In the Snakemake documentation, the includes directive can incorporate all of the rules of another workflow into the main workflow and apparently can show up in snakemake --dag -n | dot -Tsvg > dag.svg. Sub-workflows, on the other hand, can be executed prior to the main workflow should you develop rules which depend on their output.
My question is: how are these two really different? Right now, I am working on a workflow, and it seems like I can get by on just using includes and putting the name of the output in rule all of the main workflow. I could probably even place the output in the input of a main-workflow rule, making the includes workflow execute prior to that rule. Additionally, I can't visualize a DAG which includes the sub-workflow, for whatever reason. What do sub-workflows offer that the includes directive can't do?
The include doesn't "incorporate another workflow". It just adds the rules from another file, like if you add them with copy/paste (with a minor difference that include doesn't affect your target rule). The subworkflow has an isolated set of rules that work together to produce the final target file of this subworkflow. So it is well structured and isolated from both main workflow and other subworkflows.
Anyway, my personal experience shows that there are some bugs in Snakemake that make using subworkflows quite difficult. Including the file is pretty straightforward and easy.
I've never used subworkflows, but here's a case where it may be more convenient to use them rather than the include directives. (In theory, I think you don't need include and subworkflow as you could write everything in a massive Snakefile, the point is more about convenience.)
Imagine you are writing a workflow that depends on result files from a published work (or from a previous project of yours). The authors did not make public the files you need but they provide a snakemake workflow to produce them. Their snakemake workflow may be quite complex and the files you need may be just intermediate steps. So instead of making sense of the all workflow and parsing it into your own include directives, you use subworkflow to generate the required file(s). E.g.:
subworkflow jones_etal:
workdir:
"./jones_etal"
snakefile:
"./jones_etal/Snakefile"
rule all:
input:
'my_results.txt',
rule one:
input:
jones_etal('from_jones.txt'),
output:
'my_results.txt',
...
I would like to annotate the first token of a text and use that annotation in following rules. I have tried different patterns:
Token.begin == 0 (doesn't work, although there definitely is a token that begins at 0)
Token{STARTSWITH(DocumentMetaData)}; (also doesn't work)
The only pattern that works is:
Document{->MARKFIRST(First)};
But if I try to use that annotation e.g. in the following way:
First{->MARK(FirstAgain)};
it doesn't work again. This makes absolutely no sense to me. There seems to be a really weird behaviour with annotations that start at 0.
This trivial task can be a bit tricky indeed, mainly because of the visibility settings. I do not know why your rules in the question do not work without having a look at the text that should be processed.
As for UIMA Ruta 2.7.0, I prefer a rule like:
# Token{->First};
Here some additional thoughts about the rules in the question:
Token.begin == 0;
Normally, there is not token with begin at 0 since the document starts with some whitespaces or line breaks. If there is actually a token that starts at offset 0 and the rule does not match, then something invisible is covering the begin of the end of the token. This depends of course of the filtering settings, but in case that you did not change them, it could be a bom.
Token{STARTSWITH(DocumentMetaData)};
Here, either the problem above applies, or the begin offset is not identical. If the DocumentMetaData covers the complete document, then I would bet on the leading whitespaces. Another reason could be that the internal indexing is broken, e.g., the tokens or the DocumentMetaData are created by an external analysis engine which was called with EXEC and no reindexing was configured in the action. This situation could also occur with unfortunate optimizations using the config params.
Document{->MARKFIRST(First)};
First{->MARK(FirstAgain)};
MARKFIRST creates an annotation using the offset of the first RutaBasic in the matched context IIRC. If the document starts with something invisible, e.g., a line break, then the second rule cannot match.
As a general advice in situations like this when some obvious simple rules do not work correctly as expected, I recommend adding some additional rules and using the debugging config with the explanation view. As rule like Token; can directly highlight if the visibility setting are problematic for the given tokens.
DISCLAIMER: I am a developer of UIMA Ruta
My users want to store my app's settings in a version control system.
(The app targets developers and designers, and allows per-folder settings. Users often ask me to store those settings inside the folder itself, so that they can commit them to VCS.)
The settings are modified from the app's UI and are thus saved programmatically, but I want the resulting file to be human-readable. My first choice would be a pretty-printed JSON, except that it's a funny thing to merge (think those forbidden trailing commas).
That got me thinking: what is the most diff/merge-friendy human-readable text format I can possibly use?
I know many version control systems support external merge tools, but I don't want to burden the users with additional setup. My goal is to minimize accidental conflicts while keeping a reasonable, readable format and without any additional effort from the user.
The data I store is basically a list of rules, and each rule has a number of user-configurable properties. Like this:
rules:
- type: compile
source: *.less
destination: *.css
compiler: LESS 1.x
- type: compile
source: *.coffee
destination: *.js
compiler: CoffeeScript 1.3
sourceMaps: true
A line-based YAML looks like a reasonably good choice. An OpenSSH-style config format may work even better.
So two questions:
Has someone tried to solve this problem before and maybe did a write up of their experience?
Anything off the top of your head that I should consider when formatting the output file?
E.g. will it help to add 2-3 empty lines between the rules to defeat the diff context and minimize conflicts in case two users both add a new rule at the end (a pretty typical case)?
Problem
Your organization has many separate applications, some of which interact with each other (to form "systems"). You need to deploy these applications to separate environments to facilitate staged testing (for example, DEV, QA, UAT, PROD). A given application needs to be configured slightly differently in each environment (each environment has a separate database, for example). You want this re-configuration to be handled by some sort of automated mechanism so that your release managers don't have to manually configure each application every time it is deployed to a different environment.
Desired Features
I would like to design an organization-wide configuration solution with the following properties (ideally):
Supports "one click" deployments (only the environment needs to be specified, and no manual re-configuration during/after deployment should be necessary).
There should be a single "system of record" where a shared environment-dependent property is specified (such as a database connection string that is shared by many applications).
Supports re-configuration of deployed applications (in the event that an environment-specific property needs to change), ideally without requiring a re-deployment of the application.
Allows an application to be run on the same machine, but in different environments (run a PROD instance and a DEV instance simultaneously).
Possible Solutions
I see two basic directions in which a solution could go:
Make all applications "environment aware". You would pass the environment name (DEV, QA, etc) at the command line to the app, and then the app is "smart" enough to figure out the environment-specific configuration values at run-time. The app could fetch the values from flat files deployed along with the app, or from a central configuration service.
Applications are not "smart" as they are in #1, and simply fetch configuration by property name from config files deployed with the app. The values of these properties are injected into the config files at deploy-time by the install program/script. That install script takes the environment name and fetches all relevant configuration values from a central configuration service.
Question
How would/have you achieved a configuration solution that solves these problems and supports these desired features? Am I on target with the two possible solutions? Do you have a preference between those solutions? Also, please feel free to tell me that I'm thinking about the problem all wrong. Any feedback would be greatly appreciated.
We've all run into these kinds of things, particularly in large organizations. I think it's most important to manage your own expectations first, and also ask whether it's really necessary to tell every system and subsystem on a given box to "change to DEV mode" or "change to PROD mode". My personal recommendation is as follows:
Make individual boxes responsible for a different stage - i.e. "this is a DEV box", and "this is a PROD box".
Collect as much of the configuration that differs from box to box in one location, even if it requires soft links or scripts that collect the information to then print out.
A. This way, you can easily "dump this box's configuration" in two places and see what differs, for example after a new deployment.
B. You can also make configuration changes separate from software changes, at least to some degree, which is a good way to root out bugs that happen at release time.
Then have everything base its configuration on something/somewhere that is not baked-in or hard-coded - just make sure to collect and document it in that one location. It almost doesn't matter what the mechanism is, which is a good thing, because some systems just don't want to be forced to use some mechanisms or others.
Sorry if this is too general an answer - the question was very general. I've worked in several large software-based organizations before, and this seemed to be the best approach. Using a standalone server as "one unit of deployment" is the most realistic scenario (though sometimes its expensive), since applications affect each other, and no matter how careful you are, you destabilize a whole system when you move any given gear or cog.
The alternative gets very complex very quickly. You need to start rewriting the applications that you have control over in order to have them accept a "DEV" switch, and you end up adding layers of kludge to the ones you don't have control over. Usually, the ones you don't have control over at least base their properties on something defined on a system-wide level, unless they are "calling the mothership for instructions".
It's easier to redirect people to a remote location and have them "use DEV" vs "use PROD" than it is to "make this machine run like DEV" vs "make this machine run like PROD". And if you're mixing things up, like having a DEV task run together on the same box as a PROD task, then that's not a realistic scenario anyways: I guarantee that eventually you will be granting illegal DEV-only access to somebody on PROD, and you'll have a DEV task wipe out a PROD database.
Hope this helps. Let me know if you'd like to discuss more specifics involved.
I personally prefer solution 2 (the app should know itself, by its configuration, what environment it is running in). With solution 1 (pass the environment name as a startup parameter) the danger of using the wrong environment specifier is much too high. Accessing the TEST database from PROD code and vice versa may cause mayhem, if the two installed code bases are not of the same version, as is often the case.
My current project uses solution 1, but I don't like that. A previous project I worked on used a variation of solution 2: The build process generated one setup file for every environment, making sure that they contained the same code base but appropriate configuration paramters. That worked like a charm, but I know it contradicts the paradigm that the "exact same build files must be deployed everywhere".
I think I have asked a related, self-answered, question, before I read this one : How to organize code so that we can move and update it without having to edit the location of the configuration file? . So, on that basis, I provide an answer here. I don't like the idea of "smart" application (solution 1 here) for such a simple task as finding environment settings. It seems a complicated framework for something that should be simple. The idea of an install script (solution 2 here) is powerful, but it is useful to allow the user to change the content of the config file, but would it allow to change the location of this config file? What is this "central configuration service", where is it located? My answer is that I would go with option 2, if the goal is to set the content of the configuration file, but I feel that the issue of the location of this configuration file remains unanswered here.
If you're using JSON to store/transmit configuration (or can use JSON in your pre-deploy process to output to some other format) you can annotate key/property names for environment/context-specific values with arbitrary or environment-specific suffixes, and then dynamically prefer/discriminate them at build/deploy/run/render -time, while leaving un-annotated properties alone.
We have used this to avoid duplicating entire configuration files (with the associated problems well known) AND to reduce repetition. The technique is also perfect for internationalization (i18n) -- even within the same file, if desired.
Example, snippet of pre-processed JSON config:
var config = {
'ver': '1.0',
'help': {
'BLURB': 'This pre-production environment is not supported. Contact Development Team with questions.',
'PHONE': '808-867-5309',
'EMAIL': 'coder.jen#lostnumber.com'
},
'help#www.productionwebsite.com': {
'BLURB': 'Please contact Customer Service Center',
'BLURB#fr': 'S\'il vous plaît communiquer avec notre Centre de service à la clientèle',
'BLURB#de': 'Bitte kontaktieren Sie unseren Kundendienst!!1!',
'PHONE': '1-800-CUS-TOMR',
'EMAIL': 'customer.service#productionwebsite.com'
},
}
... and post-processed (in this case, at render time) given dynamic, browser-environment-known location.hostname='www.productionwebsite.com' and navigator.language of 'de'):
prefer(config,['www.productionwebsite.com','de']); // prefer(obj,string|Array<string>)
JSON.stringify(config); // {
'ver': '1.0',
'help': {
'BLURB': 'Bitte kontaktieren Sie unseren Kundendienst!!1!',
'PHONE': '1-800-CUS-TOMR',
'EMAIL': 'customer.service#productionwebsite.com'
}
}
If a non-annotated ('base') property has no competing annotated property, it is left alone (presumably global across environments) otherwise its value is replaced by an annotated value, if the suffix matches one of the inputs to the preference/discrimination function. Annotated properties that do not match are dropped entirely.
You can mix and match this behaviour to annotate configuration to achieve distinctions of global, default, specific that are (assuming you're sensible) readable with zero/minimal duplication.
The single, recursive prefer() function (as we're calling it, lacking the need or desire to make an entire project/framework out of it) we've developed so far (see jsFiddle, with inline docs) goes a bit further than this simple example, and (explained in greater detail here) handles deeply-nested configuration objects, as well as preferential ordering and (if you need to stay flat) combination of suffixes.
The function relies on JS ability to reference object properties as strings, dynamically, and tolerate # and & delimiters in property names which are not valid in dot-notation syntax but consequently (help) prevent developers from breaking this technique by accidentally referring to pre-processed/annotated attributes in code (unless they, non-conventionally don't prefer to use dot-notation.)
We have yet to have this break anything for us, nor have we been schooled on any fundamental flaws of this technique, beyond irresponsible/unintended usage or investment/fondness for existing frameworks/techniques that pre-exist. We have also not profiled it for performance (we only tend to run this once per build/session, etc.) so in your own usage, YMMV.
Most configurations transmitted client-side of course would not want to contain sensitive pre-production values, so one could (should!) use the same function to generate a production-only version (with no annotations) in pre-deploy, while still enjoying a SINGLE configuration file upstream in your process.
Further, if you're doing this for i18n, you may not want the entire wad going over the wire, so could process it server-side (cached or live, etc.) or pre-process it in build/deploy by splitting into separate files, but STILL enjoying a single source of truth as early in your workflow as possible.
We have not explored implementing the same function in Java (or C#, PERL, etc.) assuming it's even possible (with some exotic reflection maybe?) but a build environment that includes NodeJS could farm that step out easily.
Well if it suits your needs and you have no problem of storing the connection strings in the source control repository, you could create files like:
appsettings.dev.json
appsettings.qa.json
appsettings.staging.json
And choose the right one in the deployment script and rename it to the actual appsettings.json, which is then read by your app.
I am working on a project, which deals with changing the order of the rules, to make the IDS process faster and more efficient.
I just have to find where the rule generating any alert in snort alert file, is located. (I mean the rule is located on which line, in which rule file?)
Can anyone help me find out?
To locate rules within the configuration file:
you can use signature ID of snort rules.
For example,
[**] [1:5000361:0] need-to-know - suspicious spammed domain [**]
here the signature ID is 5000361.
or, you can search in the configuration file for the referenece shown in the alert
[Xref => url www.spamhaus.org/query/dbl?domain=xxxxxxx.com]
In the above line, the reference is www.spamhaus.org/query/dbl?domain=xxxxxxx.com
Snort configuration file is specified using the -c option followed by the name of the configuration file, usually named as snort.conf. Since it is specified using the option, it could be located anywhere on the system. Usually it can be found at /usr/local/etc/snort.conf or in the directory where snort is installed.
This question doesn't really make any sense. "I am working on a project, which deals with changing the order of the rules, to make the IDS process faster and more efficient."
This implies that if you change the order that the snort rules are in in a file then it will change the order in which they are evaluated, and that is completely wrong. The way snort works in terms of rule evaluation is much more complicated and to be more efficient you must make your rules more efficient. For snort the most important part of a rule is the fast_pattern keyword. Even if you do not specify a fast_pattern in a rule snort will automatically choose the longest content match in the rule that is at least 3 characters and use this as the fast_pattern. For every packet that comes in snort will build a rule evaluation tree for that packet and the order of these rules is completely unrelated to the order that they are stored in the config files. Snort will just read all rules in the configs and the order they are evaluated is determined when it receives the packet at during run time.