Thank you for your help guys. We ended up moving the db to a real filesystem
rather than a network drive. Problem solved. :)
No PHI in Email: PointClickCare and Collective Medical, A PointClickCare
Company, policies prohibit sending protected health information (PHI) by email,
which may violate
I’ve found what I believe is a bug. If you try to run compaction via the
fuseki-main `/$/compact/{ds}` endpoint on an `ja:RDFDataset` that has a
defaultGraph of `ja:InfModel`, compaction will not execute because the
resulting `DatasetGraphMapLink` type does not inherit `DatasetGraphSwitchable`
> not click or open attachments unless you recognize the sender and know the
> content is safe. If you are unsure, please contact CTS at
> hel...@pointclickcare.com.
>
>
>
> On 07/05/2021 20:44, Brandon Sara wrote:
>> I’ve found what I believe is a bug. If you try to run comp
ure, please contact CTS at
hel...@pointclickcare.com<mailto:hel...@pointclickcare.com>.
On 08/05/2021 00:05, Brandon Sara wrote:
While I can see how this will work, it is a pretty undesirable solution.
Why is that?
Are there any other options? Or is there a way to get this working for a
situation like thi
I think that even that slight change to endpoint structure would help quite a
bit.
On May 10, 2021, at 11:18 AM, Rob Vesse
mailto:rve...@dotnetrdf.org>> wrote:
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Company, policies prohibit sending protected health
My Setup:
I’m running a few fuseki servers via Docker containers. I need the storage to
be persistent across container restarts, so I’m using TDB2 for my storage. The
TDB2 database are stored on a volume that is mounted to the Docker containers.
This volume is part of our S3 instance. The
I have a very large dataset. Before compaction, it was ~51 GB. I ran
compaction (using tdb2.tdbcompact cli tool) and it dropped down to 6.7 GB.
I then wanted to see how long it would take to run compaction on an already
compacted dataset. After running it, it grew in size to 7.4 GB, then it
grew
I have a fuseki server that i communicate with remotely. I can use ARQ to
create and send the query via RDFConnection and use ARQ to handling
iterating over the results. I could also just submit an HTTP request and
use something like Jackson to map the resulting JSON-LD to my POJOs. Are
there any
DB2 uses sparse files - allocates 8M chunks but does not use all the space
> immediately. Different OS and different tools on Linux seem to report
> differently, whether it is allocated space or used space.
>
> Andy
>
> On 06/04/2021 21:43, Brandon Sara wrote:
>> I
I would love it if we could have an automatic deletion option with the compact
task, otherwise, a good amount of work can end up being needed just to ensure
that a no longer needed `Data-` folder is removed. Is this something that
the maintainers are willing to consider? If so, I’d be
> What's at 172.18.0.1:60440? Judging by the port number, is it the application
> client?
Yeah, I believe it was the host IP. I run the server in a docker container and
was hitting it with a simple REST client.
On Aug 18, 2021, at 6:43 AM, Andy Seaborne
mailto:a...@apache.org>> wrote:
Hi
Also, on subsequent requests, I get no logs like it is trying to reload the db.
It shows that the request was received, but it just waits. I’m assuming that
perhaps a lock is put on the dataset in memory and it is never let go from the
first request.
On Aug 17, 2021, at 4:38 PM, Brandon Sara
I’m having an issue with Fuseki where, once the first request is submitted, the
server never returns a response and never returns any responses for subsequent
requests either. The server also starts increasing its memory usage quite
significantly until it finally runs out of memory, a GC
n
intermediate server.
Andy
On 24/08/2021 00:28, Brandon Sara wrote:
> I’m still seeing this issue, even after the latest update of RDF-Delta.
> Anyone have any ideas?
> No PHI in Email: PointClickCare and Collective Medical, A PointClickCare
> Company, policies prohibit s
> If it is after each restart, maybe the local state has been messed up by the
> earlier problems.
I wondered this as well. However, I’ve just barely done another upload of the
data to a fresh tdb2 db and immediately after the upload, I can query all that
I want and things are super fast. But
I’ve finally tracked down the problem (at least at a high level). When using
the Transitive Reasoner, there is a block of code which caches all sub class
triples
I’m still seeing this issue, even after the latest update of RDF-Delta. Anyone
have any ideas?
No PHI in Email: PointClickCare and Collective Medical, A PointClickCare
Company, policies prohibit sending protected health information (PHI) by email,
which may violate regulatory requirements. If
I have been able to create an easily reproducible scenario that others can use
to replicate and test the issues that I’m seeing:
1. Start fuseki using the config that I’ve listed below.
2. Attempt to load the latest version of ICD-10 CM as provided freely by
BioPortal:
Can I get some recommendations on how to best tweak/setup memory for my fuseki
servers? Here is my setup:
- I’ve got a single TDB with at least several million triples (I don’t know the
exact amount yet, but perhaps around 10s of millions, maybe 100s of millions…a
the very least, I need it to
of the organization. Do
> not click or open attachments unless you recognize the sender and know the
> content is safe. If you are unsure, please contact CTS at
> hel...@pointclickcare.com.
>
>
>
> On 11/08/2021 21:21, Brandon Sara wrote:
>>> 10s of millions tri
inated from outside of the organization. Do
> not click or open attachments unless you recognize the sender and know the
> content is safe. If you are unsure, please contact CTS at
> hel...@pointclickcare.com.
>
>
>
> On 11/08/2021 21:21, Brandon Sara wrote:
>>> 10s of mil
kcare.com.
>
> And you use TDB1?
>
> TDB1 can use more memory - and between all the other components it might all
> amount to 6G if the server isn't able to do some of the background tidy-up
> work for a while.
>
> TDB2 does not have this effect.
>
>Andy
>
> On
k or open attachments unless you recognize the sender and know the
content is safe. If you are unsure, please contact CTS at
hel...@pointclickcare.com<mailto:hel...@pointclickcare.com>.
On 11/08/2021 01:17, Brandon Sara wrote:
> Can I get some recommendations on how to best tweak/setup
click or open attachments unless you recognize the sender and know the
content is safe. If you are unsure, please contact CTS at
hel...@pointclickcare.com<mailto:hel...@pointclickcare.com>.
On 11/08/2021 19:07, Brandon Sara wrote:
>> What properties are transitive?
> Right no
Currently, it seems that all cached inference (at least with the transitive
reasoner) is not loaded into cache until the first query that would query data
from a dataset is submitted to the Fuseki server. For very large ontologies,
this loading process can take quite a while. This basically
> SNOMED has a conversion to OWL - isn't that OWL functional syntax? Or do you
> have another tool that converts RF2 to RDF?
I used the SNOMED tool to convert to OWL functional syntax, then used robot to
convert that to turtle
> what OWL features are you going to use? SNOMED uses more than
Here is my scenario:
- I have a large read-only set of data and a very small mutable set of data.
- The read-only set of data can be pre-populated into a TDB2 while the mutable
set of data will start out empty but will, obviously have data injected
overtime during runtime.
- I want one Fuseki
We need the inference so that we can know equivalence between classes and
subclass relationships (eg "type 2 diabetes" is still "diabetes" because it's
is a subclass of diabetes).
Another dataset that I've never been able to get to load with any inference
enabled is SNOMED CT. Even when
> Which reasoner? IIRC SnomedCT uses various OWL features
> The default RDFS reasoner does not include the "rdf4" rule which is a
> whole-dataset rule
> A ruleset tuned to needs may work better.
I tried this to only include subclass and equivalent class using the generic
reasoner, but the
> A text index is "per dataset”.
This is what I figured, but wanted to be sure.
Thanks!
No PHI in Email: PointClickCare and Collective Medical, A PointClickCare
Company, policies prohibit sending protected health information (PHI) by email,
which may violate regulatory requirements. If sending
I was looking at the docs for Fuseki
(https://jena.apache.org/documentation/fuseki2/fuseki-data-access-control.html#https)
and tried running `fuseki-server —https=… —httpsPort=…` and all I get in
return is "Unknown argument: https”. Are the docs wrong or is there a bug?
No PHI in Email:
Andy, will you be releasing an RDF-Delta update that uses 4.3.1 soon as well?
No PHI in Email: PointClickCare and Collective Medical, A PointClickCare
Company, policies prohibit sending protected health information (PHI) by email,
which may violate regulatory requirements. If sending PHI is
Should we expect another release (like version 4.3.2) given Log4J updating to
2.16.0 in response to this other CVE:
https://cve.mitre.org/cgi-bin/cvename.cgi?name=2021-45046?
No PHI in Email: PointClickCare and Collective Medical, A PointClickCare
Company, policies prohibit sending protected
From what I've been able to find, it doesn't seem that there are any metrics
provided that show how long queries are taking to complete. I can get some
general metrics about request rates and standard Jvm metrics from a fuseki
server, but it seems that there is nothing else provided.
Am I just
I just came across CVE-2023-32200 and was wondering, is it different than
CVE-2023-22665 and, if so, how is it different?
No PHI in Email: PointClickCare and Collective Medical, A PointClickCare
Company, policies prohibit sending protected health information (PHI) by email,
which may violate
Awesome! Thanks for the quick response
> On Jul 20, 2023, at 11:13 AM, Andy Seaborne wrote:
>
> "EXTERNAL EMAIL" – Always use caution when reviewing mail from outside of the
> organization.
>
>
>
> On 20/07/2023 17:18, Brandon Sara wrote:
>> I just came
there
> still a risk/concern if I don’t have custom scripts configured at all on the
> Fuseki server?
>
> On May 31, 2023, at 12:06 PM, Andy Seaborne wrote:
>
> "EXTERNAL EMAIL" – Always use caution when reviewing mail from outside of the
> organization.
&g
n a Java17+
environment, otherwise anything may be possible.
Andy
On 01/06/2023 17:57, Brandon Sara wrote:
> Ok. When you say “arbitrary function”, could one craft and run code that
> makes HTTP calls (via XMLHttpRequest or the fetch API, for example)? We don’t
> have sensitive data in ou
om outside of the
organization.
On 31/05/2023 17:17, Brandon Sara wrote:
>
> With CVE-2023-22665, what is the risk of using Fuseki pre-4.8.0 that does not
> have custom scripts configured in any configurations? Is there only a risk if
> custom scripts are set up to be used by Fus
With CVE-2023-22665, what is the risk of using Fuseki pre-4.8.0 that does not
have custom scripts configured in any configurations? Is there only a risk if
custom scripts are set up to be used by Fuseki or is there a risk regardless of
configuration?
Thanks.
No PHI in Email: PointClickCare
ng mail from outside of the
organization.
On 02/06/2023 17:26, Brandon Sara wrote:
> And just to be clear, this code would execute on the Fuseki server, correct?
I'm not sure what "this code" refers to.
A way to be safe is to run Fuseki with a Java17 runtime.
What is appropriate in your
Does Fuseki support the creation of transactions that can span multiple
requests?
If so, would the following sequence of events be true or no?
1. I start a transaction
2. I submit a query to get some data for and update I want to perform
3. An update is submitted by a separate client
4. The
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