---
title: "Creating An AnnotationHub Package"
author: "Valerie Obenchain and Lori Shepherd"
date: "Modified: October 2016. Compiled: `r format(Sys.Date(), '%d %b %Y')`"
output:
  BiocStyle::html_document:
    toc: true
vignette: >
  % \VignetteIndexEntry{AnnotationHub: Creating An AnnotationHub Package}
  % \VignetteEngine{knitr::rmarkdown}
  % \VignetteEncoding{UTF-8}
---


# Overview

The `AnnotationHubData` package provides tools to acquire, annotate, convert
and store data for use in Bioconductor's `AnnotationHub`. BED files from the
Encode project, gtf files from Ensembl, or annotation tracks from UCSC, are
examples of data that can be downloaded, described with metadata, transformed
to standard `Bioconductor` data types, and stored so that they may be
conveniently served up on demand to users via the AnnotationHub client. While
data are often manipulated into a more R-friendly form, the data themselves
retain their raw content and are not filtered or curated like those in
[ExperimentHub](http://bioconductor.org/packages/ExperimentHub/).
Each resource has associated metadata that can be searched through the
`AnnotationHub` client interface.

# New resources

## Family of resources

Multiple, related resources are added to `AnnotationHub` by creating a software
package similar to the existing annotation packages. The package itself does
not contain data but serves as a light weight wrapper around scripts that
generate metadata for the resources added to `AnnotationHub`.

At a minimum the package should contain a man page describing the resources.
Vignettes and additional `R` code for manipulating the objects are optional.

Creating the package involves the following steps:

1. Notify `Bioconductor` team member:
   Man page and vignette examples in the software package will not work until
   the data are available in `AnnotationHub`. Adding the data to AWS S3 and the
   metadata to the production database involves assistance from a `Bioconductor`
   team member.  Please read the section "Uploading Data to S3".

2. Building the software package:
   Below is an outline of package organization. The files listed are required
   unless otherwise stated.

* inst/extdata/

    - metadata.csv:
    This file contains the metadata in the format of one row per resource
    to be added to the `AnnotationHub` database. The file should be generated
    from the code in inst/scripts/make-metadata.R where the final data are
    written out with write.csv(..., row.names=FALSE). The required column
    names and data types are specified in
    `AnnotationHubData::makeAnnotationHubMetadata`.
    See ?`AnnotationHubData::makeAnnotationHubMetadata` for details.

    If necessary, metadata can be broken up into multiple csv files instead
    having of all records in a single "metadata.csv".

* inst/scripts/

    - make-data.R:
    A script describing the steps involved in making the data object(s). This
    includes where the original data were downloaded from, pre-processing, and
    how the final R object was made. Include a description of any steps
    performed outside of `R` with third party software. Output of the script
    should be files on disk ready to be pushed to S3. If data are to be hosted
    on a personal web site instead of S3, this file should explain any
    manipulation of the data prior to hosting on the web site. For data hosted
    on a public web site with no prior manipultaion this file is not needed.

    - make-metadata.R:
    A script to make the metadata.csv file located in inst/extdata of the
    package. See ?`AnnotationHubData::makeAnnotationHubMetadata` for a
    description of the metadata.csv file, expected fields and data types. The
    `AnnotationHubData::makeAnnotationHubMetadata()` function can be used to
    validate the metadata.csv file before submitting the package.

* vignettes/

    OPTIONAL vignette(s) describing analysis workflows.

* R/

    OPTIONAL functions to enhance data exploration.

* man/

    - package man page:
    OPTIONAL. The package man page serves as a landing point and should briefly
    describe all resources associated with the package. There should be an
    \alias entry for each resource title either on the package man page or
    individual man pages.

    - resource man pages:
    OPTIONAL. Man page(s) should describe the resource (raw data source,
    processing, QC steps) and demonstrate how the data can be loaded through
    the `AnnotationHub` interface. For example, replace "SEARCHTERM*" below
    with one or more search terms that uniquely identify resources in your
    package.

    ```
    library(AnnotationHub)
    hub <- AnnotationHub()
    myfiles <- query(hub, "SEARCHTERM1", "SEARCHTERM2")
    myfiles[[1]]  ## load the first resource in the list
    ```

* DESCRIPTION / NAMESPACE
The scripts used to generate the metadata will likely use functions from
AnnotationHub or AnnotationHubData which should be listed in Depends/Imports as
necessary.


3. Data objects:
Data are not formally part of the software package and are stored
separately in AWS S3 buckets. The author should follow instructions in the
section "Uploading Data to S3"

4. Confirm valid metadata:
Confirm the data in inst/exdata/metadata.csv are valid by running
AnnotationHubData:::makeAnnotationHubMetadata() on your package. Please
address and warnings or errors.

5. Package review:
Submit the package to the
[tracker](https://github.com/Bioconductor/Contributions) for review. The
primary purpose of the package review is to validate the metadata in the csv
file(s). It is ok if the package fails R CMD build and check because the
data and metadata are not yet in place. Once the metadata.csv is approved,
records are added to the production database. At that point the package man
pages and vignette can be finalized and the package should pass R CMD build
and check.

## Individual resources

Individual objects of a standard class can be added to the hub by providing
only the data and metadata files or by creating a package as described in the
`Family of Resources` section.

OrgDb, TxDb and BSgenome objects are well defined `Bioconductor` classes and
methods to download and process these objects already exist in `AnnotationHub`.
When adding only one or two objects the overhead of creating a package may be
unnecessary.  The goal of the package is to provide structure for metadata
generation and makes sense when there are plans to update versions or add new
organisms in the future.

Make sure the OrgDb, TxDb or BSgenome object you want to add does not already
exist in the
[Biocondcutor annotation repository](http://www.bioconductor.org/packages/release/BiocViews.html#___AnnotationData)

Providing just data and metadata files involves the following steps:

1. Notify `Bioconductor` team member:
   Adding the data to AWS S3 and the metadata to the production database
   involves assistance from a `Bioconductor` team member. Please read the
   section "Uploading Data to S3".

2. Prepare the data:
   In the case of an OrgDb object, only the sqlite file is stored in S3.
   See makeOrgPackageFromNCBI() and makeOrgPackage() in the `AnnotationForge`
   package for help creating the sqlite file. BSgenome objects should be made
   according to the steps outline in the
   [BSgenome
   vignette](http://www.bioconductor.org/packages/3.4/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf). TxDb objects will be made on-the-fly from a
   GRanges with GenomicFeatures::makeTxDbFromGRanges() when the resource is
   downloaded from `AnnotationHub`. Data should be provided as a GRanges
   object. See GenomicRanges::makeGRangesFromDataFrame() or
   rtracklayer::import() for help creating the GRanges.

3. Generate metadata:
   Prepare a .R file that generates metadata for the resource(s) by calling
   the `AnnotationHubData::AnnotationHubMetadata()` constructor. Argument
   details are found on the ?`AnnotationHubMetadata` man page.

   As an example, this piece of code generates the metadata for
   the Vitis vinifera TxDb Timothée Flutre contributed to `AnnotationHub`:

```{r, TxDb_Metadata, eval=FALSE}
metadata <- AnnotationHubMetadata(
    Description="Gene Annotation for Vitis vinifera",
    Genome="IGGP12Xv0",
    Species="Vitis vinifera",
    SourceUrl="http://genomes.cribi.unipd.it/DATA/V2/V2.1/V2.1.gff3",
    SourceLastModifiedDate=as.POSIXct("2014-04-17"),
    SourceVersion="2.1",
    RDataPath="community/tflutre/",
    TaxonomyId=29760L,
    Title="Vvinifera_CRIBI_IGGP12Xv0_V2.1.gff3.Rdata",
    BiocVersion=package_version("3.3"),
    Coordinate_1_based=TRUE,
    DataProvider="CRIBI",
    Maintainer="Timothée Flutre <timothee.flutre@supagro.inra.fr",
    RDataClass="GRanges",
    DispatchClass="GRanges",
    SourceType="GFF",
    RDataDateAdded=as.POSIXct(Sys.time()),
    Recipe=NA_character_,
    PreparerClass="None",
    Tags=c("GFF", "CRIBI", "Gene", "Transcript", "Annotation"),
    Notes="chrUn renamed to chrUkn"
)
```

4. Add data to S3 and metadata to the database:
   This last step is done by the `Biocondcutor` team member.

# Additional resources

Metadata for new versions of the data can be added to the same package as they
become available.

* The titles for the new versions should be unique and not match the title of
  any resource currently in AnnotationHub. Good practice would be to
  include the version and / or genome build in the title. If the title is
  not unique, the `AnnotationHub` object will list multiple files with the
  same title. The user will need to use 'rdatadateadded' to determine which
  is the most current.

* Make data available: see section on "Uploading Data to S3"

* Update make-metadata.R with the new metadata information

* Generate a new metadata.csv file. The package should contain
  metadata for all versions of the data in AnnotationHub so the old file should
  remain.  When adding a new   version it might be helpful to write a new csv
  file named by version, e.g., metadata_v84.csv, metadata_85.csv etc.

* Bump package version and commit to git

* Notify Lori.Shepherd@Roswellpark.org that an update is ready and
  a team member will add the new metadata to the production database;
  new resources will not be visible in AnnotationHub until
  the metadata are added to the database.

Contact Lori.Shepherd@roswellpark.org or maintainer@bioconductor.org with any
questions.

# Bug fixes

A bug fix may involve a change to the metadata, data resource or both.

## Update the resource

* The replacement resource must have the same name as the original and
  be at the same location (path).

* Notify Lori.Shepherd@roswellpark.org that you want to replace the data
  and make the files available: see section "Uploading Data to S3".

## Update the metadata

New metadata records can be added for new resources but modifying existing
records is discouraged. Record modification will only be done in the case of
bug fixes.

* Notify Lori.Shepherd@roswellpark.org that you want to change the metadata

* Update make-metadata.R and regenerate the metadata.csv file

* Bump the package version and commit to git

# Remove resources

When a resource is removed from `AnnotationHub` two things happen:
the 'rdatadateremoved' field is populated with a date and the 'status'
field is populated with a reason why the resource is no longer available. Once
these changes are made, the `AnnotationHub()` constructor will not list the
resource among the available ids. An attempt to extract the resource with
'[[' and the AH id will return an error along with the status message.

In general, resources are only removed when they are no longer available
(e.g., moved from web location, no longer provided etc.).

To remove a resource from `AnnotationHub` contact Lori.Shepherd@roswellpark.org
or maintainer@bioconductor.org.

# Versioning

Versioning of resources is handled by the maintainer. If you plan to provide
incremental updates to a file for the same organism / genome build, we
recommend including a version in the title of the resource so it is easy
to distinguish which is most current.

If you do not include a version, or make the title unique in some way,
multiple files with the same title will be listed in the `AnnotationHub`
object. The user will can use the 'rdatadateadded' metadata field
to determine which file is the most current.

# Visibility

Several metadata fields control which resources are visible when
a user invokes AnnotationHub(). Records are filtered based on these criteria:

- 'snapshotdate' >= the date of the Bioconductor release being used
- 'rdatadateadded'  >= today's date
- 'rdatadateremoved' is NULL / NA
- 'biocVersion' is <= to the Bioconductor version being used

Once a record is added to AnnotationHub it is visable from that point forward
until stamped with 'rdatadateremoved'. For example, a record added on
May 1, 2017 with 'biocVersion' 3.6 will be visible in all snapshots >=
May1, 2017 and in all Bioconductor versions >= 3.6.

# Uploading Data to S3

Instead of providing the data files via dropbox, ftp, etc. we will grant
temporary access to an S3 bucket where you can upload your data. Please
email Lori.Shepherd@roswellpark.org for access.

You will be given access to the 'AnnotationContributor' user. Ensure that the
`AWS CLI` is installed on your machine. See instructions for installing `AWS
CLI` [here](https://aws.amazon.com/cli/). Once you  have requested access you
will be emailed a set of keys. There are two options to set the profile up for
AnnotationContributor

1.  Update your `.aws/config` file to include the following updating the keys
accordingly:

```
[profile AnnotationContributor]
output = text
region = us-east-1
aws_access_key_id = ****
aws_secret_access_key = ****
```
2. If you can't find the `.aws/config` file,  Run the following command entering
appropriate information from above

```
aws configure --profile AnnotationContributor
```

After the configuration is set you should be able to upload resources using

```
aws --profile AnnotationContributor s3 cp test_file.txt s3://annotation-contributor/test_file.txt --acl public-read

```

Please upload the data with the appropriate directory structure, including
subdirectories as necessary (i.e. top directory must be software package name,
then if applicable, subdirectories of versions, ...)

Once the upload is complete, email Lori.Shepherd@roswellpark.org to continue the
process