OWL-API IRIMapper usage - owl-api

I'm mapping a remote ontology to a local copy as following:
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
IRI documentIRI = IRI.create(new File("ontologies/localOntology.owl"));
IRI remoteIRI=IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl");
SimpleIRIMapper mapper = new SimpleIRIMapper(remoteIRI, documentIRI);
manager.getIRIMappers().add(mapper);
OWLOntology ontology = manager.loadOntology(remoteIRI);
manager.saveOntology(ontology, new OWLXMLDocumentFormat());
Is this the correct way to use IRIMap? What if localOntology.owl contains something different from the remote ontology? It seems that I'm manipulating the local ontology regardless the content of the remote ontology, since, for example, if we use ontology.getAxiomCount() with localOntology.owl an empty ontology, we get "0", coherently with the content of localOntology but not with the remote ontology. Should "ontology" be aligned with the remote ontology but stored in localOntology.owl after the mapping? Thank you.

The purpose of IRI mapping is just to redirect from one IRI to another - the most common use case is to avoid downloading a remote ontology multiple times. However, ensuring the local copy is in sync with the remote one (assuming the remote one is the 'master' ontology, the one other users will be using in their systems) is a task that no IRI mapper implementation undertakes.
There is no universal strategy for resolving diffs between local and remote ontology - for example, in some situations synchronizing the remote and local ontology will always be the right thing to do; when the local copy is used as a cache, losing remote updates is a bug.
In other situations, updating from the remote ontology is wrong - for example, when testing the performance of different reasoners on an ontology, if the ontology imports remote ontologies that might change during the experiment, then using an unchanging local copy is better than picking the latest updates; a change might affect the comparison results in undetectable ways, and break repeatability.
Therefore, OWL API leaves the implementation of the correct strategy to the calling code, rather than take decisions which might cause issues that are difficult to detect.

Related

Environment variable as custom metadata type in Salesforce

I am trying to represent environment variables in the Salesforce codebase and came across Custom Metadata Types. So based on which Sandbox I am in, I want to vary the baseURL of an external service that I am hitting from my apex class. I want to avoid hard coding anything in the class, and hence trying to find out an environment variable like solution.
How would you represent the URL as a custom metadata type? Also, how can I access it in the class? What happens when a qa sandbox is refreshed from prod? Do they custom metadata type records get overridden?
How are you calling that external service? If it's truly a base url you might be better of using "named credential" for it. It'll abstract the base url away for you, include authentication or certificate if you have to present any...
Failing that - custom metadata might be a poor choice. They're kind of dictionary objects, you can add more (but not from apex) but if you deploy stuff using Git/Ant/SFDX CLI rather than changesets it'd become bit pain, you'd need different custom metadata value for sandbox vs prod. Kinda defeats the purpose.
You might be better off using custom setting instead (hierarchy is enabled by default, list you'd have to flip a checkbox in setup. List is useful if you need key-value kind of pairs, similar to custom metadata): https://salesforce.stackexchange.com/questions/74049/what-is-the-difference-between-custom-settings-and-custom-metadata-types
And you can modify them with Apex too. Which means that in ideal world you could have a "postcopy" class running as soon as sandbox is refreshed that overwrites the custom setting with the non-prod value. For named credential I don't think you can pull it off, you'd need a mini deployment that changes it or manual step (have you seen https://salesforce.stackexchange.com/q/955/799 ?)

SSIS - best practices for connection managers -- compose out of parameters?

I've worked a lot with Pentaho PDI so some obvious things jump out at me.
I'll call Connection Managers "CMs" from here on out.
Obvious, Project CMs > Package CMs, for extensability/ re-usability. Seems a rare case indeed where you need a Package-level CM.
But I'm wondering another best practice. Should each Project CM itself be composed of variables? (or parameters I guess).
Let's talk in concrete terms. There are specific database sources. Let's call two of them in use Finance2000 and ETL_Log_db. These have specific connection strings (password, source, etc).
Now if you have 50 packages pulling from Finance2000 and also using ETL_Log_db ... well ... what happens if the databases change? (host, name, user, password?)
Say it's now Finance3000.
Well I guess you can go into Finance2000 and change the source, specs, and even the name itself --- everything should work then, right?
Or should you simply build a project level database called "FinanceX" or whatever and make it comprised of parameters so the connectoin string is something like #Source + # credentials + # whatever?
Or is that simply redundant?
I can see one benefit of the parameter method is that you can change the "logging database" on the fly even within the package itself during execution, instead of passing parameters merely at runtime. I think. I don't know. I don't have a mountain of experience with SSIS yet.
SSIS, starting from version 2012, has SSIS Catalog DB. You can create all your 50 packages in one Project, and all these packages share the same Project Connection Managers.
Then you deploy this Project into the SSIS Catalog; the Project automatically exposes Connection Manager parameters with CM prefix. The CM parameters are parts of the Connection Manager definition.
In the SSIS Catalog you can create so called Environments. In the Environment you define variables with name and datatype, and store its value.
Then - the most interesting part - you can associate the Environment and the uploaded Project. This allows you to bind project parameter with environment variable.
At Package Execution - you have to specify which Environment to use when specifying Connection Strings. Yes, you can have several Environments in the Catalog, and choose when starting Package.
Cool, isn't it?
Moreover, passwords are stored encrypted, so none can copy it. Values of these Environment Variables can be configured by support engineers who has no knowledge of SSIS packages.
More Info on SSIS Catalog and Environments from MS Docs.
I'll give my fair share of experience.
I recently had a similar experience at work, our 2 main databases name's changed, and i had no issue, or downtime on the schedules.
The model we use is not the best, but for this, and for other reasons, it is quite confortable to work with. We use BAT files to pass named parameters into a "Master" Job, and basically depending on 2 parameters, the Job runs on an alternate Database/Host.
The model we use is, in every KTR/KJB we use a variable ${host} and ${dbname}, these parameters are passed with each BAT file. So when we had to change the names of the hosts and databases, it was a simple Replace All Text Match in NotePad++, and done, 2.000+ BAT Files fixed, and no downtime.
Having a variable for the Host/DB Name for both Client Connection and Logging Connection lets you have that flexibility when things change radically.
You can also use the kettle.properties file for the logging connection.

storing database values in source control

We have a table in our our database that stores XSL's and XSD's that are applied to XML documents created in our application. This table is versioned in the sense that each time a change is made, a new row is created.
I'm trying to propose that we store the XSL's and XSD's as files in our Source control system instead of relying on the database to track the history. Each time a file is updated, we would deploy the new version to the database.
I don't seem to be getting much agreement on the issue. can anyone help me out with pros and cons of this approach? Perhaps I'm missing something.
XSL and XSD files are part of the application and so ought to be kept under source control. That's just obvious. Even if somebody wanted to catgorise them as data they would be reference data and so - in my book at least - would need to be kept under source control. This is because reference data is part of the application and so part of its configuration. For instance, applications which use the database to store values for drop downs or to implement business rules need to be certain that it holds the right version of the data.
The only argument for keeping multiple versions of the files in the dtabase would be if you might need to process older versions of the XML files. This depends on the nature of your application. Certainly I have worked on systems where XML files / messages came from external (third party) systems, where we really had no control over the format of the messages sent. So for a variety of reasons we needed to be able to handle incoming XML regardless of whether its structure was current or historical. But is is in addition to storing the files in a source control repository, not instead of.

Web-App : Keeping trace of the version of the application in database?

We are building a webapp which is shipped to several client as a debian package. Each client runs his own server. But the update and support is done by us.
We make regular releases of the product, with a clean version number. Most of the users get an automatic update (by Puppet), some others don't.
We want to keep a trace of the version of the application (in order to allow the user to check the version in an "about" section, and for our support to help the user more accurately).
We plan to store the version of the code and the version of the base in our database, and to keep the info up to date automatically.
Is that a good idea ?
The other alternative we see is a file.
EDIT : The code and database schema are updated together. ( if we update to version x.y.z , both code and database go to x.y.z )
Using a table to track every change to a schema as described in this post is a good practice that I'd definitely suggest to follow.
For the application, if it is shipped independently of the database (which is not clear to me), I'd embed a file in the package (and thus not use the database to store the version of the web application).
If not and thus if both the application and the database versions are maintained in sync, then I'd just use the information stored in the database.
As a general rule, I would have both, DB version and application version. The problem here is how "private" is the database. If the database is "private" to the application, and user never modifies the schema then your initial solution is fine. In my experience, databases which accumulate several years of data stop being private, it means that users add a table or two and access data using some reporting tool; from that point on the database is not exclusively used by the application any more.
UPDATE
One more thing to consider is users (application) not being able to connect to the DB and calling for support. For this case it would be better to have version, etc.. stored on file system.
Assuming there are no compelling reasons to go with one approach or the other, I think I'd go with keeping them in the database.
I'd put them in both places. Then when running your about function you quickly check that they are both the same, and if they aren't you can display extra information about the version mismatch. If they're the same then you will only need to display one of them.
I've generally found users can do "clever" things like revert databases back to old versions by manually copying directories around "because they can" so defensively dealing with it is always a good idea.

How can I put a database under git (version control)?

I'm doing a web app, and I need to make a branch for some major changes, the thing is, these changes require changes to the database schema, so I'd like to put the entire database under git as well.
How do I do that? is there a specific folder that I can keep under a git repository? How do I know which one? How can I be sure that I'm putting the right folder?
I need to be sure, because these changes are not backward compatible; I can't afford to screw up.
The database in my case is PostgreSQL
Edit:
Someone suggested taking backups and putting the backup file under version control instead of the database. To be honest, I find that really hard to swallow.
There has to be a better way.
Update:
OK, so there' no better way, but I'm still not quite convinced, so I will change the question a bit:
I'd like to put the entire database under version control, what database engine can I use so that I can put the actual database under version control instead of its dump?
Would sqlite be git-friendly?
Since this is only the development environment, I can choose whatever database I want.
Edit2:
What I really want is not to track my development history, but to be able to switch from my "new radical changes" branch to the "current stable branch" and be able for instance to fix some bugs/issues, etc, with the current stable branch. Such that when I switch branches, the database auto-magically becomes compatible with the branch I'm currently on.
I don't really care much about the actual data.
Take a database dump, and version control that instead. This way it is a flat text file.
Personally I suggest that you keep both a data dump, and a schema dump. This way using diff it becomes fairly easy to see what changed in the schema from revision to revision.
If you are making big changes, you should have a secondary database that you make the new schema changes to and not touch the old one since as you said you are making a branch.
I'm starting to think of a really simple solution, don't know why I didn't think of it before!!
Duplicate the database, (both the schema and the data).
In the branch for the new-major-changes, simply change the project configuration to use the new duplicate database.
This way I can switch branches without worrying about database schema changes.
EDIT:
By duplicate, I mean create another database with a different name (like my_db_2); not doing a dump or anything like that.
Use something like LiquiBase this lets you keep revision control of your Liquibase files. you can tag changes for production only, and have lb keep your DB up to date for either production or development, (or whatever scheme you want).
Irmin (branching + time travel)
Flur.ee (immutable + time travel + graph query)
XTDB (formerly called 'CruxDB') (time travel + query)
TerminusDB (immutable + branching + time travel + Graph Query!)
DoltDB (branching + time-travel + SQL query)
Quadrable (branching + remote state verification)
EdgeDB (no real time travel, but migrations derived by the compiler after schema changes)
Migra (diffing for Postgres schemas/data. Auto-generate migration scripts, auto-sync db state)
ImmuDB (immutable + time-travel)
I've come across this question, as I've got a similar problem, where something approximating a DB based Directory structure, stores 'files', and I need git to manage it. It's distributed, across a cloud, using replication, hence it's access point will be via MySQL.
The gist of the above answers, seem to similarly suggest an alternative solution to the problem asked, which kind of misses the point, of using Git to manage something in a Database, so I'll attempt to answer that question.
Git is a system, which in essence stores a database of deltas (differences), which can be reassembled, in order, to reproduce a context. The normal usage of git assumes that context is a filesystem, and those deltas are diff's in that file system, but really all git is, is a hierarchical database of deltas (hierarchical, because in most cases each delta is a commit with at least 1 parents, arranged in a tree).
As long as you can generate a delta, in theory, git can store it. The problem is normally git expects the context, on which it's generating delta's to be a file system, and similarly, when you checkout a point in the git hierarchy, it expects to generate a filesystem.
If you want to manage change, in a database, you have 2 discrete problems, and I would address them separately (if I were you). The first is schema, the second is data (although in your question, you state data isn't something you're concerned about). A problem I had in the past, was a Dev and Prod database, where Dev could take incremental changes to the schema, and those changes had to be documented in CVS, and propogated to live, along with additions to one of several 'static' tables. We did that by having a 3rd database, called Cruise, which contained only the static data. At any point the schema from Dev and Cruise could be compared, and we had a script to take the diff of those 2 files and produce an SQL file containing ALTER statements, to apply it. Similarly any new data, could be distilled to an SQL file containing INSERT commands. As long as fields and tables are only added, and never deleted, the process could automate generating the SQL statements to apply the delta.
The mechanism by which git generates deltas is diff and the mechanism by which it combines 1 or more deltas with a file, is called merge. If you can come up with a method for diffing and merging from a different context, git should work, but as has been discussed you may prefer a tool that does that for you. My first thought towards solving that is this https://git-scm.com/book/en/v2/Customizing-Git-Git-Configuration#External-Merge-and-Diff-Tools which details how to replace git's internal diff and merge tool. I'll update this answer, as I come up with a better solution to the problem, but in my case I expect to only have to manage data changes, in-so-far-as a DB based filestore may change, so my solution may not be exactly what you need.
There is a great project called Migrations under Doctrine that built just for this purpose.
Its still in alpha state and built for php.
http://docs.doctrine-project.org/projects/doctrine-migrations/en/latest/index.html
Take a look at RedGate SQL Source Control.
http://www.red-gate.com/products/sql-development/sql-source-control/
This tool is a SQL Server Management Studio snap-in which will allow you to place your database under Source Control with Git.
It's a bit pricey at $495 per user, but there is a 28 day free trial available.
NOTE
I am not affiliated with RedGate in any way whatsoever.
I've released a tool for sqlite that does what you're asking for. It uses a custom diff driver leveraging the sqlite projects tool 'sqldiff', UUIDs as primary keys, and leaves off the sqlite rowid. It is still in alpha so feedback is appreciated.
Postgres and mysql are trickier, as the binary data is kept in multiple files and may not even be valid if you were able to snapshot it.
https://github.com/cannadayr/git-sqlite
I want to make something similar, add my database changes to my version control system.
I am going to follow the ideas in this post from Vladimir Khorikov "Database versioning best practices". In summary i will
store both its schema and the reference data in a source control system.
for every modification we will create a separate SQL script with the changes
In case it helps!
You can't do it without atomicity, and you can't get atomicity without either using pg_dump or a snapshotting filesystem.
My postgres instance is on zfs, which I snapshot occasionally. It's approximately instant and consistent.
I think X-Istence is on the right track, but there are a few more improvements you can make to this strategy. First, use:
$pg_dump --schema ...
to dump the tables, sequences, etc and place this file under version control. You'll use this to separate the compatibility changes between your branches.
Next, perform a data dump for the set of tables that contain configuration required for your application to operate (should probably skip user data, etc), like form defaults and other data non-user modifiable data. You can do this selectively by using:
$pg_dump --table=.. <or> --exclude-table=..
This is a good idea because the repo can get really clunky when your database gets to 100Mb+ when doing a full data dump. A better idea is to back up a more minimal set of data that you require to test your app. If your default data is very large though, this may still cause problems though.
If you absolutely need to place full backups in the repo, consider doing it in a branch outside of your source tree. An external backup system with some reference to the matching svn rev is likely best for this though.
Also, I suggest using text format dumps over binary for revision purposes (for the schema at least) since these are easier to diff. You can always compress these to save space prior to checking in.
Finally, have a look at the postgres backup documentation if you haven't already. The way you're commenting on backing up 'the database' rather than a dump makes me wonder if you're thinking of file system based backups (see section 23.2 for caveats).
What you want, in spirit, is perhaps something like Post Facto, which stores versions of a database in a database. Check this presentation.
The project apparently never really went anywhere, so it probably won't help you immediately, but it's an interesting concept. I fear that doing this properly would be very difficult, because even version 1 would have to get all the details right in order to have people trust their work to it.
This question is pretty much answered but I would like to complement X-Istence's and Dana the Sane's answer with a small suggestion.
If you need revision control with some degree of granularity, say daily, you could couple the text dump of both the tables and the schema with a tool like rdiff-backup which does incremental backups. The advantage is that instead of storing snapshots of daily backups, you simply store the differences from the previous day.
With this you have both the advantage of revision control and you don't waste too much space.
In any case, using git directly on big flat files which change very frequently is not a good solution. If your database becomes too big, git will start to have some problems managing the files.
Here is what i am trying to do in my projects:
separate data and schema and default data.
The database configuration is stored in configuration file that is not under version control (.gitignore)
The database defaults (for setting up new Projects) is a simple SQL file under version control.
For the database schema create a database schema dump under the version control.
The most common way is to have update scripts that contains SQL Statements, (ALTER Table.. or UPDATE). You also need to have a place in your database where you save the current version of you schema)
Take a look at other big open source database projects (piwik,or your favorite cms system), they all use updatescripts (1.sql,2.sql,3.sh,4.php.5.sql)
But this a very time intensive job, you have to create, and test the updatescripts and you need to run a common updatescript that compares the version and run all necessary update scripts.
So theoretically (and thats what i am looking for) you could
dumped the the database schema after each change (manually, conjob, git hooks (maybe before commit))
(and only in some very special cases create updatescripts)
After that in your common updatescript (run the normal updatescripts, for the special cases) and then compare the schemas (the dump and current database) and then automatically generate the nessesary ALTER Statements. There some tools that can do this already, but haven't found yet a good one.
What I do in my personal projects is, I store my whole database to dropbox and then point MAMP, WAMP workflow to use it right from there.. That way database is always up-to-date where ever I need to do some developing. But that's just for dev! Live sites is using own server for that off course! :)
Storing each level of database changes under git versioning control is like pushing your entire database with each commit and restoring your entire database with each pull.
If your database is so prone to crucial changes and you cannot afford to loose them, you can just update your pre_commit and post_merge hooks.
I did the same with one of my projects and you can find the directions here.
That's how I do it:
Since your have free choise about DB type use a filebased DB like e.g. firebird.
Create a template DB which has the schema that fits your actual branch and store it in your repository.
When executing your application programmatically create a copy of your template DB, store it somewhere else and just work with that copy.
This way you can put your DB schema under version control without the data. And if you change your schema you just have to change the template DB
We used to run a social website, on a standard LAMP configuration. We had a Live server, Test server, and Development server, as well as the local developers machines. All were managed using GIT.
On each machine, we had the PHP files, but also the MySQL service, and a folder with Images that users would upload. The Live server grew to have some 100K (!) recurrent users, the dump was about 2GB (!), the Image folder was some 50GB (!). By the time that I left, our server was reaching the limit of its CPU, Ram, and most of all, the concurrent net connection limits (We even compiled our own version of network card driver to max out the server 'lol'). We could not (nor should you assume with your website) put 2GB of data and 50GB of images in GIT.
To manage all this under GIT easily, we would ignore the binary folders (the folders containing the Images) by inserting these folder paths into .gitignore. We also had a folder called SQL outside the Apache documentroot path. In that SQL folder, we would put our SQL files from the developers in incremental numberings (001.florianm.sql, 001.johns.sql, 002.florianm.sql, etc). These SQL files were managed by GIT as well. The first sql file would indeed contain a large set of DB schema. We don't add user-data in GIT (eg the records of the users table, or the comments table), but data like configs or topology or other site specific data, was maintained in the sql files (and hence by GIT). Mostly its the developers (who know the code best) that determine what and what is not maintained by GIT with regards to SQL schema and data.
When it got to a release, the administrator logs in onto the dev server, merges the live branch with all developers and needed branches on the dev machine to an update branch, and pushed it to the test server. On the test server, he checks if the updating process for the Live server is still valid, and in quick succession, points all traffic in Apache to a placeholder site, creates a DB dump, points the working directory from 'live' to 'update', executes all new sql files into mysql, and repoints the traffic back to the correct site. When all stakeholders agreed after reviewing the test server, the Administrator did the same thing from Test server to Live server. Afterwards, he merges the live branch on the production server, to the master branch accross all servers, and rebased all live branches. The developers were responsible themselves to rebase their branches, but they generally know what they are doing.
If there were problems on the test server, eg. the merges had too many conflicts, then the code was reverted (pointing the working branch back to 'live') and the sql files were never executed. The moment that the sql files were executed, this was considered as a non-reversible action at the time. If the SQL files were not working properly, then the DB was restored using the Dump (and the developers told off, for providing ill-tested SQL files).
Today, we maintain both a sql-up and sql-down folder, with equivalent filenames, where the developers have to test that both the upgrading sql files, can be equally downgraded. This could ultimately be executed with a bash script, but its a good idea if human eyes kept monitoring the upgrade process.
It's not great, but its manageable. Hope this gives an insight into a real-life, practical, relatively high-availability site. Be it a bit outdated, but still followed.
Update Aug 26, 2019:
Netlify CMS is doing it with GitHub, an example implementation can be found here with all information on how they implemented it netlify-cms-backend-github
I say don't. Data can change at any given time. Instead you should only commit data models in your code, schema and table definitions (create database and create table statements) and sample data for unit tests. This is kinda the way that Laravel does it, committing database migrations and seeds.
I would recommend neXtep (Link removed - Domain was taken over by a NSFW-Website) for version controlling the database it has got a good set of documentation and forums that explains how to install and the errors encountered. I have tested it for postgreSQL 9.1 and 9.3, i was able to get it working for 9.1 but for 9.3 it doesn't seems to work.
Use a tool like iBatis Migrations (manual, short tutorial video) which allows you to version control the changes you make to a database throughout the lifecycle of a project, rather than the database itself.
This allows you to selectively apply individual changes to different environments, keep a changelog of which changes are in which environments, create scripts to apply changes A through N, rollback changes, etc.
I'd like to put the entire database under version control, what
database engine can I use so that I can put the actual database under
version control instead of its dump?
This is not database engine dependent. By Microsoft SQL Server there are lots of version controlling programs. I don't think that problem can be solved with git, you have to use a pgsql specific schema version control system. I don't know whether such a thing exists or not...
Use a version-controlled database, of which there are now several.
https://www.dolthub.com/blog/2021-09-17-database-version-control/
These products don't apply version control on top of another type of database -- they are their own database engines that support version control operations. So you need to migrate to them or start building on them in the first place.
I write one of them, DoltDB, which combines the interfaces of MySQL and Git. Check it out here:
https://github.com/dolthub/dolt
I wish it were simpler. Checking in the schema as a text file is a good start to capture the structure of the DB. For the content, however, I have not found a cleaner, better method for git than CSV files. One per table. The DB can then be edited on multiple branches and merges extremely well.

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