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Re: [basex-talk] Basex Docker Container: How to Control Options
by Christian Grün 05 Apr '17

05 Apr '17

Hi Eliot, Did you try to specify the option in the local section of the .basex file (at the bottom, after all other options)? Best, Christian Am 02.04.2017 10:52 schrieb "Eliot Kimber" <ekimber(a)contrext.com>: I’ve worked around the configuration file problem by setting the options on the Java command line by setting BASEX_JVM in my Dockerfile: ENV BASEX_JVM="-Dorg.basex.CHOP=false -Dorg.basex.CATFILE=/opt/dita-ot/DITA-OT/catalog-dita.xml -Dorg.basex.DTD=true -Dorg.basex.SKIPCORRUPT=true" That seems to work. I guess I could also set this environment variable in my docker-compose.yml file, although except for CATFILE, these are invariant for this application. Cheers, E. -- Eliot Kimber http://contrext.com On 4/1/17, 10:44 PM, "Eliot Kimber" <basex-talk-bounces@mailman. uni-konstanz.de on behalf of ekimber(a)contrext.com> wrote: Perhaps a more useful question is: is there a workaround for this? That is, I need to have the DTD, CATFILE, CHOP, and SKIPCORRUPT options set when I load files into a database, which I’m doing through the remote API. Is there either a separate options file that I should be using or a way to specify these options at document load time? Cheers, E. -- Eliot Kimber http://contrext.com On 4/1/17, 10:23 PM, "Eliot Kimber" <basex-talk-bounces@mailman. uni-konstanz.de on behalf of ekimber(a)contrext.com> wrote: I dug into the code and I think this is a code bug but I don’t understand the overall flow well enough to know where the bug is, but I suspect it’s a simple change. If I debug the BasexGUI class and have a ~/.basex file that includes CATFILE=foo it will fail with an unknown option error because the option class being used is StaticOptions and StaticOptions does not define CATFILE as an option. The CATFILE option, along with a few others, is defined on MainOptions: private static final Option<?>[] INHERIT = { CHOP, INTPARSE, STRIPNS, DTD, XINCLUDE, CATFILE }; Looking at BaseXHTTP it uses HTTPContext which only uses StaticOptions, not MainOptions, which means it can never allow the INHERIT options. So something must have changed from 8.1 ish to now to change how options are handled since these options worked before I moved to the latest BaseX container and versions. But there definitely seems to be an oversight in the initial handling of the options file in the BaseXHTTP server (and in the BaseXGUI as well since I get the same behavior there as well). I would make a pull request but I don’t presume to know what policies or general practices underlie the current options mechanism deisgn. Cheers, Eliot -- Eliot Kimber http://contrext.com On 3/26/17, 10:20 PM, "Eliot Kimber" <basex-talk-bounces@mailman. uni-konstanz.de on behalf of ekimber(a)contrext.com> wrote: I found my original mail thread from January 2016: https://mailman.uni-konstanz.de/pipermail/basex-talk/2016- January/010171.html Basically I had to append my options to the existing .basex file rather than simply provide a file. However, that isn’t an option here because there is no existing /srv/.basex file (the place where the file needs to be). As an experiment I tried doing this: RUN touch /srv/.basex && \ echo "DTD=true" >> .basex && \ echo "CATFILE=/opt/dita-ot/DITA-OT/catalog-dita.xml" >> .basex && \ echo "SKIPCORRUPT=true" >> .basex && \ echo "CHOP=false" >> .basex && \ echo "DBPATH=/srv/BaseXData" >> .basex && \ echo "REPOPATH=/srv/BaseXRepo" >> .basex && \ echo "WEBPATH=/srv/BaseXWeb" >> .basex && \ chown basex /srv/.basex RUN echo "/srv/.basex:\n===========" && cat /srv/.basex && echo "=======" And I get this from the build command: /srv/.basex: =========== DTD=true CATFILE=/opt/dita-ot/DITA-OT/catalog-dita.xml SKIPCORRUPT=true CHOP=false DBPATH=/srv/BaseXData REPOPATH=/srv/BaseXRepo WEBPATH=/srv/BaseXWeb ======= When I start up this container I get this: /srv/.basex: Unknown option 'DTD'. /srv/.basex: Unknown option 'CATFILE'. /srv/.basex: Unknown option 'SKIPCORRUPT'. /srv/.basex: Unknown option 'CHOP'. /srv/.basex: writing new configuration file. Note that it’s only complaining about DTD, CATFILE, SKIPCORRUPT, and CHOP, but not DBPATH, REPOPATH, and WEBPATH. I tried reordering things, no difference in result (but the messages reflect the order change). So it must be something about how these particular options are processed rather than an issue with the .basex file, at least as far as I can see. Cheers, Eliot -- Eliot Kimber http://contrext.com On 3/26/17, 3:29 PM, "Eliot Kimber" <basex-talk-bounces@mailman. uni-konstanz.de on behalf of ekimber(a)contrext.com> wrote: Discovered that if I use USER root in the Dockerfile I have to then do USER basex before the end so that the container will be running as basex, otherwise it does not start up correctly. I also have to chown the /srv/.basex file to basex otherwise it can’t overwrite it on startup. Made some progress but something is still not working. I now have a Dockerfile based on basex/dba that results in a running system with the both the dba and my custom app runnable. However, if I then add this: COPY basex/dot_basex /srv/.basex As before, on startup I get this: docker run --name linkmgr-test -p 8984:8984 link-manager-test /srv/.basex: Unknown option 'CATFILE'. /srv/.basex: Unknown option 'DTD'. /srv/.basex: Unknown option 'SKIPCORRUPT'. /srv/.basex: Unknown option 'CHOP'. /srv/.basex: writing new configuration file. Creating /srv/BaseXWeb/WEB-INF/web.xml Creating /srv/BaseXWeb/WEB-INF/jetty.xml I think this Unknown option this is actually an issue with the file itself but I don’t recall what the exact cause and/or solution was. Cheers, E. -- Eliot Kimber http://contrext.com On 3/26/17, 1:40 PM, "Eliot Kimber" < basex-talk-bounces(a)mailman.uni-konstanz.de on behalf of ekimber(a)contrext.com> wrote: I’m trying to set up a Docker container with my own Web app using the latest official containers as a base and following the instructions in the latest BaseX docs. As part of this setup I need to add several additional options. I also want to include the dba app. Following the instructions in the docs I’m putting my additional options in /srv/.basex and these take effect. However, if I use the basex/dba image as a base, the other options, such as the custom REPOPATH and WEBPATH settings do not get used. It’s not clear to me from looking at the various Dockerfiles how the dba container sets the options and how I can then add to them without overwriting them. Of course I can duplicate the options in my Dockerfile but it seems like I should be able to add my options additively but I’m not seeing how to do it, so I feel I’m missing something. In my Dockerfile I have: COPY basex/dot_basex /srv/.basex If I don’t include this line then the container otherwise works in that my Web app is there but it requires these additional options in order to function properly. If I include it then the effective options reflect only my changes and not those required for the custom Web apps to work. Thanks, Eliot -- Eliot Kimber http://contrext.com

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Re: [basex-talk] Basex Docker Container: How to Control Options
by Eliot Kimber 02 Apr '17

02 Apr '17

Discovered that if I use USER root in the Dockerfile I have to then do USER basex before the end so that the container will be running as basex, otherwise it does not start up correctly. I also have to chown the /srv/.basex file to basex otherwise it can’t overwrite it on startup. Made some progress but something is still not working. I now have a Dockerfile based on basex/dba that results in a running system with the both the dba and my custom app runnable. However, if I then add this: COPY basex/dot_basex /srv/.basex As before, on startup I get this: docker run --name linkmgr-test -p 8984:8984 link-manager-test /srv/.basex: Unknown option 'CATFILE'. /srv/.basex: Unknown option 'DTD'. /srv/.basex: Unknown option 'SKIPCORRUPT'. /srv/.basex: Unknown option 'CHOP'. /srv/.basex: writing new configuration file. Creating /srv/BaseXWeb/WEB-INF/web.xml Creating /srv/BaseXWeb/WEB-INF/jetty.xml I think this Unknown option this is actually an issue with the file itself but I don’t recall what the exact cause and/or solution was. Cheers, E. -- Eliot Kimber http://contrext.com On 3/26/17, 1:40 PM, "Eliot Kimber" <basex-talk-bounces(a)mailman.uni-konstanz.de on behalf of ekimber(a)contrext.com> wrote: I’m trying to set up a Docker container with my own Web app using the latest official containers as a base and following the instructions in the latest BaseX docs. As part of this setup I need to add several additional options. I also want to include the dba app. Following the instructions in the docs I’m putting my additional options in /srv/.basex and these take effect. However, if I use the basex/dba image as a base, the other options, such as the custom REPOPATH and WEBPATH settings do not get used. It’s not clear to me from looking at the various Dockerfiles how the dba container sets the options and how I can then add to them without overwriting them. Of course I can duplicate the options in my Dockerfile but it seems like I should be able to add my options additively but I’m not seeing how to do it, so I feel I’m missing something. In my Dockerfile I have: COPY basex/dot_basex /srv/.basex If I don’t include this line then the container otherwise works in that my Web app is there but it requires these additional options in order to function properly. If I include it then the effective options reflect only my changes and not those required for the custom Web apps to work. Thanks, Eliot -- Eliot Kimber http://contrext.com

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Deadlock with concurrent write and reads in BaseX
by Simon Chatelain 31 Mar '17

31 Mar '17

Hello all, I am facing an issue with my application using BaseX 8.6.2. Basically what I have is one thread (Add thread) receiving data from a socket as XML fragment and storing it in BaseX. On the other hand, my application provides a REST interface to retrieve data from the DB. When retrieving data what happen is, I first execute a simple Xquery in a thread (Primary Read), and for each hit returned by this first query, I execute another query in another thread (Secondary read) to retrieve additional data. The problem is that I end up in a situation where all three threads are stopped waiting for something. The Add thread is park as it cannot acquire a write lock, while the Primary read is running, as it should be. But the Secondary read is also parked, thus blocking the Primary read, and so we end up in a kind of deadlock. The PARALLEL option in .basex is set to 4, and the FAIRLOCK option is set to true. Some technical details: In the primary read I am using session.setOutputStream(pos); session.execute(new XQuery(flwor)); where session is a LocalSession and pos is a PipedOutputStream In Secondary read, I am reading the other side of the piped stream, and for each line read from the stream, I execute another query (well not exactly in the real case scenario, but this simplification seems good enough to exhibit the problem, and is shown in the attached BaseXDeadlock.java example). You can also see the stacks of all three threads in BaseXDeadlockStacks.txt In this example, if I don’t start the Add thread, then Primary and Secondary read are running as expected. On the other hand, if I change my implementation of Primary and Secondary read, and use a blocking queue to transfer data from Primary to Secondary read like shown below: Query query = session.query(flwor) while (query.more()) { queue.put(query.next()); } And then taking from the queue in Secondary read, then it works. This implementation is shown in BaseXNoDeadlock.java. Using the latter is good enough for me, as it does the job, even if there is a small performance penalty compared to the first implementation, in my real case scenario. So my question is: is my first implementation fundamentally broken or is there something wrong on BaseX side? Best regards and many thanks to all the BaseX team for this efficient and nice to use tool. Simon Chatelain

2 1

BaseX hanging on REST/XQ pipelining
by Erik Peterson 31 Mar '17

31 Mar '17

It seems like on some RESTXQ/REST pipelining (restxq calling another restxq api) causes basex to hang. In this scenario a mock client was created to test the system. A test was written to automate mock client requests. A restxq path was created run tests. More specifically... 1) Browse to http://localhost:8984/unit-test/test where last parameter "test" maps the directiory where unit tests are located. 2) #1 is handled by a RESTXQ function where a REST URL is fetched: fetch(http://localhost:8984/rest?command=test+../webapp/mock-client/test) 3) #2 is handled by a unit-test that fetches a mock-client URL fetch(http://localhost:8984/mock-client/do-something) 4) #3 is handled by a the mock-client hitting the system fetch(http://localhost:8984/system/do-something) - #3 and #4 (mock-client) work great - #2 (the unit-test) work great when running tests from command line OR when the test is a simple unit:assert(<canary/>). But basex hangs otherwise Thanks for any insight on why the system calling back to itself may cause a system hang.

2 2

suddenly...java function x is unknown
by Erik Peterson 30 Mar '17

30 Mar '17

I've been integrating basex with 3rd party java jar files by dropping them in the basex/lib directory. This has worked fine until today when I now git "java function x is unknown". I've... - re-pulled everything from our repo to make sure all binaries are as they were when working - restarted osx - updated java - using BaseX VERSION 8.6.1 (February 24, 2017) It's working on other dev machines but not mine. Why would BaseX stop loading the classes from the lib jar files? Is there a better way I should be deploying jars? Thanks.

2 2

Performance: associating one with many, or many with one?
by Jay Straw 29 Mar '17

29 Mar '17

Hi List! I'm building an application in base-x that's sort of like a local music wiki: bands, members, venues, promoters, and albums and songs are some of what I'm representing in XML. And what I'm wondering is that, in a situation where there's one of something (a musician), and a bunch of something else they're associated with (song writting or performance credits), which node should get the reference? The numerous node gets the reference back to the one: <album name="We Might Rock You" by="The Quesadillas"> <track number="1" name="Hot Cross Buns" written-by="Joe Schmoe" /> <track number="2" name="Bicycle" written-by="Joe Schmoe" /> </album> [ etc ] Or the one refers to the many: <person name="Joe Schmoe"> <songs-written> <song name="Hot Cross Buns" /> <song name="Bicycle" /> </songs-written> </person> Example 1, I could use something like: track[@written-by="Joe Schmoe"] Example 2: person[@name="Joe Schmoe"]/songs-written/song My other thought was putting the references in both, but I'll have to do this with many types of objects I'm representing and I don't want things to get out of control (then again, if I go to export an <album/> or <band/> and I'm using the second method, I'll have to do a join) I have a feeling in a large set, the second way wins out. Even where I live, with only around 750,000 people in our entire state (Alaska), we have easily 100 - 200 acts, including bands, solo performers, traditional acts, etc, with thousands of individuals that compose them. But I want bands that are extinct, bands that are on hiatus, etc, and I hope my software is useful to others in larger cities as well. So, maybe a pointless question because my db will be so tiny compared to some folks who post on here, but just curious :-) Also, if this problem has a name I can research myself, that'd be great! Be well, Jay Straw

3 2

Basex Docker Container: How to Control Options
by Eliot Kimber 26 Mar '17

26 Mar '17

I’m trying to set up a Docker container with my own Web app using the latest official containers as a base and following the instructions in the latest BaseX docs. As part of this setup I need to add several additional options. I also want to include the dba app. Following the instructions in the docs I’m putting my additional options in /srv/.basex and these take effect. However, if I use the basex/dba image as a base, the other options, such as the custom REPOPATH and WEBPATH settings do not get used. It’s not clear to me from looking at the various Dockerfiles how the dba container sets the options and how I can then add to them without overwriting them. Of course I can duplicate the options in my Dockerfile but it seems like I should be able to add my options additively but I’m not seeing how to do it, so I feel I’m missing something. In my Dockerfile I have: COPY basex/dot_basex /srv/.basex If I don’t include this line then the container otherwise works in that my Web app is there but it requires these additional options in order to function properly. If I include it then the effective options reflect only my changes and not those required for the custom Web apps to work. Thanks, Eliot -- Eliot Kimber http://contrext.com

1 0

Possible to Access Environment Variables from XQuery?
by Eliot Kimber 25 Mar '17

25 Mar '17

I’m running BaseX in a Docker container started via docker-compose. I need to communicate some local configuration details to BaseX. Can set these as environment variables (e.g., using .env with docker-compose) but I don’t see anything in the docs that would let me access environment variables from XQuery. Is there a built-in way to do this? Thanks, Eliot -- Eliot Kimber http://contrext.com

3 3

and operator in Multiple Predicates
by Tushar Deshmukh 23 Mar '17

23 Mar '17

Namaste , and operator in predicates seems tobe not working. my xquery is as below and xml is attached herewith. declare namespace UDF="TallyUDF"; let $fromdate:=20170228 let $todate:=20170228 let $pledger_code:=57 let $pledger_status:="P" for $allitems in db:open('10096',"Vouchers")/ENVELOPE/Voucher[./Date/text() >= $fromdate and ./Date/text() <= $todate and ./AllLedgerEntries.LIST/UDF:AsPerListAllocations.LIST/UDF:ColPartyCode.LIST/UDF:ColPartyCode/text()= $pledger_code and ./AllLedgerEntries.LIST/UDF:AsPerListAllocations.LIST/UDF:MaheshCIFlag.LIST/UDF:MaheshCIFlag/text()= $pledger_status] return $allitems/MasterId Expected 2 records/nodes instead 4. Tushar Deshmukh,

2 1

Calling the sort function with two arguments
by Martin Honnen 22 Mar '17

22 Mar '17

According to https://www.w3.org/TR/xpath-functions-31/#func-sort the sort function allows one or two or three arguments, however when doing sort((5, 3, 4, 1), default-collation()) in BaseX 8.6.2 I get an error java.lang.ArrayIndexOutOfBoundsException: 2 at org.basex.query.func.fn.FnSort.iter(FnSort.java:34) at org.basex.query.QueryContext.iter(QueryContext.java:394) at org.basex.query.scope.MainModule.iter(MainModule.java:117) at org.basex.query.QueryContext.iter(QueryContext.java:330) at org.basex.query.QueryContext.cache(QueryContext.java:609) at org.basex.query.QueryProcessor.cache(QueryProcessor.java:113) at org.basex.core.cmd.AQuery.query(AQuery.java:86) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:257) at org.basex.core.Command.execute(Command.java:93) at org.basex.gui.GUI.exec(GUI.java:471) at org.basex.gui.GUI.access$300(GUI.java:44) at org.basex.gui.GUI$6.run(GUI.java:413) A similar error occurs with sort((5, 3, 4, 1), ()) Is BaseX 8.6.2 not yet in line with the freshly published spec? Regards, Martin Honnen

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