#58

.gitignore

@@ -9,6 +9,8 @@ examples/outputs
 temp/
 output/
 
+__MACOSX/
+
 # Distribution / packaging
 .Python
 build/

Makefile

@@ -1,6 +1,10 @@
 RUN = poetry run
 
-biosample_sqlite_file = ~/biosample_basex_data_good_subset.db
+#biosample_sqlite_file = ~/biosample_basex_data_good_subset.db
+# curling from NERSC portal now
+# but may want to change local destination... like a data directory?
+# NOTE: this database file will be deleted by make clean. Don't do any manual modifications in there!
+biosample_sqlite_file = biosample_basex_data_good_subset.db
 
 .PHONY: test clean all
 
@@ -28,20 +32,21 @@ clean:
 	rm -rf examples/outputs/*tsv
 	rm -rf logs/*log
 	rm -rf target/*
+	rm -rf $(biosample_sqlite_file)
 
 examples/outputs/report.tsv: examples/gold.json
 	$(RUN) annotate-sample -R $@ $<
 
 downloads/mixs6_core.tsv:
 	curl -L -s 'https://docs.google.com/spreadsheets/d/1QDeeUcDqXes69Y2RjU2aWgOpCVWo5OVsBX9MKmMqi_o/export?format=tsv&gid=178015749' > $@
 
-examples/outputs/non_attribute_metadata_sel_envs_partial.tsv:
+examples/outputs/non_attribute_metadata_sel_envs_partial.tsv: $(biosample_sqlite_file)
 	$(RUN) sqlite_client_cli \
 		--sqlite_path $(biosample_sqlite_file) \
 		--query "select * from non_attribute_metadata_sel_envs limit 9" \
 		--tsv_out $@
 
-rel_to_oxygen_example: downloads/mixs6_core.tsv
+rel_to_oxygen_example: downloads/mixs6_core.tsv $(biosample_sqlite_file)
 	$(RUN) rel_to_oxygen_example \
 		--sqlite_path $(biosample_sqlite_file) \
 		--mixs_core_path $<
@@ -56,4 +61,17 @@ downloads/bibo.owl:
 
 assets/bibo_DocumentStatus.tsv: downloads/bibo.owl bin/robot.jar
 	java -jar bin/robot.jar query --input $< --query sparql/bibo_DocumentStatus.sparql $@
-	sed --in-place=.bak 's/^\?//' $@
+	sed --in-place=.bak 's/^\?//' $@
+
+# full db at https://portal.nersc.gov/project/m3513/biosample/biosample_basex.db.gz
+# subset has few tables
+# fewer rows in XXX (corresponding to samples with reapired env package values of XXX...)
+#   see XXX
+# and fewer columns in XXX, highlighting
+downloads/biosample_basex_data_good_subset.db.zip:
+	# --location (-L) pursues redirects
+	curl --location https://portal.nersc.gov/project/m3513/biosample/biosample_basex_data_good_subset.db.zip -o $@
+
+# unzipped file goes into the cwd by default, which would usually be the root of the project
+biosample_basex_data_good_subset.db: downloads/biosample_basex_data_good_subset.db.zip
+	unzip $<

README.md

@@ -2,7 +2,24 @@
 
 # NMDC Sample Annotator API
 
-## Installing
+## Setup
+1. requires python 3.9... should we try to make this compatible with something earlier?
+2. install [poetry application](https://python-poetry.org/docs/#installation)
+3. `git clone [email protected]:microbiomedata/sample-annotator.git`
+4. `cd sample-annotator`
+5. `poetry install`
+6. `mkdir bin`... that directory _should_ already be in the repo with a placeholder.txt file, or it should be created by the Makefile
+
+test your setup with `make all`
+
+## Contributing?
+_Please_
+1. create an issue describing the problem you plan to address or the contribution you intend to make
+2. create a fork of the repo in your own GitHub account, or create a branch here in microbiomedata/sample-annotator. The name of the branch should be brief but include your issue number and a keyword or two from the issue's title
+3. start adding code, probably in the `sample_annotator` subdirectory
+4. save, `git add`, `git commit -m`, and `git push`
+5. create a pull request
+6. ask questions **any** time
 
 ## Command Line