Once it is build what is the next step #517

fbonnet08 · 2021-01-25T16:52:43Z

Hi,

would it be possible to get some proper documentation on how to install and use this framework.

Once one has build successfully what are the next steps in installing this framework?

Could someone point me towards the A to Z installation procedure.

Thanks,
F.

IvarsKarpics · 2021-02-01T12:39:52Z

You can find information for developers here: https://github.com/ispyb/ISPyB/blob/master/documentation/ISPyB_DevelopersGuide.md
To run ispyb you have to use wildlfly (formerly known as jboss). In the internet you can find scripts that allow to run the jboss server, but in a very simplified way one has to configure jboss (config example is in the documentation directory), copy ispyb.ear file to deployments directory and depending from the jboss version run /bin/standalone.sh -b 0.0.0.0 You should be able to access ispyb via http://localhost:8080/ispyb
The "old" java frontend ispyb/ispyb is deprecated and you may have a look at exi frontend (https://github.com/ispyb/EXI) and synchweb (https://github.com/DiamondLightSource/SynchWeb). There is a new python backend called pyispyb which is now in an active development: https://github.com/ispyb/py-ispyb At some point it should serve as a new ispyb backend.

Hope it helps,
Ivars

fbonnet08 · 2021-02-01T13:07:31Z

Hi Ivars, ok thanks. I am not there yet. I trying to get all the database to work and install first, via pycon.sql command. The sql configuration with mssql fails at the first command ! Do I need Microsoft SQL mssql or MySQL with the workbench Frederic.

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On Mon, Feb 1, 2021 at 1:40 PM Ivars Karpics ***@***.***> wrote: Hi @fbonnet08 <https://github.com/fbonnet08> You can find information for developers here: https://github.com/ispyb/ISPyB/blob/master/documentation/ISPyB_DevelopersGuide.md To run ispyb you have to use wildlfly (formerly known as jboss). In the internet you can find scripts that allow to run the jboss server, but in a very simplified way one has to configure jboss (config example is in the documentation directory), copy ispyb.ear file to deployments directory and depending from the jboss version run /bin/standalone.sh -b 0.0.0.0 You should be able to access ispyb via http://localhost:8080/ispyb The "old" java frontend ispyb/ispyb is deprecated and you may have a look at exi frontend (https://github.com/ispyb/EXI) and synchweb ( https://github.com/DiamondLightSource/SynchWeb). There is a new python backend called pyispyb which is now in an active development: https://github.com/ispyb/py-ispyb At some point it should serve as a new ispyb backend. Hope it helps, Ivars — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#517 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFMCZCTPUONL6S7LHF6WLLS42OKRANCNFSM4WSBK7RQ> .

-- Frederic Bonnet [email protected] ========================================================= This email message is intended only for the addressee(s) and contains information which may be confidential and / or copyright. If you are not the intended recipient please do not read, save, forward, disclose, or copy the contents of this email. If this email has been sent to you in error, please delete this email and any copies or links to this email completely and immediately from your system. No representation is made that this email is free of viruses. Virus scanning is recommended and is the responsibility of the recipient. =========================================================

IvarsKarpics · 2021-02-01T13:15:41Z

You should use MySQL or MariaDB

fbonnet08 · 2021-02-01T14:50:29Z

HI Ivars, ok thanks. I got the database MySql setup and it looks like it works. Next I will create a pxadmin account in MySQL with root full privileges and launch the configuration scripts in ## Database creation and update Run the following creation scripts from the `ispyb-ejb` module (note that this requires the `pxadmin` database user to exist and have full permissions): 1. `ispyb-ejb/db/pyconfig.sql`: This corresponds to the menu options and contains both structure and data. 2. `ispyb-ejb/db/pydb.sql`: This corresponds to the ISPyB metadata and contains only the database structure. 3. `ispyb-ejb/db/schemastatus.sql`: This corresponds to the `SchemaStatus` table and contains both structure and data. The entries indicate which update scripts have been run. 4. `ispyb-ejb/db/ispybAutoprocAttachment.sql`: This corresponds to the type and names of different autoPROC attachments. Please note that the path in the doc is not quite right and it is ispyb-ejb/db/schemastatus.sql and not ispyb-ejb/db/scripts/schemastatus.sql Once this is done I can then try to do what you mention earlier in your email or do I need other setups as well? Thanks, Frederic.

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On Mon, Feb 1, 2021 at 2:15 PM Ivars Karpics ***@***.***> wrote: You should use MySQL or MariaDB — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#517 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFMCZHULGHFEGAJHJR53QDS42SQ3ANCNFSM4WSBK7RQ> .

-- Frederic Bonnet [email protected] ========================================================= This email message is intended only for the addressee(s) and contains information which may be confidential and / or copyright. If you are not the intended recipient please do not read, save, forward, disclose, or copy the contents of this email. If this email has been sent to you in error, please delete this email and any copies or links to this email completely and immediately from your system. No representation is made that this email is free of viruses. Virus scanning is recommended and is the responsibility of the recipient. =========================================================

fbonnet08 · 2021-02-01T16:29:46Z

Hi Ivar, I got 1. `ispyb-ejb/db/pyconfig.sql` 2. `ispyb-ejb/db/pydb.sql` 3.`ispyb-ejb/db/schemastatus.sql` 4. `ispyb-ejb/db/ispybAutoprocAttachment.sql` to pass without error with the following commands: sudo mysql -u pxadmin -p pyconfig < ispyb-ejb/db/pyconfig.sql > ~/Leiden/SourceCode/MySQL/output_ispyb-ejb_pyconfig.log sudo mysql -u pxadmin -p pyconfig < ispyb-ejb/db/pydb.sql > ~/Leiden/SourceCode/MySQL/output_ispyb-ejb_pydb.log sudo mysql -u pxadmin -p pyconfig < ispyb-ejb/db/schemastatus.sql > ~/Leiden/SourceCode/MySQL/output_ispyb-ejb_schemastatus.log sudo mysql -u pxadmin -p pyconfig < ispyb-ejb/db/IspybAutoProcAttachment.sql > ~/Leiden/SourceCode/MySQL/output_ispyb-ejb_IspybAutoProcAttachment.log respectively after having created mysql> CREATE DATABASE pyconfig; mysql> CREATE DATABASE pydb; Then what do I need to do next? Thanks, Frederic.

…

On Mon, Feb 1, 2021 at 2:15 PM Ivars Karpics ***@***.***> wrote: You should use MySQL or MariaDB — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#517 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFMCZHULGHFEGAJHJR53QDS42SQ3ANCNFSM4WSBK7RQ> .

-- Frederic Bonnet [email protected] ========================================================= This email message is intended only for the addressee(s) and contains information which may be confidential and / or copyright. If you are not the intended recipient please do not read, save, forward, disclose, or copy the contents of this email. If this email has been sent to you in error, please delete this email and any copies or links to this email completely and immediately from your system. No representation is made that this email is free of viruses. Virus scanning is recommended and is the responsibility of the recipient. =========================================================

IvarsKarpics · 2021-02-01T18:07:11Z

Hi Frederic,

You have to run update scripts if you are using master branch. Info from doc:
The creation scripts are normally updated for each tag, but if you are using the master branch, you may have to run the update scripts in ispyb-ejb/db/scripts/ahead.

Cheers,
Ivars

fbonnet08 · 2021-02-01T18:44:40Z

Hi Ivars, ok thanks. I have noticed that both schemastatus and ispybAutoprocAttachment are now part of the pyconfig database and not the pydb database. is that correct? Will it still work? Thanks, Frederic.

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On Mon, Feb 1, 2021 at 7:07 PM Ivars Karpics ***@***.***> wrote: Hi Frederic, You have to run update scripts if you are using master branch. Info from doc: The creation scripts are normally updated for each tag, but if you are using the master branch, you may have to run the update scripts in ispyb-ejb/db/scripts/ahead. Cheers, Ivars — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#517 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFMCZD4RIM4AI63QUYNLOLS43UWBANCNFSM4WSBK7RQ> .

-- Frederic Bonnet [email protected] ========================================================= This email message is intended only for the addressee(s) and contains information which may be confidential and / or copyright. If you are not the intended recipient please do not read, save, forward, disclose, or copy the contents of this email. If this email has been sent to you in error, please delete this email and any copies or links to this email completely and immediately from your system. No representation is made that this email is free of viruses. Virus scanning is recommended and is the responsibility of the recipient. =========================================================

IvarsKarpics · 2021-02-02T06:31:13Z

Hmm, both table should be in pydb database. Thats a bug and should be fixed.

fbonnet08 · 2021-02-02T09:33:17Z

Hi Ivars, yes indeed there are these two tables in pydb that is why I get the following:

$ sudo mysql -u pxadmin -p pydb < ispyb-ejb/db/schemastatus.sql >

~/Leiden/SourceCode/MySQL/output_ispyb-ejb_schemastatus.log Enter password: ERROR 1050 (42S01) at line 31: Table 'SchemaStatus' already exists

$ sudo mysql -u pxadmin -p pyconfig < ispyb-ejb/db/schemastatus.sql >

~/Leiden/SourceCode/MySQL/output_ispyb-ejb_schemastatus.log Enter password: So it does not flag an error when I use pyconfig but I do when I use pydb. These two tables must have been created via the other two previous scripts. Frederic.

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On Tue, Feb 2, 2021 at 7:31 AM Ivars Karpics ***@***.***> wrote: Hmm, both table should be in pydb database. Thats a bug and should be fixed. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#517 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFMCZHHU6DWHJ4YMV4EMDTS46L37ANCNFSM4WSBK7RQ> .

-- Frederic Bonnet [email protected] ========================================================= This email message is intended only for the addressee(s) and contains information which may be confidential and / or copyright. If you are not the intended recipient please do not read, save, forward, disclose, or copy the contents of this email. If this email has been sent to you in error, please delete this email and any copies or links to this email completely and immediately from your system. No representation is made that this email is free of viruses. Virus scanning is recommended and is the responsibility of the recipient. =========================================================

fbonnet08 · 2021-02-02T13:28:31Z

Hi Ivars, I used the branch from https://ispyb.github.io/ISPyB/

$ git clone https://github.com/ispyb/ISPyB

I have ran the ahead scripts as follows: