Finish user and developer documentation

CHANGES.rst

+src/sphinx/changes.rst
\ No newline at end of file

README.md

 # Sentinel
 
-Sentinel is a JSON-based database for next-generation sequencing statistics.
+Sentinel is a JSON-based database for next-generation sequencing statistics. Queries and submissions are all done via a
+RESTful HTTP API which is specified based on [Swagger](http://swagger.io).
 
 ## Requirements
 
 - Java 8 (must be set as the default `java`)
 - Scala 2.11.6
-- MongoDB 3.0
+- MongoDB 3.0 (running on localhost port 27017 for development)
+- Python 2.7 and Sphinx (only when building the documentation)
 
-## Build & Run
+## Quick Start
 
 ```sh
 $ git clone {this-repository}
 $ cd sentinel
+$ ./scripts/bootstrap_dev.sh
 $ ./sbt
 > container:start
 > browse
@@ -22,12 +25,9 @@ If `browse` doesn't launch your browser, manually open [http://localhost:8080/](
 
 ## Support
 
-Please report issues to [the issue page](https://git.lumc.nl/sasc/sentinel/issues). Feature suggestions are also welcome.
+Report issues to [the issue page](https://git.lumc.nl/sasc/sentinel/issues). Fixes and feature suggestions are also
+welcome.
 
-## Contributing
+## More
 
-```sh
-$ grep -r 'TODO' src/
-```
-
-You can also check for unclosed issues in the issue page.
+Please see the documentation for a complete guide on the project.

src/main/scala/nl/lumc/sasc/sentinel/api/StatsController.scala

@@ -26,6 +26,7 @@ import nl.lumc.sasc.sentinel._
 import nl.lumc.sasc.sentinel.api.auth.AuthenticationSupport
 import nl.lumc.sasc.sentinel.db._
 import nl.lumc.sasc.sentinel.models._
+import nl.lumc.sasc.sentinel.processors.GenericRunsProcessor
 import nl.lumc.sasc.sentinel.processors.gentrap._
 import nl.lumc.sasc.sentinel.utils.implicits._
 
@@ -45,13 +46,10 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   protected val applicationDescription: String = "Statistics of deposited run summaries"
 
   /** Adapter for connecting to the run collections */
-  protected val runs = new RunsAdapter {
-    val mongo = self.mongo
-    def processRun(fi: FileItem, user: User, pipeline: Pipeline.Value) = Try(throw new NotImplementedError)
-  }
+  protected val runs = new GenericRunsProcessor(mongo)
 
   /** Adapter for connecting to the gentrap collection */
-  protected val gentrap = new GentrapOutputProcessor(mongo)
+  protected val gentrap = new GentrapStatsProcessor(mongo)
 
   /** Adapter for connecting to the users collection */
   protected val users = new UsersAdapter { val mongo = self.mongo }
@@ -98,6 +96,53 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   // format: OFF
   val statsGentrapAlignmentsGetOperation = (apiOperation[Seq[GentrapAlignmentStats]]("statsGentrapAlignmentsGet")
     summary "Retrieves the alignment statistics of Gentrap pipeline runs."
+    notes
+      """This endpoint returns a list containing alignment-level metrics of Gentrap pipeline runs.
+        |
+        |By default:
+        |
+        | * Each data point represents metrics from an alignment file of a sample. To return alignment metrics from
+        |   single libraries, use the `accLevel` parameter.
+        |
+        | * When the `accLevel` parameter is set to `lib`, the returned data points represent either single-end or
+        |   paired-end sequencing files. To return data points from only one library type, use the `libType` parameter.
+        |   When the `accLevel` is set to `sample`, the `libType` parameter is ignored as a single sample alignment
+        |   may be a mix of single-end and paired-end library.
+        |
+        | * Data points are returned in random order which changes in every query. To maintain a sorted order
+        |   (most-recently created first), use the `sorted` parameter.
+        |
+        | * All data points of all Gentrap runs are returned. The filter for specific data points, use the `runIds`,
+        |   `refIds`, and/or `annotIds` parameter.
+        |
+        | * All data points are unlabeled. To label the data points with their respective IDs and names, you must be
+        |   the data points' uploader and authenticate yourself using your API key. If the returned data points contain
+        |   data points you did not upload, they will remain unlabeled.
+        |
+        |Each returned data point has the following metrics:
+        |
+        | * `maxInsertSize`: Maximum insert size (only for paired-end libraries).
+        | * `median3PrimeBias`: Median value of 3' coverage biases from the top 1000 expressed transcripts (3'-most 100 bp).
+        | * `median5PrimeBias`: Median value of 5' coverage biases from the top 1000 expressed transcripts (5'-most 100 bp).
+        | * `median5PrimeTo3PrimeBias`: Median value of 5' to 3' coverage biases.
+        | * `medianInsertSize`: Median insert size (only for paired-end libraries).
+        | * `nBasesAligned`: Number of bases aligned.
+        | * `nBasesCoding`: Number of bases aligned in the coding regions.
+        | * `nBasesIntergenic`: Number of bases aligned in the intergenic regions.
+        | * `nBasesIntron`: Number of bases aligned in the intronic regions.
+        | * `nBasesRibosomal`: Number of bases aligned to ribosomal gene regions.
+        | * `nBasesUtr`: Number of bases aligned in the UTR regions.
+        | * `normalizedTranscriptCoverage`: Array representing normalized coverage along transcripts. The transcripts
+        | come from the top 1000 expressed genes and each item in the array represents 1% of the transcript length.
+        | * `nReadsAligned`: Number of reads aligned.
+        | * `nReadsSingleton`: Number of paired-end reads aligned as singletons.
+        | * `nReadsTotal`: Number of reads.
+        | * `nReadsProperPair`: Number of paired-end reads aligned as proper pairs.
+        | * `pctChimeras`: Percentage of reads aligned as chimeras (only for paired-end libraries).
+        | * `rateIndel`: How much indels are present.
+        | * `rateReadsMismatch`: Mismatch rate of aligned reads.
+        | * `stdevInsertSize`: Insert size standard deviation (only for paired-end libraries).
+      """.stripMargin
     parameters (
       queryParam[Seq[String]]("runIds")
         .description("Include only Gentrap runs with the given run ID(s).")
@@ -183,6 +228,31 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   val statsGentrapAlignmentsAggregateGetOperation = (
     apiOperation[GentrapAlignmentStatsAggr]("statsGentrapAlignmentsAggregatesGet")
       summary "Retrieves the aggregate alignment statistics of Gentrap pipeline runs."
+      notes
+        """This endpoint returns aggregate values of various alignment-level metrics. The default settings are the same
+          | as the corresponding data points endpoint. The aggregated metrics are also similar to the data points'
+          | metrics, with the following additions:
+          |
+          | * `nBasesMrna`: Number of bases aligned in the UTR and coding region.
+          | * `pctBasesCoding`: Percentage of bases aligned in the coding regions.
+          | * `pctBasesIntergenic`: Percentage of bases aligned in the intergenic regions.
+          | * `pctBasesIntron`: Percentage of bases aligned in the intronic regions.
+          | * `pctBasesMrna`: Percentage of bases aligned in the UTR and coding region.
+          | * `pctBasesRibosomal`: Percentage of bases aligned to ribosomal gene regions.
+          | * `pctBasesUtr`: Percentage of bases aligned in the UTR regions.
+          | * `pctReadsAlignedTotal`: Percentage of reads aligned (per total reads).
+          | * `pctReadsAligned`: Percentage of reads aligned (per aligned reads).
+          | * `pctReadsSingleton`: Percentage of paired-end reads aligned as singletons (per aligned reads).
+          | * `pctReadsProperPair`: Percentage of paired-end reads aligned as proper pairs (per aligned reads).
+          |
+          |The following data point attribute is not aggregated:
+          |
+          | * `normalizedTranscriptCoverage`
+          |
+          |Each aggregated metric contains the attributes `avg` (average), `max` (maximum), `min` (minimum), `median`
+          | (median), and `stdev` (standard deviation). It also contains the `nDataPoints` attribute, showing the number
+          | of data points aggregated for the metrics.
+        """.stripMargin
       parameters (
       queryParam[Seq[String]]("runIds")
         .description("Include only Gentrap runs with the given run ID(s).")
@@ -254,6 +324,44 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   // format: OFF
   val statsGentrapSequencesGetOperation = (apiOperation[Seq[SeqStats]]("statsGentrapSequencesGet")
     summary "Retrieves the sequencing statistics of Gentrap pipeline runs."
+    notes
+      """This endpoint returns a list containing sequence-level metrics of Gentrap pipeline runs.
+        |
+        |By default:
+        |
+        | * Each data point represents an input set, which may consist of a single sequence (for single-end sequencing)
+        |   or two sequences (for paired-end sequencing). Selection on library type (single, paired, or both) can be
+        |   done via the `libType` parameter. When `libType` is set to `paired`, the data point will contain a `readAll`
+        |   attribute denoting the combined metrics of both `read1` and `read2`.
+        |
+        | * The returned data points are computed from the raw sequence files. To return data points of the processed
+        |   sequence files (possibly adapter-clipped and/or trimmed), use the `qcPhase` parameter.
+        |
+        | * Data points are returned in random order which changes in every query. To maintain a sorted order
+        |   (most-recently created first), use the `sorted` parameter.
+        |
+        | * All data points of all Gentrap runs are returned. The filter for specific data points, use the `runIds`,
+        |   `refIds`, and/or `annotIds` parameter.
+        |
+        | * All data points are unlabeled. To label the data points with their respective IDs and names, you must be
+        |   the data points' uploader and authenticate yourself using your API key. If the returned data points contain
+        |   data points you did not upload, they will remain unlabeled.
+        |
+        |Each `read*` attribute contains the following metrics:
+        |
+        | * `nBases`: Total number of bases across all reads.
+        | * `nBasesA`: Total number of adenine bases across all reads.
+        | * `nBasesT`: Total number of thymines across all reads.
+        | * `nBasesG`: Total number of guanines across all reads.
+        | * `nBasesC`: Total number of cytosines across all reads.
+        | * `nBasesN`: Total number of unknown bases across all reads.
+        | * `nReads`: Total number of reads.
+        | * `nBasesByQual`: Array indicating how many bases have a given quality. The quality value corresponds to the
+        |   array index (e.g. array(10) shows how many bases have quality value 10 as quality values start from 0).
+        | * `medianQualByPosition`: Array indicating the median quality value for a given read position. The position
+        |   correspond to the array index (e.g. array(20) shows the median quality value of read position 21 since
+        |   position starts from 1).
+      """.stripMargin
     parameters (
       queryParam[Seq[String]]("runIds")
         .description("Include only Gentrap runs with the given run ID(s).")
@@ -334,6 +442,28 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   val statsGentrapSequencesAggregateGetOperation =
     (apiOperation[SeqStatsAggr[ReadStatsAggr]]("statsGentrapSequencesAggregationsGet")
       summary "Retrieves the aggregate sequencing statistics of Gentrap pipeline runs."
+      notes
+        """This endpoint returns aggregate values of various sequence-level metrics. The default settings are the same
+          | as the corresponding data points endpoint. The aggregated metrics are also similar to the data points'
+          | metrics' with the following additions:
+          |
+          | * `pctBases`: Percentage of bases across all reads.
+          | * `pctBasesA`: Percentage of adenine bases across all reads.
+          | * `pctBasesT`: Percentage of thymines across all reads.
+          | * `pctBasesG`: Percentage of guanines across all reads.
+          | * `pctBasesC`: Percentage of cytosines across all reads.
+          | * `pctBasesN`: Percentage of unknown bases across all reads.
+          | * `pctBasesGC`: Percentage of guanine and cytosine bases across all reads.
+          |
+          |The following data point attributes not aggregated:
+          |
+          | * `nBasesByQual`
+          | * `medianQualByPosition`
+          |
+          |Each aggregated metric contains the attributes `avg` (average), `max` (maximum), `min` (minimum), `median`
+          | (median), and `stdev` (standard deviation). It also contains the `nDataPoints` attribute, showing the number
+          | of data points aggregated for the metrics.
+        """.stripMargin
       parameters (
       queryParam[Seq[String]]("runIds")
         .description("Include only Gentrap runs with the given run ID(s).")

src/main/scala/nl/lumc/sasc/sentinel/models/SeqStats.scala

@@ -82,8 +82,11 @@ case class SeqStatsAggr[T <: AnyRef](read1: T, read2: Option[T] = None, readAll:
  * @param nBasesC Total number of cytosines across all reads.
  * @param nBasesN Total number of unknown bases across all reads.
  * @param nReads Total number of reads.
- * @param nBasesByQual Values indicating how many bases have a given quality.
- * @param medianQualByPosition Values indicating the median base quality of each position.
+ * @param nBasesByQual Sequence indicating how many bases have a given quality. The quality values correspond to the
+ *                     array index (e.g. Seq(10) shows many bases have quality value 10 as quality values start from 0).
+ * @param medianQualByPosition Sequence indicating the median quality value for a given read position. The position
+ *                             correspond to the array index (e.g. Seq(20) shows the median quality value of read
+ *                             position 21 since positions start from 1).
  */
 case class ReadStats(
     nBases: Long,

src/main/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapAlignmentStats.scala

@@ -36,7 +36,9 @@ import nl.lumc.sasc.sentinel.utils.pctOf
  * @param nBasesIntron Number of bases aligned in the intronic regions.
  * @param nBasesRibosomal Number of bases aligned to ribosomal gene regions.
  * @param nBasesUtr Number of bases aligned in the UTR regions.
- * @param normalizedTranscriptCoverage Values representing normalized transcript coverage.
+ * @param normalizedTranscriptCoverage Sequence representing normalized transcript coverage along transcripts. The
+ *                                     transcripts come from the top 1000 expressed genes and each item in the
+ *                                     sequence represents 1% of the transcript length.
  * @param nReadsAligned Number of reads aligned.
  * @param nReadsSingleton Number of paired-end reads aligned as singletons.
  * @param nReadsTotal Number of reads.

src/main/scala/nl/lumc/sasc/sentinel/utils/CustomObjectIdSerializer.scala

@@ -25,7 +25,7 @@ import org.json4s.mongo.ObjectIdSerializer
  * Custom ObjectId serializer for serialization between MongoDB and plain strings.
  *
  * This serializer is required so that `ObjectId`s can be serialized directly to strings instead of JSON objects, i.e.
- * `MongoDBObject("myId" -> ObjectId("1234"))` becomes `{"myId": "1234"}` instead of `{"myId": {"$oid": "1234"}}`.
+ * `MongoDBObject("myId" -> ObjectId("1234"))` becomes `{"myId": "1234"}` instead of `{"myId": {"\$oid": "1234"}}`.
  *
  * The (de)serializers are meant to be used by the controllers when sending JSON payloads.
  */

src/sphinx/api.rst

-API Reference
-=============

src/sphinx/changes.rst

+Changelog
+=========
+
+
+Release 0.1.0
+-------------
+
+`release date: July 6 2015`
+
+* First release of Sentinel, with support of the Gentrap pipeline.

src/sphinx/conf.py

@@ -16,7 +16,8 @@ import sys
 import os
 import shlex
 
-import sphinx_bootstrap_theme
+import alabaster
+
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -34,6 +35,8 @@ import sphinx_bootstrap_theme
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.todo',
+    'sphinx.ext.extlinks',
+    'alabaster',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -62,7 +65,7 @@ author = u'Wibowo Arindrarto'
 # The short X.Y version.
 version = '0.1'
 # The full version, including alpha/beta/rc tags.
-release = '0.1.0'
+release = '0.1.0-SNAPSHOT'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -75,7 +78,7 @@ language = None
 # non-false value, then it is used:
 #today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -99,6 +102,9 @@ exclude_patterns = ['_build']
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
+# Default language to highlight
+highlight_language = 'scala'
+
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
 
@@ -108,6 +114,9 @@ pygments_style = 'sphinx'
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
 
+# URL for sentinel and the live api docs
+sentinel_url = "../"
+apidoc_url = "../api-docs"
 
 # -- Options for HTML output ----------------------------------------------
 
@@ -115,15 +124,38 @@ todo_include_todos = True
 # a list of builtin themes.
 html_theme = 'alabaster'
 
+_scaladoc_url = "scaladoc/%s"
+
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {
-#    'bootswatch_theme': 'flatly',
-#}
+html_theme_options = {
+
+    'show_related': True,
+
+    'github_button': False,
+
+    'extra_nav_links': {
+        "API Documentation": apidoc_url,
+        "Source Code": "https://git.lumc.nl/sasc/sentinel",
+        "Scala Documentation": _scaladoc_url % release,
+    }
+}
+
+# Aliases for external links
+extlinks = {
+    "scaladoc": (_scaladoc_url, "ScalaDoc version "),
+    "apidoc": (apidoc_url + "%s", None),
+    "endpoint": (apidoc_url + "/#!/%s", ""),
+    }
+
+rst_prolog = """
+.. |sentinel_url| replace:: {sentinel_url}
+.. |apidoc_url| replace:: {apidoc_url}
+""".format(sentinel_url=sentinel_url, apidoc_url=apidoc_url)
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+html_theme_path = [alabaster.get_path()]
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
@@ -153,14 +185,21 @@ html_static_path = ['_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',
+        'searchbox.html',
+    ]
+}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.

src/sphinx/contribute.rst

+Contributing
+============
+
+Any type of contributions is very welcomed and appreciated :)! From bug reports to new features, there is always room
+to help out.
+
+Quick Links
+-----------
+
+* Issue tracker: `https://git.lumc.nl/sasc/sentinel/issues <https://git.lumc.nl/sasc/sentinel/issues>`_
+
+* Source code: `https://git.lumc.nl/sasc/sentinel <https://git.lumc.nl/sasc/sentinel>`_
+
+* Git: `git@git.lumc.nl:sasc/sentinel.git <git@git.lumc.nl:sasc/sentinel.git>`_
+
+Bug Reports & Feature Suggestions
+---------------------------------
+
+Feel free to report bugs and/or suggest new features about our local LUMC deployment or Sentinel in general to our
+`issue tracker <https://git.lumc.nl/sasc/sentinel/issues>`_. We do request that you be as descriptive as possible.
+Particularly for bugs, please describe in as much detail as possible what you expected to see and what you saw instead.
+
+Documentation
+-------------
+
+Documentation updates and/or fixes are very appreciated! We welcome everything from one-letter typo fixes to new 
+documentation sections, be it in the internal ScalaDoc or our user guide (the one you're reading now). You are free to
+submit a pull request for documentation fixes. If you don't feel like cloning the entire code, we are also happy if you
+open an issue on our issue tracker.
+
+Bug Fixes
+---------
+
+Bug fix contributions requires that you have a local development environment up and running. Head over to the
+:doc:`devs_setup` section for a short guide on how to do so.
+
+To find bugs to fix, you can start by browsing our issue tracker for issues labeled with ``bug``. You can also search
+through the source code for ``FIXME`` notes. Having found an issue you would like to fix, the next steps would be:
+
+1. Create a new local branch, based on the last version of `master`.
+2. Implement the fix.
+3. Make sure all test passes. If the bug has not been covered by any of our tests, we request that new tests be added
+   to protect against regressions in the future.
+4. Commit your changes.
+5. Submit a pull request.
+
+We will then review your changes. If it is all good, it will be rebased to ``master`` and we will list your name in our
+contributors list :).
+
+And yes, we did say rebase up there, not merge. We prefer to keep our git history linear, which means changes will be
+integrated to ``master`` via ``git rebase`` and not ``git merge``.
+
+New Features
+------------
+
+Feature implementations follow almost the same procedure as `Bug Fixes`_. The difference being that you are not limited
+to the feature requests we list on the issue tracker. If you have a new idea for a new feature that has not been listed
+anywhere, you are free to go ahead and implement it. We only ask that if you do wish to have the feature merged with
+the `master` branch that you communicate with us first, mainly to prevent possible duplicate works.

src/sphinx/deployment.rst

-Deployment
-==========

src/sphinx/design.rst

-Design Notes
-============

src/sphinx/devs_codebase.rst

+The Codebase
+============
+
+Before delving deeper into the code, it is useful to see how the source code is organized.
+
+Starting from the root, we see three directories:
+
+    * ``project``, where the build definition files are located.
+
+    * ``scripts``, where helper scripts are located.
+
+    * ``src``, where the actual source code files are located.
+
+Inside ``src``, we see four more directories. This may look unusual if you come from a Java background, less-so if
+you are already used to Scala. They are:
+
+    * ``main``, where the main Sentinel source files are located.
+
+    * ``test``, where unit tests are defined.
+
+    * ``it``, where integration tests are defined.
+
+    * ``sphinx``, where the raw documentation source files are located.
+
+From here on, you should already get a good grip on the contents of the deeper level directories. Some are worth noting,
+for reasons of clarity:
+
+    * ``test/resources`` contains all test files and example run summaries used for testing. It is symlinked to
+      ``it/resources`` to avoid having duplicate testing resources.
+
+    * ``main/resources`` contains run-time resource files that are loaded into the deployment JAR. In most cases, these
+      are pipeline schema files.
+
+    * ``main/webapp/api-docs`` contains a disttribution copy of the `swagger-ui <https://github.com/swagger-api/swagger-ui>`_
+      package. The package is also bundled into the deployment JAR, to help users explore the Sentinel APIs
+      interactively.

src/sphinx/devs_design.rst

+Internal Design Notes
+=====================
+
+General Aims
+------------
+
+The goal of Sentinel is to enable storing and retrieval of next-generation sequencing metrics as general as possible.
+It should not be constrained to a specific data analysis pipeline, a specific reference sequence, nor a specific
+sequencing technology. The challenge here is to have a framework that can be adapted to the need of a lab / institution
+processing large quantities of such data, when the data analysis pipelines can be so diverse with so many moving parts.
+
+This is why we decided to implement Sentinel as a service which communicates via the HTTP protocol using JSON files.
+JSON files are essentially free-form, yet it still enforces a useful structure and useful data types which can store the
+sequencing metrics. Communicating via HTTP also means that we are not constrained to a specific language. A huge number
+of tools and programming languages that can communicate via HTTP exist today.
+
+The current implementation still has a noticeable drawback, however. At the moment, if one wishes to add support to
+his / her own data analysis pipeline, he/she must clone the entire source code and implement the JSON file parsing
+functions and also the pipeline's HTTP endpoints there. More ideal is to have a single core module (e.g.
+a ``sentinel-core`` package) and other modules which implements specific pipeline support separately. This is not yet
+implemented since in order to do so, we need to be able to combine not only parsing logic, but also the HTTP endpoints
+that exposes the pipeline's metrics. While this is seems possible, we have not found a way to do so cleanly.
+
+Framework
+---------
+
+Sentinel is written in `Scala <http://www.scala-lang.org/>`_ using the `Scalatra <http://www.scalatra.org/>`_ web
+framework. Scalatra was chosen since it is has a minimal core allowing us to add / remove parts as we see fit. Other
+frameworks, such as the Play Framework, may come with features that we probably will never use (e.g. a full-blown
+templating engine).
+
+The API specification is written based on the `Swagger specification <http://swagger.io>`_. It is not the only API
+specification available out there nor is it an official specification endorsed by the W3C. It seems, however,
+to enjoy noticeable support from the programming community in general, with various third-party tools and
+libraries available (at the time of writing). The spec itself is also accompanied by useful tools such as the
+`automatic interactive documentation generator <https://github.com/swagger-api/swagger-ui>`_. Finally, Scalatra can
+generate the specification directly from the code, allowing the spec to live side-by-side with the code.
+
+
+Persistence Layer
+-----------------
+
+For the underlying database, Sentinel uses `MongoDB <https://www.mongodb.org/>`_. This is in line with what Sentinel is
+trying to achieve: to be as general as possible. MongoDB helps by not imposing any schema on its own. However, we would
+like to stress that this does not mean there is no underlying schema of any sort. While MongoDB allows JSON
+document of any structure, Sentinel does expect a certain structure from all incoming JSON summary files. They must
+represent a single pipeline run, which contain at least one sample, which contain at least one library. Internally,
+Sentinel also breaks down an uploaded run summary file into single samples. It is these single samples that are stored
+and queried in the database. One can consider that MongoDB allows us to define the 'schema' on our own, in our own code.
+
+Considering this, we strongly recommend that JSON summary files be validated against a schema. Sentinel uses 
+`JSON schema <http://json-schema.org/>`_, which itself is JSON, for the pipeline schemas.
+
+
+Data Modeling
+-------------
+
+The following list denotes some commonly-used objects inside Sentinel. Other objects exist, so this is not an
+exhaustive list.
+
+Controllers
+^^^^^^^^^^^
+
+HTTP endpoints are represented as ``Controller`` objects which subclass from the ``SentinelServlet`` class. The
+exception to this rule is the ``RootController``, since it implements only few endpoints and is the only controller
+that returns HTML for browser display. API specifications are defined inside the controllers and is tied to a specific
+route matcher of an HTTP method.
+
+Processors
+^^^^^^^^^^
+
+Pipeline support is achieved using ``Processor`` objects, implemented now in the ``nl.lumc.sasc.sentinel.processors``
+package. For a given pipeline, two processors must be implemented: a runs processor, responsible for processing
+incoming run summary files, and a stats processor, responsible for querying and aggregating metrics of the pipeline.
+
+Adapters
+^^^^^^^^
+
+Adapters are traits that are mixed into processors to add processing capabilities. For example, the
+``ReferencesAdapter`` can be mixed in to a processor so it also processes reference sequence information. Most of the
+adapters involve connection to the MongoDB database, although not all do so.
+
+Records
+^^^^^^^
+
+These objects are more loosely-defined, but most of the time they are case classes that represents a MongoDB object
+stored in the database. While it is possible to interact with raw MongoDB objects, we prefer to have these objects
+contained within case classes to minimize run time errors.

src/sphinx/devs_setup.rst

+Local Development Setup
+=======================
+
+
+Dependencies
+------------
+
+The minimum requirements for a local development environment are:
+
+* `git <https://git-scm.com/>`_ (version >= 1.9)
+* `Java <https://www.java.com/en/>`_ (version >= 1.8)
+* `MongoDB <https://www.mongodb.org/>`_ (version >= 3.0)
+
+Note that for testing, Sentinel relies on an embedded MongoDB server which it downloads and runs automatically. If you
+are only interested in running tests or are confident enough not to use any development servers, you can skip MongoDB
+installation.
+
+For building documentation, you will also need Python `Python <https://www.python.org/>`_ (version 2.7.x), since we use
+the `Sphinx <http://sphinx-doc.org/>`_ documentation generator. A complete list of python libraries is listed in the
+``dev-requirements.txt`` file in the root of the project.
+
+And finally, while the following packages are not required per se, they can make your development much easier:
+
+* `IntelliJ <https://www.jetbrains.com/idea/>`_ IDE, with the
+  `Scala plugin <https://plugins.jetbrains.com/plugin/?id=1347>`_.
+* `httpie <https://github.com/jkbrzt/httpie>`_, a command-line HTTP client for issuing HTTP requests.
+
+
+Starting Up