Skip to content

Commit

Permalink
Merge branch 'develop' into model-run-workflow
Browse files Browse the repository at this point in the history
  • Loading branch information
meetagrawal09 authored Sep 21, 2024
2 parents 69c27d6 + 09a58d2 commit a949401
Show file tree
Hide file tree
Showing 6 changed files with 129 additions and 48 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/book.yml
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ jobs:
git config --global user.email "[email protected]"
git config --global user.name "GitHub Documentation Robot"
export VERSION=$(echo $GITHUB_REF | sed 's,.*/,,' )
if [ "$VERSION" == "main" ]; then
if [ "$VERSION" = "main" ]; then
export VERSION=latest
fi
cd pecan-documentation
Expand Down
28 changes: 14 additions & 14 deletions base/db/R/dbfiles.R
Original file line number Diff line number Diff line change
Expand Up @@ -50,9 +50,8 @@ dbfile.input.insert <- function(in.path, in.prefix, siteid, startdate, enddate,


# setup parent part of query if specified
if (is.na(parentid)) {
parent <- ""
} else {
parent <- ""
if (!is.na(parentid)) {
parent <- paste0(" AND parent_id=", parentid)
}

Expand Down Expand Up @@ -242,13 +241,13 @@ dbfile.input.check <- function(siteid, startdate = NULL, enddate = NULL, mimetyp
formatid <- get.id(table = "formats", colnames = c("mimetype_id", "name"), values = c(mimetypeid, formatname), con = con)

if (is.null(formatid)) {
invisible(data.frame())
return (invisible(data.frame()))
}

# setup parent part of query if specified
if (is.na(parentid)) {
parent <- ""
} else {
parent <- ""

if (!is.na(parentid)) {
parent <- paste0(" AND parent_id=", parentid)
}

Expand Down Expand Up @@ -450,7 +449,7 @@ dbfile.posterior.check <- function(pft, mimetype, formatname, con, hostname = PE
# find appropriate pft
pftid <- get.id(table = "pfts", values = "name", colnames = pft, con = con)
if (is.null(pftid)) {
invisible(data.frame())
return (invisible(data.frame()))
}

# find appropriate format
Expand All @@ -461,7 +460,7 @@ dbfile.posterior.check <- function(pft, mimetype, formatname, con, hostname = PE
formatid <- get.id(table = "formats", colnames = c("mimetype_id", "name"), values = c(mimetypeid, formatname), con = con)

if (is.null(formatid)) {
invisible(data.frame())
return (invisible(data.frame()))
}

# find appropriate posterior
Expand All @@ -473,7 +472,7 @@ dbfile.posterior.check <- function(pft, mimetype, formatname, con, hostname = PE
con = con
)[["id"]]
if (is.null(posteriorid)) {
invisible(data.frame())
return (invisible(data.frame()))
}

invisible(dbfile.check(type = "Posterior", container.id = posteriorid, con = con, hostname = hostname))
Expand Down Expand Up @@ -639,12 +638,12 @@ dbfile.file <- function(type, id, con, hostname = PEcAn.remote::fqdn()) {

if (nrow(files) > 1) {
PEcAn.logger::logger.warn("multiple files found for", id, "returned; using the first one found")
invisible(file.path(files[1, "file_path"], files[1, "file_name"]))
return(invisible(file.path(files[1, "file_path"], files[1, "file_name"])))
} else if (nrow(files) == 1) {
invisible(file.path(files[1, "file_path"], files[1, "file_name"]))
return(invisible(file.path(files[1, "file_path"], files[1, "file_name"])))
} else {
PEcAn.logger::logger.warn("no files found for ", id, "in database")
invisible(NA)
return(invisible(NA))
}
}

Expand All @@ -662,7 +661,8 @@ dbfile.id <- function(type, file, con, hostname = PEcAn.remote::fqdn()) {
# find appropriate host
hostid <- db.query(query = paste0("SELECT id FROM machines WHERE hostname='", hostname, "'"), con = con)[["id"]]
if (is.null(hostid)) {
invisible(NA)
PEcAn.logger::logger.warn("hostid not found in database")
return (invisible(NA))
}

# find file
Expand Down
Original file line number Diff line number Diff line change
@@ -1,19 +1,20 @@
### Mac OSX {#macosx}

These are specific notes for installing PEcAn on Mac OSX and will be referenced from the main [installing PEcAn](Installing-PEcAn) page. You will at least need to install the build environment and Postgres sections. If you want to access the database/PEcAn using a web browser you will need to install Apache. To access the database using the BETY interface, you will need to have Ruby installed.
These are specific notes for installing PEcAn on Mac OSX and referenced from the [installing PEcAn](Installing-PEcAn) page.

This document also contains information on how to install the Rstudio server edition as well as any other packages that can be helpful.
Build environment and Postgres sections are required to install and use PEcAn.

Optional software includes Apache, Rails, and Rstudio. Apache is required to run the BETYdb UI and the web-based version of PEcAn - both are optional. Rails is requred to use the BETYdb web interface. Rstudio is a commonly used IDE for R.

#### Install build environment

```bash
# install R
# download from http://cran.r-project.org/bin/macosx/
##### Option 1: Download and install

R: download from http://cran.r-project.org/bin/macosx/

# install gfortran
# download from http://cran.r-project.org/bin/macosx/tools/
gfortran: download from http://cran.r-project.org/bin/macosx/tools/

```bash
# install OpenMPI
curl -o openmpi-1.6.3.tar.gz http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.3.tar.gz
tar zxf openmpi-1.6.3.tar.gz
Expand Down Expand Up @@ -42,14 +43,63 @@ sudo make install
cd ..
```

#### Install Postgres
##### Option 2: Homebrew

```bash
# R
brew install --cask r
# gfortran
brew install gcc
# OpenMPI
brew install open-mpi
# szip
brew install szip
# HDF5
brew install hdf5
## homebrew should configure hdf5 with fortran and cxx, otherwise:
## brew install hdf5 --with-fortran --with-cxx
```

For those on a Mac I use the following app for postgresql which has
postgis already installed (http://postgresapp.com/)

To get postgis run the following commands in psql:
#### Install Postgres and PostGIS

##### Option 1:

For MacOS, the Postgres.app provides Postgres with PostGIS
already installed (http://postgresapp.com/).

To run Postgres:
* Open Postgres.app.
* In the menu bar, click the elephant icon and select “Open psql”.

##### Option 2: install using homebrew:

```bash
# optional: remove existing postgres installations with:
# brew uninstall --force postgresql

# install Postgres, fixed at v12 (officially supported by BETYdb):
brew install postgres@12
brew pin postgres@12

# PostGIS
brew install postgis

# to run Postgres:
brew services start postgresql
```

#### Enable PostGIS

To enable PostGIS, you should start Postgres:

```bash
psql postgres
```

And then run the following commands:

```sql
##### Enable PostGIS (includes raster)
CREATE EXTENSION postgis;
##### Enable Topology
Expand All @@ -60,23 +110,42 @@ CREATE EXTENSION fuzzystrmatch;
CREATE EXTENSION postgis_tiger_geocoder;
```

To check your postgis run the following command again in psql: `SELECT PostGIS_full_version();`
To check your postgis run the following command again in psql:

```sql
SELECT PostGIS_full_version();`
```

#### Additional installs


##### Install JAGS

Download JAGS from http://sourceforge.net/projects/mcmc-jags/files/JAGS/3.x/Mac%20OS%20X/JAGS-Mavericks-3.4.0.dmg/download

##### Option 1: using homebrew

```bash
brew install jags
```

##### Option 2: Download

Download JAGS from http://sourceforge.net/projects/mcmc-jags/files/JAGS/3.x/Mac%20OS%20X/JAGS-Mavericks-3.4.0.dmg/download.


##### Install udunits

Installing udunits-2 on MacOSX is done from source.
##### Option 1: Install using homebrew:

```bash
brew install udunits
```

##### Option 2: Install udunits-2 on MacOSX is done from source.

* download most recent [version of Udunits here](http://www.unidata.ucar.edu/downloads/udunits/index.jsp)
* instructions for [compiling from source](http://www.unidata.ucar.edu/software/udunits/udunits-2/udunits2.html#Obtain)


```bash
curl -o udunits-2.1.24.tar.gz ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.1.24.tar.gz
tar zxf udunits-2.1.24.tar.gz
Expand All @@ -86,7 +155,7 @@ make
sudo make install
```

#### Apache Configuration
#### Apache Configuration (Optional)

Mac does not support pdo/postgresql by default. The easiest way to install is use: http://php-osx.liip.ch/

Expand All @@ -102,10 +171,24 @@ Alias /pecan ${PWD}/pecan/web
EOF
```

#### Ruby
#### Ruby (Optional)

_Note: it is recommended that BETYdb be run using Docker because the application uses unsupported versions of Ruby and Rails._

The BETYdb application requires Ruby version 2.7.7, as specified in [PecanProject/bety/.ruby-version](https://github.com/PecanProject/bety/blob/develop/.ruby-version).

```bash
brew install rbenv
rbenv init
rbenv install 2.7.7
```

#### Rstudio (Optional)

The default version of ruby should work. Or use [JewelryBox](https://jewelrybox.unfiniti.com/).
For MacOS, you can download [Rstudio Desktop](http://www.rstudio.com/).

#### Rstudio Server
Or using homebrew:

For the mac you can download [Rstudio Desktop](http://www.rstudio.com/).
```bash
brew install --cask rstudio
```
21 changes: 11 additions & 10 deletions modules/data.atmosphere/R/met.process.R
Original file line number Diff line number Diff line change
Expand Up @@ -255,13 +255,14 @@ met.process <- function(site, input_met, start_date, end_date, model,
#--------------------------------------------------------------------------------------------------#
# Change to Site Level - Standardized Met (i.e. ready for conversion to model specific format)
if (stage$standardize) {
standardize_result <- list()

id_stdized <- list()
ready.id <- list(input.id = NULL, dbfile.id = NULL)

for (i in seq_along(cf.id[[1]])) {

if (register$scale == "regional") {
#### Site extraction
standardize_result[[i]] <- .extract.nc.module(cf.id = list(input.id = cf.id$container_id[i],
id_stdized <- .extract.nc.module(cf.id = list(input.id = cf.id$container_id[i],
dbfile.id = cf.id$id[i]),
register = register,
dir = dir,
Expand All @@ -277,7 +278,7 @@ met.process <- function(site, input_met, start_date, end_date, model,
# Expand to support ensemble names in the future
} else if (register$scale == "site") {
##### Site Level Processing
standardize_result[[i]] <- .metgapfill.module(cf.id = list(input.id = cf.id$input.id[i], dbfile.id = cf.id$dbfile.id[i]),
id_stdized <- .metgapfill.module(cf.id = list(input.id = cf.id$input.id[i], dbfile.id = cf.id$dbfile.id[i]),
register = register,
dir = dir,
met = met,
Expand All @@ -288,15 +289,15 @@ met.process <- function(site, input_met, start_date, end_date, model,
host = host,
overwrite = overwrite$standardize,
ensemble_name = i)
} else {
# No action taken. These ids will be dropped from ready.id
id_stdized <- NULL
}

ready.id$input.id <- c(ready.id$input.id, id_stdized$input.id)
ready.id$dbfile.id <- c(ready.id$dbfile.id, id_stdized$dbfile.id)

} # End for loop
ready.id <- list(input.id = NULL, dbfile.id = NULL)

for (i in seq_along(standardize_result)) {
ready.id$input.id <- c(ready.id$input.id, standardize_result[[i]]$input.id)
ready.id$dbfile.id <- c(ready.id$dbfile.id, standardize_result[[i]]$dbfile.id)
}

} else {
ready.id <- input_met$id
Expand Down
1 change: 0 additions & 1 deletion modules/uncertainty/R/sensitivity.R
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@
##' @export
##' @author Ryan Kelly, David LeBauer, Rob Kooper, Mike Dietze, Istem Fer
#--------------------------------------------------------------------------------------------------#
##' @author Ryan Kelly, David LeBauer, Rob Kooper, Mike Dietze
read.sa.output <- function(traits, quantiles, pecandir, outdir, pft.name = "",
start.year, end.year, variable, sa.run.ids = NULL, per.pft = FALSE) {

Expand Down
2 changes: 0 additions & 2 deletions modules/uncertainty/man/read.sa.output.Rd

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

0 comments on commit a949401

Please sign in to comment.