I have a set of statistical data (about 100M size), which is organized in key-value pairs, some of the values are just numbers (e.g. like person's age or weight) and some are hierarchical (e.g. like person's employments - it can have a set of employment records, each again containing key/value pairs, etc.). The real data is not exactly these but the structure is similar.
I need to query these data with arbitrary set of criteria - i.e. I may want to ask something like "where 20 oldest persons worked 3 years ago" or "what is the sum of all salaries for all people that ever worked at company X for more than a year", or "give me all you know on people that found a new job recently", etc.
I can program each individual query pretty easily but since there can be many of them and they vary all the time it becomes tedious to program each one anew, so the question is if there's an existing tool that would make it easier for me to do such queries (if it has a nice GUI that's a bonus :). Something like SQL wouldn't work well because data fields aren't really fixed and making hierarchy work in SQL would be too much trouble IMHO. So is there a tool that I could use with relative ease for this task (i.e. not learning a whole new language for that - I'd better stay with hand-coding the queries then)?
You may want to look at MongoDB. It is a JSON data store, so it essentially works with key/value pairs, and you can nest JSON within JSON. It uses JavaScript as the query language. Of course, you'd need to convert your data to JSON, but this is not difficult.
Another option may be a graph database like Neo4j. Each record is a node and you can define relationships between nodes (visualized as edges).
I do not think either of these have any type of GUI, but they are pretty easy to query. MongoDB uses JS with bindings you can use to call the DB. Neo4j uses Java, but there are some bindings for other languages.
SQL queries would be challenging, but it would work. I will also throw PostgreSQL as an option since it is somewhat object oriented, but I am more familiar with the others.
Related
I'm trying to build a web application where users can upload a file (specifically the MDF file format) and view the data in forms of various charts. The files can contain any number of time based signals (various numeric data types) and users may name the signals wildly.
My thought on saving the data involves 2 steps:
Maintain a master table as an index, to save such meta information as file names, who uploaded it, when, etc. Records (rows) are added each time a new file is uploaded.
Create a new table (I'll refer to this as data tables) for each file uploaded, within the table each column will be one signal (first column being timestamps).
This brings the problem that I can't pre-define the Model for the data tables because the number, name, and datatype of the fields will differ among virtually all uploaded files.
I'm aware of some libs that help to build runtime dynamic models but they're all dated and questions about them on SO basically get zero answers. So despite the effort to make it work, I'm not even sure my approach is the optimal way to do what I want to do.
I also came across this Postgres specifc model field which can take nested arrays (which I believe fits the 2-D time based signals lists). In theory I could parse the raw uploaded file and construct such an array and basically save all the data in one field. Not knowing the limit of size of data, this could also be a nightmare for the queries later on, since to create the charts it usually takes only a few columns of signals at a time, compared to a total of up to hundreds of signals.
So my question is:
Is there a better way to organize the storage of data? And how?
Any insight is greatly appreciated!
If the name, number and datatypes of the fields will differ for each user, then you do not need an ORM. What you need is a query builder or SQL string composition like Psycopg. You will be programatically creating a table for each combination of user and uploaded file (if they are different) and programtically inserting the records.
Using postgresql might be a good choice, you might also create a GIN index on the arrays to speed up queries.
However, if you are primarily working with time-series data, then using a time-series database like InfluxDB, Prometheus makes more sense.
I am new to clojure. I want to fetch x records with fields from database and want to insert records into database. Which once should I use between defrecord and defschema in this scenario?
Are those the same?
defschema and defrecord do not refer to database schema ("shape of database") nor to records (i.e., rows in relational DBs).
Schema is a library for describing the shape of your data, and validating whether some data conforms to this shape. It is similar to the more recent clojure.spec. Clojure Records are custom datatypes, which look a bit like Java-classes.
It is easy to be tempted to write "Object Oriented" DB communication with Records for each entity. However, all database contains is data, which is just lists, maps, sets, and some basic data types. I suggest you keep your data in built-in Clojure data structures, ready at hand, and don't hide it in unnecessary abstractions. (Side note: your DB component, instead of DB entity, may very well be a Clojure Record. For example, lifecycle management with Component uses Records.)
A good place to start would be Honey SQL, which allows you to build SQL queries as Clojure data structures. You get back data and can operate on that data with the full might of Clojure.
Then, when you are comfortable with "laying all your data open (without encapsulation)", go and describe the shape of your data, what is valid and what is not. clojure.spec is a powerful tool for that.
I'm working to optimize a Django application that's (mainly) backed by MongoDB. It's dying under load testing. On the current problematic page, New Relic shows over 700 calls to pymongo.collection:Collection.find. Much of the code was written by junior coders and normally I would look for places to add indicies, make smarter joins and remove loops to reduce query calls, but joins aren't an option here. What I have done (after adding indicies based on EXPLAINs) is tried to reduce the cost in loops by making a general query and then filtering that smaller set in the loops*. While I've gotten the number down from 900 queries, 700 still seems insane even with the intense amount of work being done on the page. I thought perhaps find was called even when filtering an existing queryset, but the code suggests it's always a database query.
I've added some logging to mongoengine to see where the queries come from and to look at EXPLAIN statements, but I'm not having a ton of luck sifting through the wall of info. mongoengine itself seems to be part of the performance problem: I switched to mongomallard as a test and got a 50% performance improvement on the page. Unfortunately, I got errors on a bunch of other pages (as best I can tell it appears Mallard doesn't do well when filtering an existing queryset; the error complains about a call to deepcopy that's happening in a generator, which you can't do-- I hit a brick wall there). While Mallard doesn't seem like a workable replacement for us, it does suggest a lot of the proessing time is spent converting objects to and from Python in mongoengine.
What can I do to further reduce the calls? Or am I focusing on the wrong thing and should be attacking the problem somewhere else?
EDIT: providing some code/ models
The page in question displays the syllabus for a course, showing all the modules in the course, their lessons and the concepts under the lessons. For each concept, the user's progress in the concept is also shown. So there's a lot of looping to get the hierarchy teased out (and it's not stored according to any of the patterns the Mongo docs suggest).
class CourseVersion(Document):
...
course_instances = ListField(ReferenceField('CourseInstance'))
courseware_containers = ListField(EmbeddedDocumentField('CoursewareContainer'))
class CoursewareContainer(EmbeddedDocument):
id = UUIDField(required=True, binary=False, default=uuid.uuid4)
....
courseware_containers = ListField(EmbeddedDocumentField('self'))
teaching_element_instances = ListField(StringField())
The course's modules, lessons and concepts are stored in courseware_containers; we need to get all of the concepts so we can get the list of ids in teaching_element_instances to find the most recent one the user has worked on (if any) for that concept and then look up their progress.
* Just to be clear, I am using a profiler and looking at times and doings things The Right Way as best I know, not simply changing things and hoping for the best.
The code sample isn't bad per-sae but there are a number of areas that should be considered and may help improve performance.
class CourseVersion(Document):
...
course_instances = ListField(ReferenceField('CourseInstance'))
courseware_containers = ListField(EmbeddedDocumentField('CoursewareContainer'))
class CoursewareContainer(EmbeddedDocument):
id = UUIDField(required=True, binary=False, default=uuid.uuid4)
....
courseware_containers = ListField(EmbeddedDocumentField('self'))
teaching_element_instances = ListField(StringField())
Review
Unbounded lists.
course_instances, courseware_containers, teaching_element_instances
If these fields are unbounded and continuously grow then the document will move on disk as it grows, causing disk contention on heavily loaded systems. There are two patterns to help minimise this:
a) Turn on Power of two sizes. This will cost disk space but should lower the amount of io churn as the document grows
b) Initial Padding - custom pad the document on insert so it gets put into a larger extent and then remove the padding. Really an anti pattern but it may give you some mileage.
The final barrier is the maximum document size - 16MB you can't grow your data bigger than that.
Lists of ReferenceFields - course_instances
MongoDB doesn't have joins so it costs an extra query to look up a ReferenceField - essentially they are an in app join. Which isn't bad per-sae but its important to understand the tradeoff. By default mongoengine won't automatically dereference the field only doing course_version.course_instances will it do another query and then populate the whole list of references. So it can cost you another query - if you don't need the data then exclude() it from the query to stop any leaking queries.
EmbeddedFields
These fields are part of the document, so there is no cost for them, other than the wire costs of transmitting and loading the data. **As they are part of the document, you don't need select_related to get this data.
teaching_element_instances
Are these a list of id's? It says its a StringField in the code sample above. Either way, if you don't need to dereference the whole list then storing the _ids as a StringField and manually dereferencing may be more efficient if coded correctly - especially if you just need the latest (last?) id.
Model complexity
The CoursewareContainer is complex. For any given CourseVersion you have n CoursewareContainers with themselves have a list of n containers and those each have n containers and on...
Finding the most recent instances
We need to get all of the concepts so we can get the list of ids in
teaching_element_instances to find the most recent one the user has
worked on (if any) for that concept and then look up their progress.
I'm unsure if there is a single instance you are after or one per Container or one per Course. Either way - the logic for querying the data should be examined. If its a single instance you are after - then that could be stored against the user so to simplify the logic of looking this up. If its per course or container then to improve performance ensure you minimise the number of queries - if possible collect all the ids and then at the end issue a single $in query, rather than doing a query per container.
Mongoengine costs
Currently, there is a performance cost to loading the data into Mongoengine classes - if you don't need the classes and are happy to work with simple dictionaries then either issue a raw pymongo query or use as_pymongo.
Schema design
The schema looks logical enough but is it suitable for the use case - in essence is it using MongoDB's strengths or is it putting a relational peg in a document database shaped hole? I can't answer than for you but I do know the way to the happy path with MongoDB is design the schema based on its use case. With relational databases schema design from the outset is simple - you normalise, with document databases how the data is used is a primary factor.
MongoDB best practices
There are many other best practices and mongodb have a guide which might be of interest: MongoDB Operations Best Practices.
Feel free to contact me via the Mongoengine mailing list to discuss further and if needs be discuss in private.
Ross
Question to all Cassandra experts out there.
I have a column family with about a million records.
I would like to query these records in such a way that I should be able to perform a Not-Equal-To kind of operation.
I Googled on this and it seems I have to use some sort of Map-Reduce.
Can somebody tell me what are the options available in this regard.
I can suggest a few approaches.
1) If you have a limited number of values that you would like to test for not-equality, consider modeling those as a boolean columns (i.e.: column isEqualToUnitedStates with true or false).
2) Otherwise, consider emulating the unsupported query != X by combining results of two separate queries, < X and > X on the client-side.
3) If your schema cannot support either type of query above, you may have to resort to writing custom routines that will do client-side filtering and construct the not-equal set dynamically. This will work if you can first narrow down your search space to manageable proportions, such that it's relatively cheap to run the query without the not-equal.
So let's say you're interested in all purchases of a particular customer of every product type except Widget. An ideal query could look something like SELECT * FROM purchases WHERE customer = 'Bob' AND item != 'Widget'; Now of course, you cannot run this, but in this case you should be able to run SELECT * FROM purchases WHERE customer = 'Bob' without wasting too many resources and filter item != 'Widget' in the client application.
4) Finally, if there is no way to restrict the data in a meaningful way before doing the scan (querying without the equality check would returning too many rows to handle comfortably), you may have to resort to MapReduce. This means running a distributed job that would scan all rows in the table across the cluster. Such jobs will obviously run a lot slower than native queries, and are quite complex to set up. If you want to go this way, please look into Cassandra Hadoop integration.
If you want to use not-equals operator on a specific partition key and get all other data from table then you can use a combination of range queries and TOKEN function from CQL to achieve this
For example, if you want to fetch all rows except the ones having partition key as 'abc' then you execute below 2 queries
select <column1>,<column2> from <keyspace1>.<table1> where TOKEN(<partition_key_column_name>) < TOKEN('abc');
select <column1>,<column2> from <keyspace1>.<table1> where TOKEN(<partition_key_column_name>) > TOKEN('abc');
But, beware that result is going to be huge (depending on size of table and fields you need). So you might want to use this in conjunction with dsbulk kind of utility. Also note that there is no guarantee of ordering in your result. This is just a kind of data dump which will most probably be useful for some kind of one-time data migration like scenarios.
I'm rewriting an application which handles a lot of data (about 100 GB) which is designed as a relational model.
The application is very complex; it is some kind of conversion tool for open street map data of huge sizes (the whole world) and converts it into a map file for our own route planning software. The converter application for example holds the nodes in the open street map with their coordinate and all its tags (a lot of more than that, but this should serve as an example in this question).
Current situation:
Because this data is very huge, I split it into several files: Each file is a map from an ID to an atomic value (let's assume that the list of tags for a node is an atomic value; it is not but the data storage can treat it as such). So for nodes, I have a file holding the node's coords, one holding the node's name and one holding the node's tags, where the nodes are identified by (non-continuous) IDs.
The application once was split into several applications. Each application processes one step of the conversion. Therefore, such an application only needs to handle some of the data stored in the files. For example, not all applications need the node's tags, but a lot of them need the node's coords. This is why I split the relations into files, one file for each "column".
Each processing step can read a whole file at once into a data structure within RAM. This ensures that lookups can be very efficient (if the data structure is a hash map).
I'm currently rewriting the converter. It should now be one single application. And it should now not use separated files for each "column". It should rather use some well-known architecture to hold external data in a relational manner, like a database, but much faster.
=> Which library can provide the following features?
Requirements:
It needs to be very fast in iterating over the existing data (while not modifying the set of rows, but some values in the current row).
It needs to provide constant or near-constant lookup, similar to hash maps (while not modifying the whole relation at all).
Most of the types of the columns are constantly sized, but in general they are not.
It needs to be able to append new rows to a relation in constant or logarithmic time per row. Live-updating some kind of search index will not be required. Updating (rebuilding) the index can happen after a whole processing step is complete.
Some relations are key-value-based, while others are an (continuously indexed) array. Both of them should provide fast lookups.
It should NOT be a separate process, like a DBMS like MySQL would be. The number of queries will be enormous (around 10 billions) and will be totally the bottle neck of the performance. However, caching queries would be a possible workaround: Iterating over a whole table can be done in a single query while writing to a table (from which no data will be read in the same processing step) can happen in a batch query. But still: I guess that serializing, inter-process-transmitting and de-serializing SQL queries will be the bottle neck.
Nice-to-have: easy to use. It would be very nice if the relations can be used in a similar way than the C++ standard and Qt container classes.
Non-requirements (Why I don't need a DBMS):
Synchronizing writing and reading from/to the same relation. The application is split into multiple processing steps; every step has a set of "input relations" it reads from and "output relations" it writes into. However, some steps require to read some columns of a relation while writing in other columns of the same relation.
Joining relations. There are a few cross-references between different relations, however, they can be resolved within my application if lookup is fast enough.
Persistent storage. Once the conversion is done, all the data will not be required anymore.
The key-value-based relations will never be re-keyed; the array-based relations will never be re-indexed.
I can think of several possible solutions depending on lots of factors that you have not quantified in your question.
If you want a simple store to look things up and you have sufficient disk, SQLite is pretty efficient as a database. Note that there is no SQLite server, the 'server' is linked into your application.
Personally this job smacks of being embarrassingly parallel. I would think that a small Hadoop cluster would make quick work of the entire job. You could spin it up in AWS, process your data, and shut it down pretty inexpensively.