Help me in creating Hypergraphdb

[mscsf...@pucit.edu.pk]

Hi everyone,

I have tried with many ways but no progress. 

1) I imported the 1.3 release. Then i add the simple java class with following code.

import org.hypergraphdb.*; // top-level API classes are in this package public class HGDBCreateSample { public static void main(String [] args) { String databaseLocation = args[0]; HyperGraph graph; // ... try { graph = new HyperGraph(databaseLocation); } catch (Throwable t) { t.printStackTrace(); } finally { graph.close(); } } }

But no output.

2) Then i Made a new simple java project and a java class with above code and manually add the hgdb, hgdbje , hgdbp2p and others folders but still no progress.

Now what should i do?

[Borislav Iordanov]

What output do you expect in your case (1) below? You are creating a new database and then closing. There is no output to be expected there as far I can tell.

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[mscsf...@pucit.edu.pk]

Hi Boris,

Its not compiling successfully. I need some records as an output.

[Borislav Iordanov]

Hi,

It seems like you need help with general Java programming. I can answer HGDB related question, but when it comes to programming in general, there is plenty of online material to help you. 

Essentially, HGDB is an API that you can use to store and retrieve graph-like data. You can use it to store Java beans too. And the tutorials give some examples. 

I can’t help with “it’s not compiling successfully”  - you need to learn Java, or some JVM based language and then you can call the API.

Best,

Boris

[ZARYAB ARIF]

Hi Boris,

Thank you so much for your help. I have successfully created the hypergraph database. 

In my output folder there are four files. 

1)00000000.jdb

2)hgdbversion

3)je.info.o

4)je.lck

Will you please explain that? 

On Wed, Jul 25, 2018 at 8:02 AM, Borislav Iordanov <borislav...@gmail.com> wrote:

Hi,

It seems like you need help with general Java programming. I can answer HGDB related question, but when it comes to programming in general, there is plenty of online material to help you. 

Essentially, HGDB is an API that you can use to store and retrieve graph-like data. You can use it to store Java beans too. And the tutorials give some examples. 

I can’t help with “it’s not compiling successfully”  - you need to learn Java, or some JVM based language and then you can call the API.

Best,

Boris

On Jul 25, 2018, at 3:45 AM, mscsf...@pucit.edu.pk wrote:

Hi Boris,

Its not compiling successfully. I need some records as an output.

On Tuesday, July 24, 2018 at 11:11:16 AM UTC-7, mscsf...@pucit.edu.pk wrote:

Hi everyone,

I have tried with many ways but no progress. 

1) I imported the 1.3 release. Then i add the simple java class with following code.

import org.hypergraphdb.*; // top-level API classes are in this package public class HGDBCreateSample { public static void main(String [] args) { String databaseLocation = args[0]; HyperGraph graph; // ... try { graph = new HyperGraph(databaseLocation); } catch (Throwable t) { t.printStackTrace(); } finally { graph.close(); } } }

But no output.

2) Then i Made a new simple java project and a java class with above code and manually add the hgdb, hgdbje , hgdbp2p and others folders but still no progress.

Now what should i do?

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[Borislav Iordanov]

Those are binary files constituting the database. To read back your data you need to query it using the API - checkout http://hypergraphdb.org/?project=hypergraphdb&page=IntroQuerying

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[ZARYAB ARIF]

There are four files in output folders. But  what is the by default storage extension for HGDB?

[Borislav Iordanov]

It’s BerkeleyDB Java Edition.

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[ZARYAB ARIF]

".jdb" ??

[Borislav Iordanov]

You really don’t need to be concerned with those files. The folder contains the data. It’s managed by BerkeleyDB and whatever B-Tree binary format and log format that implementation has defined. I’ve never needed to dig into that, except occasionally deleting the .lck file which might be left over from an improperly shutdown application :)

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[ZARYAB ARIF]

Actually I have two parameters one is path, 2nd one is the by default extension of db file. That's why I was asking :)

[ZARYAB ARIF]

Hi Boris,

Through the below code i can only read the x value. What i will do if i have lots of other values in my database?

 HyperGraph graph; 
     // ...
    try
{

       graph = new HyperGraph("E:/temp/HGraph1");
       String x="testing";
   HGHandle Handle = graph.add(x);

        graph.open("E:/temp/HGraph1");

    System.out.println(graph.get(Handle));

[Borislav Iordanov]

You query:

http://hypergraphdb.org/?project=hypergraphdb&page=IntroQuerying

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[ZARYAB ARIF]

I have read this. But the Book class which you have used for an example has been obsoleted.

[ZARYAB ARIF]

Hi Boris,

I wanna run update function like 

graph.update(Handle);

But it shows the following error

org.hypergraphdb.HGException: Could not find HyperGraph handle for atom c441af6a-2fb8-4b82-a2ff-ccce7ed70c50

at org.hypergraphdb.HyperGraph.update(HyperGraph.java:1142)

at src.Test1.HGclientTest.main(HGclientTest.java:35)

What does it mean??

[Borislav Iordanov]

Hi,

graph.update takes the actual object, the atom, not its handle. So if you have the handle, do graph.update(graph.get(handle)) instead.

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[ZARYAB ARIF]

Thanks I have solved the problem :)

Now please help me in following issue.

try {
    //insert
    graph = new HyperGraph("E:/temp/HGrapht2");
    String x = "Hello";
    Handle = graph.add(x);
    String y="new";
    graph.add(y);
    System.out.println(graph.get(Handle));   //Here what should i do, so that i can display the all data in files like Hello, new??

    //update
          String z="new hello";

         graph.update(z);
       
     System.out.println(graph.get(Handle));       //here i want to display the updated file but there is no function for that purpose.
   
    //delete
    graph.remove(Handle);
    System.out.println(graph.get(Handle));          // Here it should be removed but still shows an output.

    }

[Borislav Iordanov]

I’m not sure what the issue is, but the graph.update call below is incorrect because ‘z’ is not an atom already added to the database. In Java string are immutable, so update on the same string object won’t work. You have to call graph.replace(handle, newValue), so in your casE:

graph.replace(Handle, z)

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[ZARYAB ARIF]

How can I read more than one values?? 

One value can be read by 

Graph.get(Handle). 

But if more than one HGhandle have been added to database. How can I display them? 

[Borislav Iordanov]

You have to do a query: 

http://hypergraphdb.org/?project=hypergraphdb&page=IntroQuerying

For example, to display all strings:

graph.getAll(hg.type(String.class)).forEach(System.out::println)

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[ZARYAB ARIF]

okay Thanks :)

[ZARYAB ARIF]

Hey,

To update the database below code is correct?

 String z="new hello";

         graph.update(z);

I just want to update the database  not replace the existing strings. I also use the code 

graph.update(graph.get(Handle));  But in this case first i have to get the handle by adding atoms. Like 

HGHandle Handle=graph.add(z); If i first add in database then update, Then why we are using update? Without update we can add the atoms earlier then why update?

[Borislav Iordanov]

On Aug 20, 2018, at 1:48 PM, ZARYAB ARIF <mscsf...@pucit.edu.pk> wrote:

Hey,

To update the database below code is correct?

 String z="new hello";

         graph.update(z);

No, that’s not correct. What do you mean by “update the database”? The graph.update(atom) method updates an atom which is assumed to already be in the database. Updating an atom is one possible way to “update the database” - others are adding atoms or removing atoms. If you want to “update the database” by adding a new atom, you do “graph.add(atom)”. Those are standard operations in DBMS, see https://en.wikipedia.org/wiki/Create,_read,_update_and_delete for example. 

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[ZARYAB ARIF]

OK got it. I was thinking update function means update the database, not update the atoms. That's why I was confused between update and add functions. Thanks for making me correct :) 

[ZARYAB ARIF]

I have a variable having String data type. By that variable i want to access the record from database. 

I am using in this way.

Public status read(String key)

{

hypergraph.get(key);

}

hypergraph is an object of Hypergraph. But the above code shows an error. What should i do?

[ZARYAB ARIF]

Hi boris,

I hope you are fine. There is a function in getIndexManager()       "getIndex()". This function has two parameters (keyValue, valuetype). Will you explain these two parameters? I am little bit confused.

Actually i have a string value and i want to find the index of that value in database. Now what should i do??

[Borislav Iordanov]

This is an internal function that you shouldn’t be using normally. To add indices, see here:

http://hypergraphdb.org/?project=hypergraphdb&page=IndicesHowto

if you just have a string valued atom, there is no need to add index. You can just lookup the atom with that value via hg.eq(stringValue)

B

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[ZARYAB ARIF]

Hi Boris,

I need your help i am stuck at a point. I have searched allot but couldn't find the solution. 

I have a function in which i want to read the database from a specified point.

I have a key value when it matches in database, I have to read database after that match record. But i could not find such function. I found the match record by using following function.

hypergraph.find(hg.eq(key));

But after this line i wish to start from the specified location where i find this. How can i do this??

[ZARYAB ARIF]

Hi Boris,

I am getting the error from the following line. Please have a look.

HGSearchResult<HGHandle> rs = graph.find(HGQuery.hg.eq(key));/

and the error msg is 

Exception in thread "main" java.lang.NullPointerException

at src.Test1.HGclientTest.deletetest(HGclientTest.java:40)

at src.Test1.HGclientTest.main(HGclientTest.java:123)

what does it means?

[ZARYAB ARIF]

Hi Boris,

String  key="found";
       HGSearchResult<HGHandle> record =graph.find(HGQuery.hg.eq(key));
try{
           HGHandle handle=record.next();
           System.out.println("search1"+graph.get(handle));
        

           graph.remove(handle);  //at this line code stuck, it shows application running but no output.
}
            finally{
             record.close();}

This code is not working. Please tell me whats wrong in it. 

okay Thanks :)

You query:

http://hypergraphdb.org/?project=hypergraphdb&page=IntroQuerying

".jdb" ??

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[Borislav Iordanov]

This looks perfectly fine to me. 

One quirk about the graph.remove method is that when called with keepIncidentLinks=false (which is the default and how ur calling it), it will recursively remove all links pointing to that atom and all links pointing to them etc. So what might be happening is this atom is part of a large graph component this way, it might simply take a lot of time to delete the whole thing.

[ZARYAB ARIF]

How much time? I waited for 20 minutes but still its running.

[Borislav Iordanov]

That’s probably too much…

I’ve never seen this problem though. How are you sure it’s stuck at that line? Can you create a test program that reproduces that problem? Are you using 1.4-SNAPSHOT or 1.3?

[ZARYAB ARIF]

I am using 1.4 SNAPSHOT. I have been created a test code then I debug the code. Each line is executing successfully but at this line

Graph.remove(handle);

Debugger window shows application is running. 

 

okay Thanks :)

You query:

http://hypergraphdb.org/?project=hypergraphdb&page=IntroQuerying

".jdb" ??

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[Borislav Iordanov]

Hmm, I have no explanation of why that would happen. But I’m very much interested in getting to the bottom of it. So if you can provide some means to reproduce the issue such as a test program, I would greatly appreciate!

Best,

Boris

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[ZARYAB ARIF]

Okay sure.

[ZARYAB ARIF]

Please share your email id. Where i can send the test code which is reproducing this issue. 

Okay sure.

okay Thanks :)

You query:

http://hypergraphdb.org/?project=hypergraphdb&page=IntroQuerying

".jdb" ??

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[Borislav Iordanov]

borislav...@gmail.com 

Thanks! :)

[ZARYAB ARIF]

 Email Sent...

[Borislav Iordanov]

Hi,

Thanks for the small sample reproducing the problem! The issue is an open cursor on the same piece of data that you are trying to delete. This ends up creating an internal deadlock in BerkeleyDB: the remove waits for the lock obtained by the cursor to be released.So if you close the result set (record.close() in your case) before the call to remove, it will work.

Best,
Boris

[ZARYAB ARIF]

Hi Boris,

I have modified the code but there is an error.

org.hypergraphdb.HGException: java.lang.IllegalStateException: Database still has 1 open cursors while trying to close.

at org.hypergraphdb.storage.bje.DefaultIndexImpl.close(DefaultIndexImpl.java:167)

at org.hypergraphdb.storage.bje.BJEStorageImplementation.shutdown(BJEStorageImplementation.java:176)

at org.hypergraphdb.HGStore.close(HGStore.java:382)

at org.hypergraphdb.HyperGraph.close(HyperGraph.java:419)

at deletetest.main(deletetest.java:30)

Caused by: java.lang.IllegalStateException: Database still has 1 open cursors while trying to close.

at com.sleepycat.je.Database.closeInternal(Database.java:503)

at com.sleepycat.je.Database.close(Database.java:348)

at org.hypergraphdb.storage.bje.DefaultIndexImpl.close(DefaultIndexImpl.java:163)

... 4 more

org.hypergraphdb.HGException: java.lang.IllegalStateException: Database still has 1 open cursors while trying to close.

at org.hypergraphdb.storage.bje.DefaultIndexImpl.close(DefaultIndexImpl.java:167)

at org.hypergraphdb.storage.bje.BJEStorageImplementation.shutdown(BJEStorageImplementation.java:176)

at org.hypergraphdb.HGStore.close(HGStore.java:382)

at org.hypergraphdb.HyperGraph.close(HyperGraph.java:419)

at deletetest.main(deletetest.java:30)

Caused by: java.lang.IllegalStateException: Database still has 1 open cursors while trying to close.

at com.sleepycat.je.Database.closeInternal(Database.java:503)

at com.sleepycat.je.Database.close(Database.java:348)

at org.hypergraphdb.storage.bje.DefaultIndexImpl.close(DefaultIndexImpl.java:163)

... 4 more

Problem: 2 locks left

---- LSN: 0x0/0x1181c----

 ThinLockAddr:32501037 Owner:18315851 -1_main_ThreadLocker Waiters: (none)

---- LSN: 0x0/0x1265c----

 ThinLockAddr:19432779 Owner:7905343 -1_main_ThreadLocker Waiters: (none)

Local Cache Usage = 112

Cache Layout: Allocation of resources in the cache.

adminBytes=0

cacheTotalBytes=3,145,840

dataBytes=0

lockBytes=112

sharedCacheTotalBytes=0

Exception in thread "main" java.lang.NullPointerException: HGStore.getLink called with a null handle.

at org.hypergraphdb.HGStore.getLink(HGStore.java:182)

at org.hypergraphdb.HyperGraph$8.call(HyperGraph.java:1667)

at org.hypergraphdb.HyperGraph$8.call(HyperGraph.java:1)

at org.hypergraphdb.transaction.HGTransactionManager.transact(HGTransactionManager.java:400)

at org.hypergraphdb.transaction.HGTransactionManager.ensureTransaction(HGTransactionManager.java:327)

at org.hypergraphdb.HyperGraph.loadAtom(HyperGraph.java:1664)

at org.hypergraphdb.HyperGraph.get(HyperGraph.java:824)

at deletetest.main(deletetest.java:23)

[ZARYAB ARIF]

Resolved this error :) 

[ZARYAB ARIF]

Resolved this error :) 

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>>
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>
>
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> You received this message because you are subscribed to the Google Groups "HyperGraphDB" group.

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