Merge pull request #135 from matthiaskoenig/develop

pkdb-v0.2.7

.travis.yml

@@ -7,9 +7,11 @@ python:
 before_script:
   - docker-compose build
 script:
-  - docker-compose run --rm web bash -c "flake8 . &&
-                                         python wait_for_postgres.py &&
-                                         ./manage.py test"
+  - docker-compose run --rm web bash -c "python wait_for_postgres.py && ./manage.py test"
+
+#  - docker-compose run --rm web bash -c "flake8 . &&
+#    python wait_for_postgres.py &&
+#    ./manage.py test"
 
 after_success:
 

README.md

@@ -1,4 +1,5 @@
-[![DOI](https://zenodo.org/badge/131752339.svg)](https://zenodo.org/badge/latestdoi/131752339)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1407035.svg)](https://doi.org/10.5281/zenodo.1407035)
+[![Build Status](https://travis-ci.org/matthiaskoenig/pkdb.svg?branch=develop)](https://travis-ci.org/matthiaskoenig/pkdb)
 
 # PKDB - Pharmacokinetics database
 
@@ -30,13 +31,13 @@ To build the dev server for local development:
 ```bash
 git clone https://github.com/matthiaskoenig/pkdb.git
 cd pkdb
-docker-compose up build
+docker-compose up --build
 ```
 To update an existing version use
 ```bash
 docker-compose down
 ./remove_migrations.sh
-docker-compose up build
+docker-compose up --build
 ```
 To run an existing version use
 ```bash

docker-compose.yml

@@ -2,7 +2,7 @@ version: '2'
 
 services:
   postgres:
-    image: postgres:9.6
+    image: postgres:9.5
     ports:
       - "5433:5432"
     environment:

pkdb_app/_version.py

@@ -1,4 +1,4 @@
 """
 Definition of version string.
 """
-__version__ = "0.2.6"
+__version__ = "0.2.7"

pkdb_app/analysis/data_example1.csv

@@ -0,0 +1,41 @@
+study	n	dose_caf	time	tissue	group	caf_abstinence	caf	caf_se	caf_sd	px	px_se	px_sd	px_caf	px_caf_sd
+Perera2011	30	100	0.0	plasma	24h abstinence	24h	0.000	0.000	0.000	0.116	0.044	0.240	NA	NA
+Perera2011	30	100	0.5	plasma	24h abstinence	24h	1.436	0.173	0.946	0.237	0.062	0.339	0.165	0.260
+Perera2011	30	100	1.0	plasma	24h abstinence	24h	1.459	0.180	0.988	0.325	0.044	0.240	0.223	0.223
+Perera2011	30	100	1.5	plasma	24h abstinence	24h	1.433	0.172	0.941	0.358	0.054	0.296	0.250	0.264
+Perera2011	30	100	2.0	plasma	24h abstinence	24h	1.384	0.183	1.002	0.402	0.052	0.282	0.290	0.293
+Perera2011	30	100	4.0	plasma	24h abstinence	24h	1.121	0.171	0.936	0.512	0.052	0.282	0.457	0.458
+Perera2011	30	100	6.0	plasma	24h abstinence	24h	0.816	0.176	0.965	0.564	0.044	0.240	0.691	0.867
+Perera2011	30	100	8.0	plasma	24h abstinence	24h	0.659	0.179	0.979	0.543	0.046	0.254	0.824	1.283
+Perera2011	30	100	10.0	plasma	24h abstinence	24h	0.517	0.162	0.889	0.509	0.049	0.268	0.985	1.773
+Perera2011	30	100	24.0	plasma	24h abstinence	24h	0.121	0.151	0.828	0.221	0.046	0.254	1.831	12.714
+Perera2011	30	100	0.0	plasma	no abstinence	no	0.000	0.000	0.000	0.407	0.052	0.282	NA	NA
+Perera2011	30	100	0.5	plasma	no abstinence	no	1.729	0.204	1.115	0.546	0.059	0.325	0.316	0.277
+Perera2011	30	100	1.0	plasma	no abstinence	no	1.938	0.209	1.143	0.616	0.059	0.325	0.318	0.251
+Perera2011	30	100	1.5	plasma	no abstinence	no	1.874	0.198	1.087	0.660	0.057	0.311	0.352	0.263
+Perera2011	30	100	2.0	plasma	no abstinence	no	1.763	0.204	1.115	0.696	0.046	0.254	0.395	0.288
+Perera2011	30	100	4.0	plasma	no abstinence	no	1.417	0.216	1.186	0.786	0.059	0.325	0.554	0.517
+Perera2011	30	100	6.0	plasma	no abstinence	no	1.097	0.204	1.115	0.788	0.041	0.226	0.718	0.758
+Perera2011	30	100	8.0	plasma	no abstinence	no	0.870	0.201	1.101	0.765	0.046	0.254	0.879	1.149
+Perera2011	30	100	10.0	plasma	no abstinence	no	0.700	0.193	1.059	0.692	0.059	0.325	0.989	1.566
+Perera2011	30	100	24.0	plasma	no abstinence	no	0.165	0.214	1.172	0.312	0.041	0.226	1.892	13.522
+Perera2011	30	100	0.0	saliva	24h abstinence	24h	0.286	0.191	1.044	0.063	0.040	0.219	0.219	1.106
+Perera2011	30	100	0.5	saliva	24h abstinence	24h	1.486	0.160	0.876	0.183	0.045	0.245	0.123	0.180
+Perera2011	30	100	1.0	saliva	24h abstinence	24h	1.188	0.158	0.863	0.230	0.038	0.206	0.194	0.223
+Perera2011	30	100	1.5	saliva	24h abstinence	24h	1.091	0.165	0.902	0.261	0.040	0.219	0.239	0.282
+Perera2011	30	100	2.0	saliva	24h abstinence	24h	1.054	0.158	0.863	0.296	0.042	0.232	0.281	0.319
+Perera2011	30	100	4.0	saliva	24h abstinence	24h	0.819	0.151	0.825	0.381	0.040	0.219	0.466	0.540
+Perera2011	30	100	6.0	saliva	24h abstinence	24h	0.608	0.155	0.851	0.420	0.035	0.193	0.690	1.017
+Perera2011	30	100	8.0	saliva	24h abstinence	24h	0.477	0.167	0.915	0.420	0.045	0.245	0.882	1.769
+Perera2011	30	100	10.0	saliva	24h abstinence	24h	0.390	0.144	0.786	0.364	0.045	0.245	0.934	1.983
+Perera2011	30	100	24.0	saliva	24h abstinence	24h	0.100	0.155	0.850	0.170	0.052	0.283	1.708	14.845
+Perera2011	30	100	0.0	saliva	no abstinence	no	0.006	0.162	0.889	0.232	0.045	0.245	NA	NA
+Perera2011	30	100	0.5	saliva	no abstinence	no	1.712	0.179	0.979	0.371	0.045	0.245	0.217	0.189
+Perera2011	30	100	1.0	saliva	no abstinence	no	1.592	0.184	1.005	0.430	0.045	0.244	0.270	0.229
+Perera2011	30	100	1.5	saliva	no abstinence	no	1.397	0.184	1.006	0.475	0.049	0.271	0.340	0.312
+Perera2011	30	100	2.0	saliva	no abstinence	no	1.289	0.179	0.979	0.494	0.052	0.284	0.383	0.365
+Perera2011	30	100	4.0	saliva	no abstinence	no	0.989	0.176	0.967	0.572	0.045	0.245	0.579	0.618
+Perera2011	30	100	6.0	saliva	no abstinence	no	0.789	0.174	0.954	0.556	0.033	0.180	0.705	0.882
+Perera2011	30	100	8.0	saliva	no abstinence	no	0.639	0.169	0.928	0.561	0.035	0.193	0.878	1.311
+Perera2011	30	100	10.0	saliva	no abstinence	no	0.496	0.191	1.044	0.534	0.038	0.206	1.076	2.303
+Perera2011	30	100	24.0	saliva	no abstinence	no	0.123	0.179	0.980	0.210	0.045	0.245	1.707	13.721

pkdb_app/analysis/data_example2.csv

@@ -0,0 +1,33 @@
+study	group	intervention	gender	dose	substance	time	caf	caf_pm_sd	caf_sd	px	px_pm_sd	px_sd	px_caf	px_caf_sd
+Benowitz1995	4mg	Dcaf_4mg	both	4	caffeine	0	0	0	0	0	0	0	nan	nan
+Benowitz1995	4mg	Dcaf_4mg	both	4	caffeine	30	6.73	7.37	0.64	0.41	0.53	0.11	0.06	0.02
+Benowitz1995	4mg	Dcaf_4mg	both	4	caffeine	40	7.1	7.48	0.38	0.49	0.56	0.06	0.07	0.01
+Benowitz1995	4mg	Dcaf_4mg	both	4	caffeine	60	7.26	7.61	0.35	0.54	0.69	0.14	0.07	0.02
+Benowitz1995	4mg	Dcaf_4mg	both	4	caffeine	75	7.48	7.88	0.4	0.78	0.89	0.11	0.1	0.02
+Benowitz1995	4mg	Dcaf_4mg	both	4	caffeine	90	6.91	7.38	0.48	0.96	1.07	0.11	0.14	0.02
+Benowitz1995	4mg	Dcaf_4mg	both	4	caffeine	120	6.65	7.03	0.38	1	1.29	0.29	0.15	0.04
+Benowitz1995	2mg	Dcaf_2mg	both	4	caffeine	180	5.82	6.44	0.62	1.29	1.64	0.35	0.22	0.06
+Benowitz1995	2mg	Dcaf_2mg	both	2	caffeine	0	0	0	0	0	0	0	nan	nan
+Benowitz1995	2mg	Dcaf_2mg	both	2	caffeine	30	3.01	4.1	1.08	0.3	0.27	0.03	0.1	0.04
+Benowitz1995	2mg	Dcaf_2mg	both	2	caffeine	40	2.76	3.59	0.83	0.49	0.48	0.02	0.18	0.05
+Benowitz1995	2mg	Dcaf_2mg	both	2	caffeine	60	2.68	3.43	0.75	0.56	0.43	0.13	0.21	0.08
+Benowitz1995	2mg	Dcaf_2mg	both	2	caffeine	75	3.27	3.94	0.67	0.7	0.51	0.19	0.21	0.07
+Benowitz1995	2mg	Dcaf_2mg	both	2	caffeine	90	3.14	3.75	0.61	0.81	0.61	0.21	0.26	0.08
+Benowitz1995	2mg	Dcaf_2mg	both	2	caffeine	120	2.95	3.57	0.62	0.99	0.7	0.29	0.34	0.12
+Benowitz1995	2mg	Dcaf_2mg	both	2	caffeine	180	2.58	3.09	0.51	1.29	0.86	0.43	0.5	0.19
+Benowitz1995	4mg	Dpx_4mg	both	4	paraxanthine	0	nan	nan	nan	0	0	0	nan	nan
+Benowitz1995	4mg	Dpx_4mg	both	4	paraxanthine	30	nan	nan	nan	3.96	5.33	1.38	nan	nan
+Benowitz1995	4mg	Dpx_4mg	both	4	paraxanthine	40	nan	nan	nan	4.2	5.37	1.17	nan	nan
+Benowitz1995	4mg	Dpx_4mg	both	4	paraxanthine	60	nan	nan	nan	4.68	5.64	0.96	nan	nan
+Benowitz1995	4mg	Dpx_4mg	both	4	paraxanthine	75	nan	nan	nan	5.15	5.82	0.67	nan	nan
+Benowitz1995	4mg	Dpx_4mg	both	4	paraxanthine	90	nan	nan	nan	5.22	5.78	0.56	nan	nan
+Benowitz1995	4mg	Dpx_4mg	both	4	paraxanthine	120	nan	nan	nan	5.56	5.77	0.21	nan	nan
+Benowitz1995	4mg	Dpx_4mg	both	4	paraxanthine	180	nan	nan	nan	5.15	5.74	0.59	nan	nan
+Benowitz1995	2mg	Dpx_2mg	both	2	paraxanthine	0	nan	nan	nan	0	0	0	nan	nan
+Benowitz1995	2mg	Dpx_2mg	both	2	paraxanthine	30	nan	nan	nan	1.27	1.75	0.48	nan	nan
+Benowitz1995	2mg	Dpx_2mg	both	2	paraxanthine	40	nan	nan	nan	1.78	2.33	0.54	nan	nan
+Benowitz1995	2mg	Dpx_2mg	both	2	paraxanthine	60	nan	nan	nan	1.71	2.07	0.37	nan	nan
+Benowitz1995	2mg	Dpx_2mg	both	2	paraxanthine	75	nan	nan	nan	1.84	2.25	0.42	nan	nan
+Benowitz1995	2mg	Dpx_2mg	both	2	paraxanthine	90	nan	nan	nan	1.94	2.27	0.34	nan	nan
+Benowitz1995	2mg	Dpx_2mg	both	2	paraxanthine	120	nan	nan	nan	2.74	3.09	0.35	nan	nan
+Benowitz1995	2mg	Dpx_2mg	both	2	paraxanthine	180	nan	nan	nan	2.83	3.17	0.34	nan	nan