Merge pull request #441 from PNNL-CompBio/build_2.2_bug_fixes

Build 2.2 Bug Fixes - Large PR

Author: jjacobson95

README.md

@@ -36,22 +36,22 @@ please see the [schema description](schema/README.md).
 
 ## Building a local version
 
-The build process can be found in our [build
-directory](build/README.md). Here you can follow the instructions to
+The build process can be found in our [coderbuild
+directory](coderbuild/README.md). Here you can follow the instructions to
 build your own local copy of the data on your machine. 
 
 ## Adding a new dataset
 
-We have standardized the build process so an additional dataset can be
+We have standardized the build (coderbuild) process so an additional dataset can be
 built locally or as part of the next version of coder. Here are the
 steps to follow:
 
-1. First visit the [build
-directory](build/README.md) and ensure you can build a local copy of
+1. First visit the [coderbuild
+directory](coderbuild/README.md) and ensure you can build a local copy of
 CoderData. 
 
 2. Checkout this repository and  create a subdirectory of the
-[build directory](build) with your own build files. 
+[coderbuild directory](coderbuild) with your own build files. 
 
 3. Develop your scripts to build the data files according to our
 [LinkML Schema](schema/coderdata.yaml]). This will require collecting
@@ -66,10 +66,10 @@ validator](https://linkml.io/linkml/data/validating-data) together
 with our schema file. 
 
 You can use the following scripts as part of your build process:
-- [build/utils/fit_curve.py](build/utils/fit_curve.py): This script
+- [coderbuild/utils/fit_curve.py](coderbuild/utils/fit_curve.py): This script
   takes dose-response data and generates the dose-response statistics
   required by CoderData/
-- [build/utils/pubchem_retrieval.py](build/utils/pubchem_retreival.py):
+- [coderbuild/utils/pubchem_retrieval.py](coderbuild/utils/pubchem_retreival.py):
   This script retreives structure and drug synonym information
   required to populate the `Drug` table. 
 
@@ -78,13 +78,13 @@ and arguments:
 
 | shell script     | arguments                | description         |
 |------------------|--------------------------|---------------------|
-| `build_samples.sh` | [latest_samples] | Latest version of samples generated by coderdata build |
+| `build_samples.sh` | [latest_samples] | Latest version of samples generated by coderbuild |
 | `build_omics.sh` | [gene file] [samplefile] | This includes the `genes.csv` that was generated in the original build as well as the sample file generated above. |
 | `build_drugs.sh` | [drugfile1,drugfile2,...]       | This includes a comma-delimited list of all drugs files generated from previous build  |
 | `build_exp.sh`| [samplfile ] [drugfile] | sample file and drug file generated by previous scripts |
 
 5. Put the Docker container file inside the [Docker
-directory](./build/docker) with the name
+directory](./coderbuild/docker) with the name
 `Dockerfile.[datasetname]`. 
 
 6. Run `build_all.py` from the root directory, which should now add in