got earlier was obviously
because I forgot to update the Mac bundle after the change of namespace,
but I assume you figured that out yourself then!
Thank you so much for giving the new architecture a try - I was lucky
that your workflow did not rely on one of the features that are still
not migrated (such as the extensions).
Antonin
>
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Owen Stephens
Feb 3, 2021, 5:19:09 AM2/3/21
to OpenRefine
Hi Joe,
In terms of the nested IF statements to map from coded values to real values (e.g. 1 -> AFRICAN & AFRO-AM), you could do that using a "cross" function to lookup the values across two projects, but I'm inclined to suggest trying using facets/mass edits to change the values instead. This is probably more work to setup, but once you've set them up, you can reuse them. My instinct (and its just instinct, I've not tested) is that doing each change as a Mass edit will give you better performance.
You can setup a Mass Edit in two ways:
1. Make text facet, and then use the "Edit" option for the value in the facet
2. Edit a single cell with the appropriate value and click "Apply to all identical cells"
In both cases, the transformation in the Undo/Redo JSON will be like:
[
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"1"
],
"fromBlank": false,
"fromError": false,
"to": "AFRICAN & AFRO-AM"
}
],
"description": "Mass edit cells in column Department/affiliation"
}
]
You can do these one by one to build up a list of mass-edit statements for all the value mappings - and once you have these, you can then use these as segments of Undo/Redo history to apply. If you want to save time, as long as you are careful to get it right, you can generate the required JSON automatically from a list of values (method of your choice), and then apply the JSON.
Best wishes
Owen
example JSON for mapping all the Department/affiliation values (I generated this from a table of codes + values in an OpenRefine project using the templating export to put in the rest of the JSON around the values):
[{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"1"
],
"fromBlank": false,
"fromError": false,
"to": "AFRICAN & AFRO-AM"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"2"
],
"fromBlank": false,
"fromError": false,
"to": "ALUMNI COLLEGE"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"3"
],
"fromBlank": false,
"fromError": false,
"to": "ANATOMY"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"4"
],
"fromBlank": false,
"fromError": false,
"to": "ANESTHESIOLOGY"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"5"
],
"fromBlank": false,
"fromError": false,
"to": "ANTHROPOLOGY"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"6"
],
"fromBlank": false,
"fromError": false,
"to": "ART HISTORY"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"7"
],
"fromBlank": false,
"fromError": false,
"to": "ASIAN STUDIES"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"8"
],
"fromBlank": false,
"fromError": false,
"to": "BIOCHEMISTRY"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"9"
],
"fromBlank": false,
"fromError": false,
"to": "BIOLOGY"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"10"
],
"fromBlank": false,
"fromError": false,
"to": "CANE"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"11"
],
"fromBlank": false,
"fromError": false,
"to": "CHEMISTRY"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"12"
],
"fromBlank": false,
"fromError": false,
"to": "CLASSICS"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"13"
],
"fromBlank": false,
"fromError": false,
"to": "CLIPP"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"14"
],
"fromBlank": false,
"fromError": false,
"to": "BIOMED-SPECIAL"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"15"
],
"fromBlank": false,
"fromError": false,
"to": "COMM & FAM MED"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"16"
],
"fromBlank": false,
"fromError": false,
"to": "COMP & INFO SCI"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"17"
],
"fromBlank": false,
"fromError": false,
"to": "COMPARATIVE LIT"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"18"
],
"fromBlank": false,
"fromError": false,
"to": "CLERGY"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"19"
],
"fromBlank": false,
"fromError": false,
"to": "DART-COLL-ADMIN"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"20"
],
"fromBlank": false,
"fromError": false,
"to": "INSTITUE FOR WRITING/RHETORIC"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"21"
],
"fromBlank": false,
"fromError": false,
"to": "DARTMOUTH INST."
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"22"
],
"fromBlank": false,
"fromError": false,
"to": "MHMH-GENERAL"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"23"
],
"fromBlank": false,
"fromError": false,
"to": "MHMH-NURSE"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"24"
],
"fromBlank": false,
"fromError": false,
"to": "DMS-GENERAL"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"25"
],
"fromBlank": false,
"fromError": false,
"to": "DMS-NURSE"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"26"
],
"fromBlank": false,
"fromError": false,
"to": "Pluralism and Leadership (OPAL)"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"27"
],
"fromBlank": false,
"fromError": false,
"to": "DRAMA & FILM STUD"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"28"
],
"fromBlank": false,
"fromError": false,
"to": "EARTH SCIENCES"
}
],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
"engineConfig": {
"facets": [],
"mode": "row-based"
},
"columnName": "Department/affiliation",
"expression": "value",
"edits": [
{
"from": [
"29"
],
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],
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{
"op": "core/mass-edit",
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],
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},
{
"op": "core/mass-edit",
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],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
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"fromError": false,
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],
"description": "Mass edit cells in column Department/affiliation"
},
{
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"op": "core/mass-edit",
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{
"op": "core/mass-edit",
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"fromError": false,
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"op": "core/mass-edit",
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"description": "Mass edit cells in column Department/affiliation"
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{
"op": "core/mass-edit",
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],
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"op": "core/mass-edit",
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"op": "core/mass-edit",
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],
"description": "Mass edit cells in column Department/affiliation"
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"op": "core/mass-edit",
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],
"description": "Mass edit cells in column Department/affiliation"
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"op": "core/mass-edit",
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],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
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],
"description": "Mass edit cells in column Department/affiliation"
},
{
"op": "core/mass-edit",
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],
"description": "Mass edit cells in column Department/affiliation"
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],
"description": "Mass edit cells in column Department/affiliation"
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],
"description": "Mass edit cells in column Department/affiliation"
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}]
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