Skip to content

Commit

Permalink
Update doc with new repo to hold data files
Browse files Browse the repository at this point in the history
  • Loading branch information
howff committed Feb 21, 2024
1 parent e163c08 commit 2c87807
Show file tree
Hide file tree
Showing 3 changed files with 10 additions and 14 deletions.
5 changes: 1 addition & 4 deletions doc/annotation_database.md
Original file line number Diff line number Diff line change
Expand Up @@ -20,10 +20,7 @@ jq

Download:

- https://cogstack.rosalind.kcl.ac.uk/exports/customised_handlers.tar.gz
- http://netix.dl.sourceforge.net/project/gate/gate/8.1/gate-8.1-build5169-ALL.zip
- https://cogstack.rosalind.kcl.ac.uk/exports/bio-yodie-1.2.1-se.tar.gz
- https://cogstack.rosalind.kcl.ac.uk/exports/bio-yodie-resource-prep-output.2019.fixed.zip
- https://git.ecdf.ed.ac.uk/SMI/data.git

## Install the required software

Expand Down
5 changes: 5 additions & 0 deletions doc/install.md
Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,8 @@ git clone https://github.com/SMI/nlp2phenome
git clone https://git.ecdf.ed.ac.uk/SMI/service-docs.git
git clone https://git.ecdf.ed.ac.uk/SMI/metacat.git
git clone https://github.com/SMI/CogStack-SemEHR
sudo yum install git-lfs
git clone https://git.ecdf.ed.ac.uk/SMI/data.git
```

## Install SemEHR annotation database via Docker
Expand All @@ -101,6 +103,9 @@ sudo chmod g+w /opt/semehr/
ln -s ~/src/CogStack-SemEHR /opt/semehr/CogStack-SemEHR
```

If you want to use the annotation features you'll need some additional
files, see the [annotation database](annotation_database.md) document.

## Python virtual environment

```
Expand Down
14 changes: 4 additions & 10 deletions src/tools/install.sh
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -

sudo apt-get update
sudo apt-get install ant curl openjdk-11-jdk subversion unzip vim git apt-transport-https
sudo apt-get install ant curl openjdk-11-jdk subversion unzip vim git git-lfs apt-transport-https
sudo apt-get install python3 python3-pip python3-virtualenv python3-setuptools python3-dev python3-testresources
sudo apt-get install postgresql-13 mongodb libpq-dev

Expand Down Expand Up @@ -37,6 +37,7 @@ cd ~/SemEHR
git clone https://github.com/SMI/StructuredReports
git clone https://github.com/SMI/CogStack-SemEHR
git clone https://github.com/SMI/nlp2phenome
git clone https://git.ecdf.ed.ac.uk/SMI/data.git

git clone https://github.com/SMI/SmiServices
cd SmiServices/src/common/Smi_Common_Python
Expand All @@ -54,15 +55,8 @@ cd ~/SemEHR/CogStack-SemEHR/installation
echo ~/SemEHR/ | bash install_semehr.sh
sudo apt remove -y python2-dev

cd ~/SemEHR
wget https://cogstack.rosalind.kcl.ac.uk/exports/bio-yodie-resource-prep-output.2019.fixed.zip
unzip bio-yodie-resource-prep-output.2019.fixed.zip
rm -fr __MACOSX
mv ~/SemEHR/gcp/bio-yodie-1-2-1/bio-yodie-resources/en/databases ~/SemEHR/gcp/bio-yodie-1-2-1/bio-yodie-resources/en/databases.old
mv ~/SemEHR/gcp/bio-yodie-1-2-1/bio-yodie-resources/en/gazetteer-en-bio ~/SemEHR/gcp/bio-yodie-1-2-1/bio-yodie-resources/en/gazetteer-en-bio.old
mv output/en/{databases,gazetteer-en-bio} ~/SemEHR/gcp/bio-yodie-1-2-1/bio-yodie-resources/en/
rm bio-yodie-resource-prep-output.2019.fixed.zip
rmdir output/databases output/en output
cd ~/SemEHR/data/CogStack-SemEHR
./install.sh

cd ~/SemEHR/structuredreports/src/tools
./mtsamples_ihi_extract.py
Expand Down

0 comments on commit 2c87807

Please sign in to comment.