---
title: "cheetSheet"
author: "Lori Shepherd"
output:
    html_document:
      toc: true
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Cheat Sheet for adding Annotations

This doc describes how to add resources to AnnotationHub. In general, these instructions pertain to core team members only.

***

# AnnotationHub

***
## Run Periodically - whenever updated

### ensembl release

This requires generating two types of resources

1. GTF -> GRanges on the fly conversion
2. 2Bit

#### GTF

On Local Machine:

1. Navigate to the AnnotationHub_docker directory or create such a directory by
following the instructions [here](https://github.com/Bioconductor/auxiliary_docker_containers/tree/master/annotationhub).

2. Start the docker:

```
export MYSQL_REMOTE_PASSWORD=***  (See credentials doc)
sudo docker-compose up
```

3. In a new terminal start R:

```
options(AH_SERVER_POST_URL="http://localhost:3000/resource")
options(ANNOTATION_HUB_URL="http://localhost:3000")
library(AnnotationHubData)
# change the appropraite release number
# to populate S3 bucket need metadataOnly = FALSE
# metadataOnly will control population of S3 bucket
# insert controls inserting into database
meta <- updateResources(getwd(),
			  BiocVersion = "3.6",
			  preparerClasses = "EnsemblGtfImportPreparer",
			  metadataOnly = TRUE, insert = FALSE,
			  justRunUnitTest = FALSE, release = "89")
# test/check meta
url <- getOption("AH_SERVER_POST_URL")
pushMetadata(meta, url)

# you could rerun updateResources with insert=TRUE to do the push but I like to check resource data
```
4. exit R

5. Convert db to sqlite (puts the file in the data/ directory)
```
sudo docker exec annotationhub_annotationhub_1 bash /bin/backup_db.sh
```
6. If satisfied, copy this file to annotationhub.bioconductor.org and follow
instructions for updating production database

#### 2Bit

On EC2 Instance:

The files will be downloaded, converted and pushed to S3 bucket. This should
be done on the EC2 instance val_annotations. If it is not running, start the EC2
instance on AWS and log as user ubuntu.

Because this can take awhile, it is recommended to use the screen application.
Some usefule screen calls:
```
- start screen by typing 'screen'
- cd to directory you want to be in, start the process or code you want to run
- exit the screen session with 'ctl-a' 'd'
- list screen sessions with 'screen -ls'
- reconnect to a specific session (e.g., XYZ) with 'screen -r XYZ'
```

1. Start screen
2. Navigate to directory to run code
3. In R:

```
library(AnnotationHubData)
# to populate S3 bucket need metadataOnly = FALSE
# metadataOnly will control population of S3 bucket
# insert controls inserting into database
meta <- updateResources(getwd(),
			BiocVersion = "3.6",
			preparerClasses = "EnsemblTwoBitPreparer",
			metadataOnly = FALSE, insert = FALSE,
			justRunUnitTest = FALSE, release = "89")

# a suggested step is to save(meta, file="metadataForTwoBit")
# and scp to local machine
```

4. Check S3 bucket is being populated.
5. Once finished close everything and stop EC2 instance

On Local Machine:

1. Navigate to the AnnotationHub_docker directory

2. Start the docker:

```
export MYSQL_REMOTE_PASSWORD=***  (See credentials doc)
sudo docker-compose up
```

3. In a new terminal start R:

```
options(AH_SERVER_POST_URL="http://localhost:3000/resource")
options(ANNOTATION_HUB_URL="http://localhost:3000")
library(AnnotationHubData)

# option 1:
meta <- updateResources(getwd(),
			BiocVersion = "3.6",
			preparerClasses = "EnsemblTwoBitPreparer",
			metadataOnly = TRUE, insert = FALSE,
			justRunUnitTest = FALSE, release = "89")


# option 2:
# if you saved the meta from the EC2 instance
load("metadataForTwoBit")

url <- getOption("AH_SERVER_POST_URL")
pushMetadata(meta, url)

# you could rerun updateResources with insert=TRUE to do the push but I like to check resource data
```
4. exit R

5. Convert db to sqlite (puts the file in the data/ directory)
```
sudo docker exec annotationhub_annotationhub_1 bash /bin/backup_db.sh
```
6. If satisfied, copy this file to annotationhub.bioconductor.org and follow
instructions for updating production database

***

After GTF or 2bits are added to production database, you should be able to
get the resources and see the updated timestamp of database with something like
the following

```
library(AnnotationHub)
hub = AnnotationHub()
length(query(hub, c("ensembl", "gtf", "release-89")))
length(query(hub, c("fasta", "release-89", "twobit")))
```


### User Contributed Resources

Contributors will generally reach out when wanting to update or include
Annotations to the AnnotationHub. In the past they have provided the annotations
through an application like dropbox; we have since updated the process and now
will directly upload files to S3 in a temporary location. Send them the
instructions found [here](https://github.com/Bioconductor/AnnotationHubData/blob/master/vignettes/IntroductionToAnnotationHubData.Rmd)

A key will have to be generated for them to access and use the
`AnnotationContributor` account.  Go to [here](https://console.aws.amazon.com/iam/home?region=us-east-1#/users/AnnotationContributor)
Under the 'Security credentials' tab click 'Create access key'. Send the
Access key ID to the contributor and the Secret access key is stored in AWS.
When the contributor is done you can delete the key (small 'x' at the right of
the key row).

Advise that their data should be in a directory the same name as the software
package that will access the annotations; subdirectories to keep track of versions
is strongly encouraged.

Once the data is uploaded to S3 move the data to the proper location.

We will need a copy of the package to generate and test the annotaitons. Request
link to package from user.

Follow instructions [here](https://github.com/Bioconductor/AnnotationHubData/blob/master/inst/scripts/addContributedResources.txt)

In general, generate the list of AnnotationHubMetadata objects with
`makeAnnotationHubMetadata()` or `updateResources`. To test that the
metadata.csv is properly formatted, run `makeAnnotationHubMetadata`.

Some suggested testing procedures can be found [here](https://github.com/Bioconductor/auxiliary_docker_containers/blob/master/annotationhub/README.md#test)

When satisfied start the AnnotationHub docker and add resource to docker.

1. Navigate to the AnnotationHub_docker directory

2. Start the docker:

```
export MYSQL_REMOTE_PASSWORD=***  (See credentials doc)
sudo docker-compose up
```

3. In a new terminal start R:

```
options(AH_SERVER_POST_URL="http://localhost:3000/resource")
options(ANNOTATION_HUB_URL="http://localhost:3000")
library(AnnotationHubData)

# run approprate makeAnnotationHubMetadata() call and
#url <- getOption("AH_SERVER_POST_URL")
#pushMetadata(meta, url)
```
4. exit R

5. Convert db to sqlite (puts the file in the data/ directory)
```
sudo docker exec annotationhub_annotationhub_1 bash /bin/backup_db.sh
```
6. If satisfied, copy this file to annotationhub.bioconductor.org and follow
instructions for updating production database


## Run Release time after new builds of annotations

### makeStandardOrgDbs

This recipe should be run after the new OrgDb packages have been built
for the release are available in the devel repo. The code essentially
loads the current packages, extracts the sqlite file and creates some
basic metadata.

The BiocVersion should be whatever the next release version will be,
the current devel soon to be release. The
OrgDb resources get the same name when they are regenerated - they
aren't tied to a genome build so that's not a distinguishing feature in
the title. We only want 1 OrgDb for each species available in a release
and the BiocVersion is what we use to filter records exposed.

On AWS:

Create S3 bucket based on rdatapath: annotationhub/ncbi/standard/<BiocVersion>

On Local Machine:

1. Navigate to the AnnotationHub_docker directory

2. Start the docker:

```
export MYSQL_REMOTE_PASSWORD=***  (See credentials doc)
sudo docker-compose up
```

3. In a new terminal start R:

```
options(AH_SERVER_POST_URL="http://localhost:3000/resource")
options(ANNOTATION_HUB_URL="http://localhost:3000")
library(AnnotationHubData)

# see the man page for clarification on testing and actively pushing
# ?makeStandardOrgDbsToAHM
# to populate S3 bucket need metadataOnly = FALSE
# metadataOnly will control population of S3 bucket
# insert controls inserting into database
meta <- updateResources(getwd(),
			BiocVersion = "3.5",
			preparerClasses = "OrgDbFromPkgsImportPreparer",
			metadataOnly = TRUE, insert = FALSE,
			justRunUnitTest = FALSE,
			downloadOrgDbs=TRUE)
# downloadOrgDbs can be FALSE for subsequent runs

url <- getOption("AH_SERVER_POST_URL")
pushMetadata(meta, url)
```
4. exit R

5. Convert db to sqlite (puts the file in the data/ directory)
```
sudo docker exec annotationhub_annotationhub_1 bash /bin/backup_db.sh
```
6. If satisfied, copy this file to annotationhub.bioconductor.org and follow
instructions for updating production database

7. After uploaded to production you can test that they are available in release
and devel

```
query(hub, "OrgDb")
table(mcols(query(hub, "OrgDb"))$rdatadateadded)
```
If before the release occurs, `debug(AnnotationHub:::.uid0)` so that query2's biocversion
is the desired test version.

### makeStandardTxDbs

This recipe should be run after the new TxDbs have been built and are in
the devel repo. The code loads the packages, extracts the sqlite file
and creates metadata.

The BiocVersion should be whatever the next release version will be,
the current devel soon to be release. The
OrgDb resources get the same name when they are regenerated - they
aren't tied to a genome build so that's not a distinguishing feature in
the title. We only want 1 OrgDb for each species available in a release
and the BiocVersion is what we use to filter records exposed.

On AWS:

Create S3 bucket based on rdatapath: annotationhub/ucsc/standard/<BiocVersion>

On Local Machine:

1. Navigate to the AnnotationHub_docker directory

2. Start the docker:

```
export MYSQL_REMOTE_PASSWORD=***  (See credentials doc)
sudo docker-compose up
```

3. In a new terminal start R:

```
options(AH_SERVER_POST_URL="http://localhost:3000/resource")
options(ANNOTATION_HUB_URL="http://localhost:3000")
library(AnnotationHubData)

# see the man page for clarification on testing and actively pushing
# follow example in man page
# will need the list of updated or added TxDbs to make a character list of files

?makeStandardTxDbsToAHM



#
# The following will hopefully be implemented in the future
#
#meta <- updateResources(getwd(),
#                        BiocVersion = "3.5",
#                        preparerClasses = "TxDbFromPkgsImportPreparer",
#                        metadataOnly = TRUE, insert = FALSE,
#                        justRunUnitTest = FALSE,
#                        downloadTxDbs=TRUE)
# downloadTxDbs can be FALSE for subsequent runs



url <- getOption("AH_SERVER_POST_URL")
pushMetadata(meta, url)
```
4. exit R

5. Convert db to sqlite (puts the file in the data/ directory)
```
sudo docker exec annotationhub_annotationhub_1 bash /bin/backup_db.sh
```
6. If satisfied, copy this file to annotationhub.bioconductor.org and follow
instructions for updating production database

7. After uploaded to production you can test that they are available in release
and devel

```
query(hub, "TxDb")
table(mcols(query(hub, "TxDb"))$rdatadateadded)
```

### makeNCBIToOrgDbs (Non Standard Orgs)

This code generates ~1000 non-standard
OrgDb sqlite files from ucsc. These are less comprehensive and the
standard OrgDb packages. It's best to run this on an EC2 instance.

The BiocVersion should be whatever the next release version will be,
the current devel soon to be release. The
OrgDb resources get the same name when they are regenerated - they
aren't tied to a genome build so that's not a distinguishing feature in
the title. We only want 1 OrgDb for each species available in a release
and the BiocVersion is what we use to filter records exposed.

Before running, make sure the `AnnotationForge/inst/extdata/viableIDs.rda` and
`GenomeInfoDbData/data/specData.rda` files have been updated and pushed in their
respective packages. The scripts to generate these data files are in the packages
`inst/scripts` directories as viableIDs.R and updateGenomeInfoDbData.R respectively.

On AWS:

Create S3 bucket: annotationhub/ncbi/uniprot/<BiocVersion>

On EC2 Instance:

The files will be downloaded, converted and pushed to S3 bucket. This should
be done on the EC2 instance val_annotations. If it is not running, start the EC2
instance on AWS and log as user ubuntu.

Because this can take awhile, it is recommended to use the screen application.
Some usefule screen calls:
```
- start screen by typing 'screen'
- cd to directory you want to be in, start the process or code you want to run
- exit the screen session with 'ctl-a' 'd'
- list screen sessions with 'screen -ls'
- reconnect to a specific session (e.g., XYZ) with 'screen -r XYZ'
```

1. Start screen
2. Navigate to directory to run code
3. In R:

```
library(AnnotationHubData)

# see the man page for clarification on testing and actively pushing
# ?makeNCBIToOrgDbsToAHM
# to populate S3 bucket need metadataOnly = FALSE
# metadataOnly will control population of S3 bucket
# insert controls inserting into database
meta <- updateResources(getwd(),
			BiocVersion = "3.5",
			preparerClasses = "NCBIImportPreparer",
			metadataOnly = TRUE, insert = FALSE,
			justRunUnitTest = FALSE)

# a suggested step is to save(meta, file="metadataForTwoBit")
# and scp to local machine
```

4. Check S3 bucket is being populated.
5. Once finished close everything and stop EC2 instance

On Local Machine:

1. Navigate to the AnnotationHub_docker directory

2. Start the docker:

```
export MYSQL_REMOTE_PASSWORD=***  (See credentials doc)
sudo docker-compose up
```

3. In a new terminal start R:

```
options(AH_SERVER_POST_URL="http://localhost:3000/resource")
options(ANNOTATION_HUB_URL="http://localhost:3000")
library(AnnotationHubData)

# option 1:
meta <- updateResources(getwd(),
			BiocVersion = "3.5",
			preparerClasses = "NCBIImportPreparer",
			metadataOnly = TRUE, insert = FALSE,
			justRunUnitTest = FALSE)


# option 2:
# if you saved the meta from the EC2 instance
load("metadataForTwoBit")


# Note: Eventually get smarter in code
# but put in fixes to make sure data was uploaded
# need to filter out files that failed 

temp = rep(NA, length(meta))
for(i in 1:length(meta)){
       tit = metadata(meta[[i]])$Title
       temp[i] = tit
}
aws = system("aws s3 ls s3://annotationhub/ncbi/uniprot/3.5 --recursive",
    intern=TRUE)
library(stringr)
aws = gsub("\\s+", " ", str_trim(aws))

temp2 = rep(NA, length(aws))
for(i in 1:length(aws)){
    tit = basename(strsplit(aws[i], " ")[[1]][4])
    temp2[i] = tit
}

idx = which(temp %in% temp2)
meta2 = meta[idx]


url <- getOption("AH_SERVER_POST_URL")
pushMetadata(meta2, url)

```
4. exit R

5. Convert db to sqlite (puts the file in the data/ directory)
```
sudo docker exec annotationhub_annotationhub_1 bash /bin/backup_db.sh
```
6. If satisfied, copy this file to annotationhub.bioconductor.org and follow
instructions for updating production database


***


# ExperimentHub

ExperimentHub Resources are added upon request or when it is recommended a
package be an Experiment Data Package rather than Software package. The
package that will use such data will reach out. It is then a similar process to
The AnnotationHubData adding contributor resources.

The user will upload files to S3 in a temporary location. Send them the
instructions found [here]()

A key will have to be generated for them to access and use the
`AnnotationContributor` account.  Go to [here](https://console.aws.amazon.com/iam/home?region=us-east-1#/users/AnnotationContributor)
Under the 'Security credentials' tab click 'Create access key'. Send the
Access key ID to the contributor and the Secret access key is stored in AWS.
When the contributor is done you can delete the key (small 'x' at the right of
the key row).

Advise that their data should be in a directory the same name as the software
package that will use the Experiment Data when uploading (ie. software package
`Test` would upload files to S3 in a folder `Test` ->  `Test\file1`,
`Test\file2`, etc). If subdirectories are needed that is okay but ensure the
`RDataPath` in the metadata.csv reflects this structure.

Once the data is uploaded to S3 move the data to the proper location.

We will need a copy of the package to generate and test the annotaitons. Request
link to package from user. The following should be sent to user to ensure the
package is sent up correctly: [instructions](https://github.com/Bioconductor/ExperimentHubData/blob/master/vignettes/ExperimentHubData.Rmd).

In general, generate the list of ExperimentHubMetadata objects with
`makeExperimentHubMetadata()` or `addResources`. To test that the
metadata.csv is properly formatted,run  `makeAnnotationHubMetadata`.

 Info on [ExperimentHub docker](https://github.com/Bioconductor/ExperimentHub_docker)
 and how to set up docker directory.

When satisfied start the AnnotationHub docker and add resource to docker.

1. Navigate to the AnnotationHub_docker directory

2. Start the docker:

```
export MYSQL_REMOTE_PASSWORD=***  (See credentials doc)
sudo docker-compose up
```

3. In a new terminal start R:

```
options(EXPERIMENT_HUB_SERVER_POST_URL="http://localhost:4000/resource")
options(EXPERIMENT_HUB_URL="http://localhost:4000")
library(ExperimentHubData)

# run approprate makeExperimentHubMetadata() call and following if necessary
#url <- getOption("EXPERIMENT_HUB_SERVER_POST_URL")
#pushMetadata(meta, url)
```

4. exit R

5. Test
From the list of dockers running `sudo docker ps` find the process with `db` in
the name. Example `test_db1`. Connect to the container with
`sudo docker exec -ti test_db bash`. Log into mysql with `mysql -p -u hubuser`
(The password will be the same as the exported MYSQL_REMOTE_PASSWORD). Explore
with mysql commands like `select * from resources order by id desc limit 5;`

6. Convert db to sqlite (puts the file in the data/ directory)
```
sudo docker exec experimenthubdocker_experimenthub_1 bash /bin/backup_db.sh
```
7. If satisfied, copy this file to annotationhub.bioconductor.org and follow
instructions for updating production database

Some other Notes and helpful hints:

1.  If a new recipe needed to be added, the recipe is added in AnnotationHub.
Be sure to then update the version of AnnotationHub dependency in the DESCRIPTION
of ExperimentHub and increase the version in ExperimentHub.

2. Remember when an ExperimentHub package is accepted it is uploaded to a different
repo.
