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Working on #1 - FDA import process works. 3 hours for first import, 1.25 hours on subsequent updates.

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This commit is contained in:
Andrew Kesterson
2013-10-27 18:35:35 -04:00
parent e0232aa02d
commit 0a7bf8f174
21 changed files with 759 additions and 472 deletions
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173
Makefile
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@@ -1,90 +1,85 @@
MAJOR:=$(shell bash -c 'source version.sh ; echo $$MAJOR')
BUILD:=$(shell bash -c 'source version.sh ; echo $$BUILD')
OS_NAME:=$(shell bash -c 'source version.sh ; echo $$OS_NAME')
ifeq "$(OS_NAME)" "win"
PIP=$(shell pwd)/virtualenv/Scripts/pip
VIRTUALENV_PKGS_DIR=$(shell pwd)/virtualenv/Lib/site-packages
else
PIP=$(shell pwd)/virtualenv/bin/pip
VIRTUALENV_PKGS_DIR=$(shell pwd)/virtualenv/lib/site-packages
endif
VIRTUALENV=$(shell which virtualenv)
PYTHON=$(shell which python)
PYTHON_FILES=setup.py mercy/version.py $(shell find mercy -iname "*py")
PYTHON_SDIST=./dist/mercy-$(MAJOR)-$(BUILD).tar.gz
.PHONY: clean
clean:
rm -fr dist/*
find mercy -iname "*pyc" -exec rm -vf \{\} \;
cd puppet && make clean
############## Targets for puppet module
puppet/version.sh: version.sh
cp version.sh $@
.PHONY: puppet
puppet: puppet_dist
.PHONY: puppet_dist
puppet_dist: puppet/version.sh
cd puppet && make dist
.PHONY: puppet_install
puppet_install: puppet/version.sh
cd puppet && make install
.PHONY: puppet_uninstall
puppet_uninstall: puppet/version.sh
cd puppet && make uninstall
################ /puppet module
############### Targets for python app
dist: $(PYTHON_SDIST) puppet
sdist: $(PYTHON_SDIST)
mercy/version.py: version.sh
bash -c 'source version.sh && echo "VERSION=\"$${MAJOR}-$${BUILD}\"" > $@'
$(PYTHON_SDIST): $(PYTHON_FILES)
$(PYTHON) setup.py sdist --formats=gztar
uninstall:
rm -fr $(VIRTUALENV_PKGS_DIR)/mercy-* || echo 'not installed'
install: $(PYTHON_SDIST) virtualenv
$(PIP) install $(PYTHON_SDIST) --upgrade
.PHONY: virtualenv
virtualenv:
if [ ! -e $(PIP) ]; then \
$(VIRTUALENV) --no-site-packages --distribute virtualenv ; \
fi
################## /python app
################## Targets for supporting development work
databases: databases/fda_ndc.zip databases/drugbank.xml.zip
.PHONY: databases/fda_ndc.zip
databases/fda_ndc.zip:
rm -fr databases/fda_ndc*
mkdir -p databases/fda_ndc
rm -f fda_ndc.zip
DBPAGE=$$(wget -O - http://www.fda.gov/Drugs/InformationOnDrugs/default.htm --quiet | grep -Eo 'National Drug Code Directory Search(</strong>)*(</a>)*(<br />)*<a href="[a-zA-Z0-9\:/\.]+">More information about the database</a>' | cut -d \" -f 2); \
LINK=$$(wget -O - http://www.fda.gov/$${DBPAGE} --quiet | grep ">NDC Database File" | cut -d \" -f 2) ; \
wget -O $@ http://www.fda.gov/$${LINK}
cd databases/fda_ndc && unzip -e ../fda_ndc.zip
.PHONY: databases/drugbank.xml.zip
databases/drugbank.xml.zip:
rm -fr databases/drugbank*
mkdir -p databases/drugbank
wget -O $@ http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip
MAJOR:=$(shell bash -c 'source version.sh ; echo $$MAJOR')
BUILD:=$(shell bash -c 'source version.sh ; echo $$BUILD')
OS_NAME:=$(shell bash -c 'source version.sh ; echo $$OS_NAME')
PIP=$(shell pwd)/virtualenv/bin/pip
VIRTUALENV_PKGS_DIR=$(shell pwd)/virtualenv/lib/python2.7/site-packages
VIRTUALENV=$(shell which virtualenv)
PYTHON=$(shell which python)
PYTHON_FILES=setup.py mercy/version.py $(shell find mercy -iname "*py")
PYTHON_SDIST=./dist/mercy-$(MAJOR)-$(BUILD).tar.gz
.PHONY: clean
clean:
rm -fr dist/*
find mercy -iname "*pyc" -exec rm -vf \{\} \;
cd puppet && make clean
############## Targets for puppet module
puppet/version.sh: version.sh
cp version.sh $@
.PHONY: puppet
puppet: puppet_dist
.PHONY: puppet_dist
puppet_dist: puppet/version.sh
cd puppet && make dist
.PHONY: puppet_install
puppet_install: puppet/version.sh
cd puppet && make install
.PHONY: puppet_uninstall
puppet_uninstall: puppet/version.sh
cd puppet && make uninstall
################ /puppet module
############### Targets for python app
dist: $(PYTHON_SDIST) puppet
sdist: $(PYTHON_SDIST)
mercy/version.py: version.sh
bash -c 'source version.sh && echo "VERSION=\"$${MAJOR}-$${BUILD}\"" > $@'
$(PYTHON_SDIST): $(PYTHON_FILES)
$(PYTHON) setup.py sdist --formats=gztar
uninstall:
rm -fr $(VIRTUALENV_PKGS_DIR)/mercy-* || echo 'not installed'
install: $(PYTHON_SDIST) virtualenv
$(PIP) install $(PYTHON_SDIST) --upgrade
.PHONY: virtualenv
virtualenv:
if [ ! -e $(PIP) ]; then \
$(VIRTUALENV) --no-site-packages --distribute virtualenv ; \
fi
################## /python app
################## Targets for supporting development work
databases: databases/fda_ndc.zip databases/drugbank.xml.zip
.PHONY: databases/fda_ndc.zip
databases/fda_ndc.zip:
rm -fr databases/fda_ndc*
mkdir -p databases/fda_ndc
rm -f fda_ndc.zip
DBPAGE=$$(wget -O - http://www.fda.gov/Drugs/InformationOnDrugs/default.htm --quiet | grep -Eo 'National Drug Code Directory Search(</strong>)*(</a>)*(<br />)*<a href="[a-zA-Z0-9\:/\.]+">More information about the database</a>' | cut -d \" -f 2); \
LINK=$$(wget -O - http://www.fda.gov/$${DBPAGE} --quiet | grep ">NDC Database File" | cut -d \" -f 2) ; \
wget -O $@ http://www.fda.gov/$${LINK}
cd databases/fda_ndc && unzip -e ../fda_ndc.zip
.PHONY: databases/drugbank.xml.zip
databases/drugbank.xml.zip:
rm -fr databases/drugbank*
mkdir -p databases/drugbank
wget -O $@ http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip
cd databases/drugbank && unzip -e ../drugbank.xml.zip