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[Updated] Install instructions for Mac and Linux
Richard Stanley edited this page Aug 30, 2017
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This is a manual installation that follows as closely as possible the packaging in Debian except that it can run under any user and does not require superuser privileges. Requirements are a JRE, PHP, Git, wget, unzip.
# for example, on a fresh Ubuntu Linux
sudo apt-get install git wget unzip default-jre openjdk-7-jre php5
This is written for Bash, particularly the array declarations. So, modify if you need to use another shell.
Download the BaseX zip archive and unzip it. We'll create an openinfoman folder to store all of the relevant files both of OpenInfoMan and BaseX. This mirrors the approach used in the PPA packaging in Linux.
Note: Do not install via Homebrew as it is not the correct version and it creates BaseXData, BaseXWeb, BaseXRepo, instead of the dirs named data, webapp, and repo. If you installed the Homebrew version, remove the basex dotfiles and BaseX dirs in $HOME.
cd $HOME
wget http://files.basex.org/releases/8.5.3/BaseX853.zip
unzip BaseX853.zip
mkdir openinfoman
cp -R basex/* openinfoman/
cp basex/.basexhome openinfoman/
# remove if you wish
# rm -rf basex/
Add the openinfoman/bin directory to your $PATH however you wish to do so. Download the OpenInfoMan source repo and copy into the openinfoman folder the relevant files.
mkdir openinfoman/repo-src
git clone https://github.com/openhie/openinfoman openinfomangh
cp openinfomangh/repo/* openinfoman/repo-src/
cp -R openinfomangh/resources openinfoman/
cp ~/openinfomangh/webapp/*xqm ~/openinfoman/webapp
mkdir -p ~/openinfoman/webapp/static
cp -R ~/openinfomangh/webapp/static/* ~/openinfoman/webapp/static
basex -Vc "CREATE DATABASE provider_directory"
echo "module namespace csd_webconf = 'https://github.com/openhie/openinfoman/csd_webconf';
declare variable \$csd_webconf:db := 'provider_directory';
declare variable \$csd_webconf:baseurl := '';
declare variable \$csd_webconf:remote_services := ();
" > $HOME/openinfoman/repo-src/generated_openinfoman_webconfig.xqm
basex -Vc "REPO INSTALL http://files.basex.org/modules/expath/functx-1.0.xar"
cd openinfoman/repo-src
basex -Vc "repo install "generated_openinfoman_webconfig.xqm""
# use the list of funcs from the debian install.
declare -a arr=("csd_webapp_ui.xqm" "csd_base_library.xqm" "csd_base_library_updating.xqm" "csd_base_stored_queries.xqm" "csd_document_manager.xqm" "csd_load_sample_directories.xqm" "csd_query_updated_services.xqm" "csd_poll_service_directories.xqm" "csd_local_services_cache.xqm" "csd_merge_cached_services.xqm" "csr_processor.xqm" "svs_load_shared_value_sets.xqm" "async_fake.xqm");\
for i in "${arr[@]}"; do basex -Vc "repo install $i"; done
basex -Vc "RUN $HOME/openinfoman/resources/scripts/init_db.xq"
cd $HOME/openinfoman
declare -a arr=("stored_query_definitions/facility_search.xml" "stored_query_definitions/adhoc_search.xml" "stored_query_definitions/service_search.xml" "stored_query_definitions/organization_search.xml" "stored_query_definitions/provider_search.xml" "stored_query_definitions/modtimes.xml" "stored_updating_query_definitions/service_create.xml" "stored_updating_query_definitions/mark_duplicate.xml" "stored_updating_query_definitions/simple_merge.xml" "stored_updating_query_definitions/mark_potential_duplicate.xml" "stored_updating_query_definitions/delete_potential_duplicate.xml" "stored_updating_query_definitions/organization_create.xml" "stored_updating_query_definitions/provider_create.xml" "stored_updating_query_definitions/facility_create.xml" "stored_updating_query_definitions/delete_duplicate.xml" "stored_updating_query_definitions/merge_by_identifier.xml" "stored_updating_query_definitions/extract_hierarchy.xml");\
for i in "${arr[@]}"; do resources/scripts/install_stored_function.php resources/$i; done
cd $HOME/openinfoman/resources/shared_value_sets
declare -a arr=("1.3.6.1.4.1.21367.200.101" "1.3.6.1.4.1.21367.200.102" "1.3.6.1.4.1.21367.200.103" "1.3.6.1.4.1.21367.200.104" "1.3.6.1.4.1.21367.200.105" "1.3.6.1.4.1.21367.200.106" "1.3.6.1.4.1.21367.200.108" "1.3.6.1.4.1.21367.200.109" "1.3.6.1.4.1.21367.200.110" "2.25.1098910207106778371035457739371181056504702027035" "2.25.17331675369518445540420660603637128875763657" "2.25.18630021159349753613449707959296853730613166189051" "2.25.259359036081944859901459759453974543442705863430576" "2.25.265608663818616228188834890512310231251363785626032" "2.25.309768652999692686176651983274504471835.999.400" "2.25.309768652999692686176651983274504471835.999.401" "2.25.309768652999692686176651983274504471835.999.402" "2.25.309768652999692686176651983274504471835.999.403" "2.25.309768652999692686176651983274504471835.999.404" "2.25.309768652999692686176651983274504471835.999.405" "2.25.309768652999692686176651983274504471835.999.406" "2.25.9830357893067925519626800209704957770712560");\
for i in "${arr[@]}"; do basex -q"import module namespace svs_lsvs = 'https://github.com/openhie/openinfoman/svs_lsvs';' (svs_lsvs:load($i))'" ; done
Done. Launch the web server with:
cd $HOME/openinfoman && basexhttp &
# gracefully stop the server
basexhttp stop
Visit http://localhost:8984/CSD
Note: The basexhttp script must be run from $HOME/openinfoman or some path resolutions will fail.
This installs the following OpenInfoMan libraries:
- Configurable Export to CSV
- RapidPro
- Health Worker Registry
- Inter-Linked Health Worker Registry Validation
- DHIS2
cd $HOME
git clone https://github.com/openhie/openinfoman-csv
cd ~/openinfoman-csv/repo
basex -Vc "REPO INSTALL openinfoman_csv_adapter.xqm"
# this may not be needed
cp ~/openinfoman-csv/webapp/*xqm ~/openinfoman/webapp
Note: openinfoman-rapidpro is dependent on openinfoman-csv
cd $HOME
git clone https://github.com/openhie/openinfoman-rapidpro
cp ~/openinfoman-rapidpro/resources/stored_query_definitions/* ~/openinfoman/resources/stored_query_definitions
cd $HOME/openinfoman
declare -a arr=("stored_query_definitions/get_csv_for_import.xml" "stored_query_definitions/phone_stats.xml" "stored_query_definitions/select_facility.xml" "stored_query_definitions/get_json_for_import.xml");\
for i in "${arr[@]}"; do resources/scripts/install_stored_function.php resources/$i; done
Not in the postinst, but including.
cp ~/openinfoman-rapidpro/webapp/openinfoman_rapidpro_bindings.xqm ~/openinfoman/webapp
There are also additional tools in openinfoman-rapidpro under the tools directory.
cd $HOME
git clone https://github.com/openhie/openinfoman-ilr
cp ~/openinfoman-ilr/resources/stored_query_definitions/* ~/openinfoman/resources/stored_query_definitions
cd $HOME/openinfoman
resources/scripts/install_stored_function.php resources/stored_query_definitions/validate_provider_facility_service.xml
cd $HOME
git clone https://github.com/openhie/openinfoman-hwr
cp ~/openinfoman-hwr/resources/stored_query_definitions/* ~/openinfoman/resources/stored_query_definitions/
cp ~/openinfoman-hwr/resources/stored_updating_query_definitions/* ~/openinfoman/resources/stored_updating_query_definitions/
cd $HOME/openinfoman
declare -a arr=("stored_query_definitions/health_worker_urn_search_by_id.xml" "stored_query_definitions/health_worker_indices_address.xml" "stored_query_definitions/health_worker_indices_provider_facility.xml" "stored_query_definitions/health_worker_read_name.xml" "stored_query_definitions/health_worker_indices_service.xml" "stored_query_definitions/health_worker_read_otherids.xml" "stored_query_definitions/facility_indices_otherid.xml" "stored_query_definitions/health_worker_read_credential.xml" "stored_query_definitions/health_worker_read_org_address.xml" "stored_query_definitions/facility_name_search.xml" "stored_query_definitions/health_worker_read_provider.xml" "stored_query_definitions/facility_read_organization.xml" "stored_query_definitions/facility_read_otherid.xml" "stored_query_definitions/facility_indices_address.xml" "stored_query_definitions/organization_get_urns.xml" "stored_query_definitions/facility_read_contact_point.xml" "stored_query_definitions/organization_read_address.xml" "stored_query_definitions/facility_indices_contact_point.xml" "stored_query_definitions/health_worker_read_service.xml" "stored_query_definitions/health_worker_indices_provider_organization.xml" "stored_query_definitions/facility_read_service.xml" "stored_query_definitions/health_worker_indices_org_contact_point.xml" "stored_query_definitions/bulk_health_worker_read_otherids_json.xml" "stored_query_definitions/organization_indices_otherid.xml" "stored_query_definitions/health_worker_get_urns.xml" "stored_query_definitions/health_worker_read_provider_organization.xml" "stored_query_definitions/health_worker_read_provider_facility.xml" "stored_query_definitions/health_worker_indices_otherid.xml" "stored_query_definitions/health_worker_indices_credential.xml" "stored_query_definitions/health_worker_read_org_contact_point.xml" "stored_query_definitions/organization_indices_address.xml" "stored_query_definitions/facility_indices_organization.xml" "stored_query_definitions/health_worker_indices_contact_point.xml" "stored_query_definitions/health_worker_read_address.xml" "stored_query_definitions/organization_name_search.xml" "stored_query_definitions/health_worker_read_otherids_json.xml" "stored_query_definitions/health_worker_indices_org_address.xml" "stored_query_definitions/health_worker_indices_name.xml" "stored_query_definitions/organization_indices_contact_point.xml" "stored_query_definitions/organization_read_credential.xml" "stored_query_definitions/health_worker_read_otherid.xml" "stored_query_definitions/health_worker_indices_operating_hours.xml" "stored_query_definitions/health_worker_read_operating_hours.xml" "stored_query_definitions/facility_indices_service.xml" "stored_query_definitions/organization_read_otherid.xml" "stored_query_definitions/service_get_urns.xml" "stored_query_definitions/facility_get_urns.xml" "stored_query_definitions/provider_name_search.xml" "stored_query_definitions/organization_indices_credential.xml" "stored_query_definitions/organization_read_contact_point.xml" "stored_query_definitions/facility_read_address.xml" "stored_query_definitions/health_worker_read_contact_point.xml" "stored_updating_query_definitions/health_worker_delete_org_contact_point.xml" "stored_updating_query_definitions/health_worker_update_contact_point.xml" "stored_updating_query_definitions/health_worker_delete_otherid.xml" "stored_updating_query_definitions/health_worker_create_org_address.xml" "stored_updating_query_definitions/health_worker_delete_provider_facility.xml" "stored_updating_query_definitions/health_worker_update_service.xml" "stored_updating_query_definitions/health_worker_update_provider_facility.xml" "stored_updating_query_definitions/health_worker_update_provider_organization.xml" "stored_updating_query_definitions/health_worker_create_service.xml" "stored_updating_query_definitions/health_worker_create_provider_organization.xml" "stored_updating_query_definitions/health_worker_delete_address.xml" "stored_updating_query_definitions/health_worker_update_provider.xml" "stored_updating_query_definitions/health_worker_create_org_contact_point.xml" "stored_updating_query_definitions/health_worker_delete_operating_hours.xml" "stored_updating_query_definitions/health_worker_create_provider.xml" "stored_updating_query_definitions/health_worker_delete_credential.xml" "stored_updating_query_definitions/health_worker_update_operating_hours.xml" "stored_updating_query_definitions/health_worker_update_name.xml" "stored_updating_query_definitions/health_worker_delete_name.xml" "stored_updating_query_definitions/health_worker_create_credential.xml" "stored_updating_query_definitions/health_worker_delete_org_address.xml" "stored_updating_query_definitions/health_worker_create_contact_point.xml" "stored_updating_query_definitions/health_worker_update_otherid.xml" "stored_updating_query_definitions/health_worker_create_provider_facility.xml" "stored_updating_query_definitions/health_worker_create_address.xml" "stored_updating_query_definitions/health_worker_delete_service.xml" "stored_updating_query_definitions/health_worker_update_address.xml" "stored_updating_query_definitions/health_worker_delete_provider_organization.xml" "stored_updating_query_definitions/health_worker_update_org_contact_point.xml" "stored_updating_query_definitions/health_worker_update_credential.xml" "stored_updating_query_definitions/health_worker_create_operating_hours.xml" "stored_updating_query_definitions/health_worker_delete_contact_point.xml" "stored_updating_query_definitions/health_worker_delete_provider.xml" "stored_updating_query_definitions/health_worker_update_org_address.xml" "stored_updating_query_definitions/health_worker_create_name.xml" "stored_updating_query_definitions/health_worker_create_otherid.xml" );\
for i in "${arr[@]}"; do resources/scripts/install_stored_function.php resources/$i; done
cd $HOME
git clone https://github.com/openhie/openinfoman-dhis
cp openinfoman-dhis/repo/* openinfoman/repo-src/
cp ~/openinfoman-dhis/resources/stored_query_definitions/* ~/openinfoman/resources/stored_query_definitions/
cp ~/openinfoman-dhis/resources/stored_updating_query_definitions/* ~/openinfoman/resources/stored_updating_query_definitions/
cd $HOME/openinfoman/repo-src
declare -a arr=("dxf2csd.xqm" "dxf_1_0.xqm" "util.xqm");\
for i in "${arr[@]}"; do basex -Vc "repo install $i"; done
cd $HOME/openinfoman
declare -a arr=("stored_query_definitions/aggregate_hw_export.xml" "stored_query_definitions/csd2dxf.xml" "stored_query_definitions/transform_to_dxf.xml" "stored_updating_query_definitions/dxf_to_svs.xml" "stored_updating_query_definitions/dxf_to_csd.xml" "stored_updating_query_definitions/extract_from_dxf.xml");\
for i in "${arr[@]}"; do resources/scripts/install_stored_function.php resources/$i; done
cp ~/openinfoman-dhis/webapp/openinfoman_dhis2_bindings.xqm ~/openinfoman/webapp
cp -R ~/openinfoman-dhis/resources/service_directories/* ~/openinfoman/resources/service_directories/
cd ~/openinfoman/bin && ./basexhttp &