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So I'm designing this blog engine and I'm trying to just keep my blog data without considering comments or membership system or any other type of multi-user data.
The blog itself is surrounded around 2 types of data, the first is the actual blog post entry which consists of: title, post body, meta data (mostly dates and statistics), so it's really simple and can be represented by simple json object. The second type of data is the blog admin configuration and personal information. Comment system and other will be implemented using disqus.
My main concern here is the ability of such engine to scale with spiked visits (I know you might argue this but lets take it for granted). So since I've started this project I'm moving well with the rest of my stack except the data layer. Now I've been having this dilemma choosing the database, I've considered MongoDB but some reviews and articles/benchmarking were suggesting slow reads after collections read certain size. Next I was looking at Redis and using its persistence features RDB and AOF, while Redis is good at both fast reading/writing I'm afraid of using it because I'm not familiar with it. And this whole search keeps going on to things like "PostgreSQL 9.4 is now faster than MongoDB for storing JSON documents" etc.
So is there any way I can settle this issue for good? considering that I only need to represent my data in key,value structure and only require fast reading but not writing and the ability to be fault tolerant.
Thank you
If I were you I would start small and not try to optimize for big data just yet. A lot of blogs you read about the downsides of a NoSQL solution are around large data sets - or people that are trying to do relational things with a database designed for de-normalized data.
My list of databases to consider:
Mongo. It has huge community support and based on recent funding - it's going to be around for a while. It runs very well on a single instance and a basic replica set. It's easy to set up and free, so it's worth spending a day or two running your own tests to settle the issue once and for all. Don't trust a blog.
Couchbase. Supports key/value storage and also has persistence to disk. http://www.couchbase.com/couchbase-server/features Also has had some recent funding so hopefully that means stability. =)
CouchDB/PouchDB. You can use PouchDB purely on the client side and it can connect to a server side CouchDB. CouchDB might not have the same momentum as Mongo or Couchbase, but it's an actively supported product and does key/value with persistence to disk.
Riak. http://basho.com/riak/. Another NoSQL that scales and is a key/value store.
You can install and run a proof-of-concept on all of the above products in a few hours. I would recommend this for the following reasons:
A given database might scale and hit your points, but be unpleasant to use. Consider picking a database that feels fun! Sort of akin to picking Ruby/Python over Java because the syntax is nicer.
Your use case and domain will be fairly unique. Worth testing various products to see what fits best.
Each database has quirks and you won't find those until you actually try one. One might have quirks that are passable, one will have quirks that are a show stopper.
The benefit of trying all of them is that they all support schemaless data, so if you write JSON, you can use all of them! No need to create objects in your code for each database.
If you abstract the database correctly in code, swapping out data stores won't be that painful. In other words, your code will be happier if you make it easy to swap out data stores.
This is only an option for really simple CMSes, but it sounds like that's what you're building.
If your blog is super-simple as you describe and your main concern is very high traffic then the best option might be to avoid a database entirely and have your CMS generate static files instead. By doing this, you eliminate all your database concerns completely.
It's not the best option if you're doing anything dynamic or complex, but in this small use case it might fit the bill.
This is linked to my other question when to move from a spreadsheet to RDBMS
Having decided to move to an RDBMS from an excel book, here is what I propose to do.
The existing data is loosely structured across two sheets in a work-book. The first sheet contains main record. The second sheet allows additional data.
My target DBMS is mysql, but I'm open to suggestions.
Define RDBMS schema
Define, say, web-services to interface with the database so the same can be used for both, UI and migration.
Define a migration script to
Read each group of affiliated rows from the spreadsheet
Apply validation/constraints
Write to RDBMS using the web-service
Define macros/functions/modules in spreadsheet to enforce validation where possible. This will allow use of the existing system while the new comes up. At the same time, ( i hope ) it will reduce migration failures when the move is eventually made.
What strategy would you follow?
There are two aspects to this question.
Data migration
Your first step will be to "Define RDBMS schema" but how far are you going to go with it? Spreadsheets are notoriously un-normalized and so have lots of duplication. You say in your other question that "Data is loosely structured, and there are no explicit constraints." If you want to transform that into a rigourously-defined schema (at least 3NF) then you are going to have to do some cleansing. SQL is the best tool for data manipulation.
I suggest you build two staging tables, one for each worksheet. Define the columns as loosely as possible (big strings basically) so that it is easy to load the spreadsheets' data. Once you have the data loaded into the staging tables you can run queries to assess the data quality:
how many duplicate primary keys?
how many different data formats?
what are the look-up codes?
do all the rows in the second worksheet have parent records in the first?
how consistent are code formats, data types, etc?
and so on.
These investigations will give you a good basis for writing the SQL with which you can populate your actual schema.
Or it might be that the data is so hopeless that you decide to stick with just the two tables. I think that is an unlikely outcome (most applications have some underlying structure, we just have to dig deep enough).
Data Loading
Your best bet is to export the spreadsheets to CSV format. Excel has a wizard to do this. Use it (rather than doing Save As...). If the spreadsheets contain any free text at all the chances are you will have sentences which contain commas, so make sure you choose a really safe separator, such as ^^~
Most RDBMS tools have a facility to import data from CSV files. Postgresql and Mysql are the obvious options for an NGO (I presume cost is a consideration) but both SQL Server and Oracle come in free (if restricted) Express editions. SQL Server obviously has the best integration with Excel. Oracle has a nifty feature called external tables which allow us to define a table where the data is held in a CSV file, removing the need for staging tables.
One other thing to consider is Google App Engine. This uses Big Table rather than an RDBMS but that might be more suited to your loosely-structured data. I suggest it because you mentioned Google Docs as an alternative solution. GAE is an attractive option because it is free (more or less, they start charging if usage exceeds some very generous thresholds) and it would solve the app sharing issue with those other NGOs. Obviously your organisation may have some qualms about Google hosting their data. It depends on what field they are operating in, and the sensitivity of the information.
Obviously, you need to create a target DB and the necessary table structure.
I would skip the web services and write a groovy script which reads the .xls (using the POI library), validates and saves the data in the database.
In my view, anything more involved (web services, GUI...) is not justified: these kinds of tasks are very well suited for scripts because they're concise and extremely flexible while things like performance, code base scalability and such are less of an issue here. Once you have something that works, you will be able to adapt the script to any future document with different data anomalies you run into in a matter of minutes or a few hours.
This is all assuming your data isn't in perfect order and needs to be filtered and/or cleaned.
Alternatively, if the data and validation rules aren't too complex, you can probably get good results with using a visual data transfer tool like Kettle: you just define the .xls as your source, the database table as the table, some validation/filter rules if needed and trigger the loading process. Quite painless.
If you'd rather use a tool that roll your own, check out SeekWell, which lets you write to your database from Google Sheets. Once you define your schema, Select the tables into a Sheet, then edit or insert the records and mark them for the appropriate action (e.g., update, insert, etc.). Set the schedule for the update and you're done. Read more about it here. Disclaimer--I'm a co-founder.
Hope that helps!
You might be doing more work than you need to. Excel spreadsheets can be saved as CVS or XML files and many RDBMS clients support importing these files directly into tables.
This could allow you skip writing web service wrappers and migration scripts. Your database constraints would still be properly enforced during any import. If your RDBMS data model or schema is very different from your Excel spreadsheets, however, then some translation would of course have to take place via scripts or XSLT.
I'm in the process of choosing database for my application. I have been using MySQL for the longest time but for my current application Performance and Scalability is important and I know MySQL has its limitation and I have been hearing a lot about key-value stores, column-based DBs and document-based DBs and others. I have looked into:
Cassandra
MongoDB
Redis
CouchDB
They all seem (or claim) to be faster than relational DBs such as MySQL.
I'm using Ruby on Rails and there are clients for all the above so it shouldn't be a problem.
My data model is simple for the most part which is centered on a user object(with rich profile and preferences) related to different items such as photos, videos, posts...etc and each one of these has one tag or more.
The fact that these databases are new there doesn't seem to be a lot of resources for them online. Plus they are in a way structurally different so it will not be trivial to switch from one to another later.
I wish you can give me your input on what DB you think would be most suit my application that will have good performance and scale.
Thanks,
Tam
Step 1) Create your design using whatever technology you are strongest with.
Step 2) Release your social network, begin on researching non-relational databases and master whichever you feel most comfortable with.
Step 3) Refactor your data tier so you could potentially replace MySQL quickly and easily with your newly learned DB technology.
Step 4) Wait for your website to become so big that the need to replace MySQL comes around and begin to plug the holes.
I know this seems kind of cheeky, but really my point is just release your software and start to worry about scale etc. when it actually becomes a concern.
The primary benefit of something like a document database, at least for your app, is that you can treat the entire User glob of info as a single document. You don't have to worry about adding table for properties, or new features, or whatever, rather you can keep the bulk of it in the user document and update it dynamically.
For read often, write rarely, this works a treat.
Now you don't need a "document database" to do something like this. MySQL et al will work just fine with a primary key and a CLOB (text) / BLOB field to hold the document.
Where something like CouchDB (the one that I'm most familiar with in this space) can help is that it has well supported replication, and it's straightforward to create views on specific attributes of the documents (for example, you want all "premiere" members, or whatever).
Plus, since CouchDB is HTTP, it works well with the modern caches and such that are available, which can help you in scaling, especially in, again, read heavy operations.
A lot of this is more about overall architecture than actual tools, so make sure you consider that first.
There is also Tokyo Cabinet which is used by some large sites.
I have not yet used on but my understanding is that when site like Twitter need to turn large numbers of messages round very quickly the overhead of the RDBMS is just to great and starts to slow the response times down significantly.
What you would need to do is look at the advantages you get from an RDBMS and weigh that against it's speed then do the same in reverse for a nosql type database.
RDBMS's give you a standard, they give you security, integrity and a general purpose language based on sets to make data manipulation easier. However if you do not need all or any of that structure you are loosing out on speed.
Prior to SQL was CODASYL and network databases. SQL took ove because of portability and transferability of skills etc. But i think the mobile wired world is changing this and it would be worth investigating.
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I have used Relational DB's a lot and decided to venture out on other types available.
This particular product looks good and promising: http://neo4j.org/
Has anyone used graph-based databases? What are the pros and cons from a usability prespective?
Have you used these in a production environment? What was the requirement that prompted you to use them?
I used a graph database in a previous job. We weren't using neo4j, it was an in-house thing built on top of Berkeley DB, but it was similar. It was used in production (it still is).
The reason we used a graph database was that the data being stored by the system and the operations the system was doing with the data were exactly the weak spot of relational databases and were exactly the strong spot of graph databases. The system needed to store collections of objects that lack a fixed schema and are linked together by relationships. To reason about the data, the system needed to do a lot of operations that would be a couple of traversals in a graph database, but that would be quite complex queries in SQL.
The main advantages of the graph model were rapid development time and flexibility. We could quickly add new functionality without impacting existing deployments. If a potential customer wanted to import some of their own data and graft it on top of our model, it could usually be done on site by the sales rep. Flexibility also helped when we were designing a new feature, saving us from trying to squeeze new data into a rigid data model.
Having a weird database let us build a lot of our other weird technologies, giving us lots of secret-sauce to distinguish our product from those of our competitors.
The main disadvantage was that we weren't using the standard relational database technology, which can be a problem when your customers are enterprisey. Our customers would ask why we couldn't just host our data on their giant Oracle clusters (our customers usually had large datacenters). One of the team actually rewrote the database layer to use Oracle (or PostgreSQL, or MySQL), but it was slightly slower than the original. At least one large enterprise even had an Oracle-only policy, but luckily Oracle bought Berkeley DB. We also had to write a lot of extra tools - we couldn't just use Crystal Reports for example.
The other disadvantage of our graph database was that we built it ourselves, which meant when we hit a problem (usually with scalability) we had to solve it ourselves. If we'd used a relational database, the vendor would have already solved the problem ten years ago.
If you're building a product for enterprisey customers and your data fits into the relational model, use a relational database if you can. If your application doesn't fit the relational model but it does fit the graph model, use a graph database. If it only fits something else, use that.
If your application doesn't need to fit into the current blub architecture, use a graph database, or CouchDB, or BigTable, or whatever fits your app and you think is cool. It might give you an advantage, and its fun to try new things.
Whatever you chose, try not to build the database engine yourself unless you really like building database engines.
We've been working with the Neo team for over a year now and have been very happy. We model scholarly artifacts and their relationships, which is spot on for a graph db, and run recommendation algorithms over the network.
If you are already working in Java, I think that modeling using Neo4j is very straight forward and it has the flattest / fastest performance for R/W of any other solutions we tried.
To be honest, I have a hard time not thinking in terms of a Graph/Network because it's so much easier than designing convoluted table structures to hold object properties and relationships.
That being said, we do store some information in MySQL simply because it's easier for the Business side to run quick SQL queries against. To perform the same functions with Neo we would need to write code that we simply don't have the bandwidth for right now. As soon as we do though, I'm moving all that data to Neo!
Good luck.
Two points:
First, on the data I've been working with the past 5 years in SQL Server, I've recently hit the scalability wall with SQL for the type of queries we need to run (nested relationhsips...you know...graphs). I've been playing around with neo4j, and my lookup times are several orders of magnitude faster when I need this kind of lookup.
Second, to the point that graph databases are outdated. Um...no. Early on, as people were trying to figure out how to store and lookup data efficiently, they created and played with graph and network style database models. These were designed so the physical model reflected the logical model, so their efficiency wasnt that great. This type of data structure was good for semi-structured data, but not as good for structured dense data. So, this IBM dude named Codd was researching efficient ways to arrange and store structured data and came up with the idea for the relational database model. And it was good, and people were happy.
What do we have here? Two tools for two different purposes. Graph database models are very good for representing semi-structured data and the relationships between entities (that may or may not exist). Relational databases are good for structured data that has a very static schema, and where join depths do not go very deep. One is good for one kind of data, the other is good for other kinds of data.
To coin the phrase, there is no Silver Bullet. Its very short sighted to say that graph database models are out of date and to use one gives up 40 years of progress. That's like saying using C is giving up all the technological progress we've gone through to get things like Java and C#. That's not true though. C is a tool that is needed for certain tasks. And Java is a tool for other tasks.
I've been using MySQL for years to manage engineering data, and it worked well, but one of the problems we had (but didn't realise we had) was that we always had to plan the schema up-front. Another problem we knew we had was mapping the data up to domain objects and back.
Now we've just started trying out neo4j and it looks like it is solving both problems for us. The ability to add different properties to each node (and relation) has allowed us to re-think our entire approach to data. It is like dynamic versus static languages (Ruby versus Java), but for databases. Building the data model in the database can be done in a much more agile and dynamic way, and that is dramatically simplifying our code.
And since the object model in code is generally a graph structure, mapping from the database is also simpler, with less code and consequently fewer bugs.
And as a additional bonus, our initial prototype code for loading our data into neo4j is actually performing faster than the previous MySQL version. I have no solid numbers on this (yet), but that was a nice additional feature.
But at the end of the day, the choice probably should be based mostly on the nature of your domain model. Does it map better to tables or graphs? Decide by doing some prototypes, load the data and play with it. Use neoclipse to look at different views of the data. Once you've done that, hopefully you know if you're on to a good thing or not.
Here is a good article that talks about the needs that non relational databases fill: http://www.readwriteweb.com/enterprise/2009/02/is-the-relational-database-doomed.php
It does a good job at pointing out (aside from the name) that relational databases arent flawed or wrong, its just that these days people are starting to process more and more data in mainstream software and web sites, and that relational databases just wont scale for these needs.
I am building an intranet at my company.
I am interested in understanding how to load data that was stored in tables (Oracle, MySQL, SQL Server, Excel, Access, various random lists) and loading it into Neo4J, or some other graph database. Specifcally, what happens when common data overlaps existing data already in the system.
Yes, I know some data is best modeled in RDBMS, but I have this idea itching me, that when you need to superimpose several distinct tables, the graph model is better than the table structure.
For instance, I work in a manufacturing environment. There is a major project we are working on and because of the complexity, each department has created a seperate Excel spreadsheet that has a BOM (Bill Of Materials) hierarchy in a column on the left and then several columns of notes and checks made by individuals who made these sheets.
So one of the problems is merging all these notes together into one "view" so that someone can see all the issues that need to be addressed in any particular part.
The second problem is that an Excel spreadsheet sucks at representing a hierarchial BOM when a common component is used in more than one subassembly. Meaning that, if someone writes a note about the P34 relay in the ignition subassembly, the same comment should be associated with the P34 relays used in the motor driver subassembly. This won't occur in the excel spreadsheet.
For the company intranet, I want to be able to search for anything easily. Such as data related to a part number, a BOM structure, a phone number, an email address, a company policy, or procedure. I want to even extend this to manage computer hardware assets, and installed software.
I envision that once the information network starts to get populated you can start doing cool traversals such as "I want to write an email to everyone working on the XYZ project". People will have been associated with the project because they will be tagged as creating and modifying the data within the XYZ project. So by using the XYZ project as a search key, a huge set with everything related to the XYZ project will be created. Including links to people who built the XYZ project. The people links will connect to their email addresses. So by their involvement in the XYZ project, they will be included in my email. This is in stark contrast to some secretary trying to maintain a list of people work on the project. We generate a lot of lists. We spend a lot of time maintaining lists and making sure they are up to date. And most of it doesn't add any value to our products.
Another cool traversal could report all the computers that have a certain piece of software installed, by version. That report could be used to generate tasks to remove extra copies of old software and to update people who need to have the latest copy. It would also be useful for license tracking.
might be a bit late, but there is a growing number of projects using Neo4j, the better known ones listed at Neo4j . Also NeoTechnology, the company behind Neo4j, has some references at their customers page
Note: I am part of the Neo4j team
When dealing with small projects, what do you feel is the break even point for storing data in simple text files, hash tables, etc., versus using a real database? For small projects with simple data management requirements, a real database is unnecessary complexity and violates YAGNI. However, at some point the complexity of a database is obviously worth it. What are some signs that your problem is too complex for simple ad-hoc techniques and needs a real database?
Note: To people used to enterprise environments, this will probably sound like a weird question. However, my problem domain is bioinformatics. Most of my programming is prototypes, not production code. I'm primarily a domain expert and secondarily a programmer. Most of my code is algorithm-centric, not data management-centric. The purpose of this question is largely for me to figure out how much work I might save in the long run if I learn to use proper databases in my code instead of the more ad-hoc techniques I typically use.
1) Concurrency. Do you have multiple people accessing the same dataset? Then it's going to get pretty involved to broker all of the different readers and writers in a scalable fashion if you roll your own system.
2) Formatting and relationships: Is your data something that doesn't fit neatly into a table structure? Long nucleotide sequences and stuff like that? That's not really conveniently tabular data.
Another example: Nobody would consider implementing software like Photoshop to store PSDs in a relational format, because the data structures don't really lend themselves to that type of storage or query pattern.
3) ACID (sort of a corollary to #1): If Atomicity, Consistency, Integrity, and Durability are not challenges with a flat file, then go with a flat file.
For me, the line is crossed once I have to query my data in ways that involve more than a single relationship. Relating two flat data structures on disk is fairly simple, but once we get beyond that, a set-based language like SQL and formal database relationships actually reduce complexity.
I think at some point you'll miss the querying capabilities of a database, but you can consider some minimalistic database alternatives:
SQLite (Great, almost SQL-92 standard compliant)
shsql
SQL Server Compact
I would only write my own on-disk format under very special circumstances. Reusing someone else's code is nearly always faster.
For relational data, I would use SQLite. For key/value pairs, I would use BerkeleyDB (perhaps via KiokuDB). For simple objects, I would use JSON or YAML, but only if I only had a few.
With SQLite and BDB, "a real database" is literally two lines of code away. It is hard to beat that.
The problem with small projects is that they become bigger before we know it. And once they do , we start missing the sql capabilities.
Always design such that a db can be utilized later on if required without ripping apart half of the application.
It depends entirely on the domain-specific application needs. A lot of times direct text file/binary files access can be extremely fast, efficient, as well as providing you all the file access capabilities of your OS's file system.
Furthermore, your programming language most likely already has a built-in module (or is easy to make one) for specific parsing.
If what you need is many appends (INSERTS?) and sequential/few access little/no concurrency, files are the way to go.
On the other hand, when your requirements for concurrency, non-sequential reading/writing, atomicity, atomic permissions, your data is relational by the nature etc., you will be better off with a relational or OO database.
There is a lot that can be accomplished with SQLite3, which is extremely light (under 300kb), ACID compliant, written in C/C++, and highly ubiquitous (if it isn't already included in your programming language -for example Python-, there is surely one available). It can be useful even on db files as big as 1GB, possible more.
If your requirements where bigger, there wouldn't even be a discussion, go for a full-blown RDBMS.
For the kind of applications you are developing in bioinformatics, you are often doing one-shot applications (often scripts that define a workflow of calculations) that answer a specific questions, and you are not likely to be reusing these applications after you answered your question.
Often, you should therefore avoid creating databases to store the results, as after all you are not going to use their features very much.
You will probably be querying some webservices, files, or databases, run some local algorithms on the data gathered from different sources, and produce some tabular or structured output format (xml, json, etc).
For that, I would suggest you to use workflow tools like Knime (or a commercial solution like Inforsense KDE, Accelrys's Pipeline pilot, or Snaplogic, as they allow you to query data in a variety of formats and locations (rdbms, flat files, webservices), run algorithms, and build powerful web apps that allow you to easily publish your workflows to your users and let them interact at specific points).
If your prototype "grows" and you have to build more functionality on top of the data your workflows output, and if the output of your prototype is not likely to change everyday, then it's a wise decision to store a subset of the results in a database. This allows you to plug in powerful reporting tools like BusinessObjects, Crystal reports, jasper reports or whatever reporting solution available out there and show data to your users in a better shape than a spreadsheet or a csv file.
Finally, some development frameworks will make your choices more obvious : if you build a web application using an MVC framework, it is likely that your data will reside in an RDBMS (but please, don't put genomic sequences in a table column :-)).
All in all, it's a case by case choice, depending on your needs for each particular application.
In software I can usually get away with storing values in a XML configuration file or in the registry, e.g. software options. Once I need to persist objects I move to a database because the upfront cost is not that bad compared to the long term effects that relations and reporting can offer.
For bioinformatics you may be interested on that: Blast on DB. The guy who is working on that is a friend of mine and has a work on fast similarity sequence search, he found out to make his own binary storage better than using databases at this point.
I don't know specific details about his solution but you probably can exchange one or two ideias mailing the guy, even sharing code.
Do you need/want SQL queries?
Are multiple people going to want to access the data?
Is your data relational?
If you answered no to those questions, you (probably) don't need a full on database.
First, I'd consider:
How large will the database initially be: # of tables, # of rows
How quickly will it grow?
Is the data frequently queried?
If I were to create a personal recipe app, for example, I know I might add 50 favorite recipes to start and add no more than 5 recipes a year. With that being said, I could easily get by without a database since the size of the data store will have minimal impact on queries.
That said, I would probably use a database for any application where data entry and queries occur (even a small personal recipe app). I don't think it adds a lot of overhead especially when your framework (e.g. Rails) allows you to keep your database dumb (primarily tables, indexes, and constraints). It alleviates the chance that I'll have to eventually port to a database if I decide to scale up.
If you know the format of your data, flat files, if faster/easier to develop with, will be fine. If you expect your record formats to change frequently during development then I'd suggest that ALTER TABLE is your friend. Flat files will also tend to be faster (if you care about speed) unless you expect to implement the equivalent of joins across many combinations of files.
The real benefit of using a RDBMS during development is the flexibility with which you can modify your data schema and the ease with which you can access your data via queries.
Good design will ensure that you keep your data access layer relatively isolated (because of separation of concerns) so it should be a fairly straightforward (if tedious) matter to rework to a database later should it be worthwhile. Or, of course, if you use a database to develop your structures you may subsequently take the app back to flat/indexed files once those structures are crystallized in order to gain performance.
Use whatever persistence technology you're most comfortable with, and scales sufficiently.
YAGNI at least means "Don't add a new technology to your personal stack unless you can't be productive with whatever is already there."
For many (most?) of us, our comfort zone for data persistence is SQL. For some, it might be XML. Just don't write your own until (see paragraph 2).
As someone also doing research in Bioinformatics, I would suggest NOT using a database for these kinds of prototype projects unless you are sure it needs it. If you are on the fence, go with the databaseless solution and stick with flat files. It is also important to note that traditionally Bioinformatics researchers have go the flat file route, which means there are well defined file formats for most types of data in the feild. If you decide to go with a database solution, it may hurt your compatibility with existing research projects.