Issue 30 (#31)

* Initial relative import changes

* - Adds a requirements file (for testing)

- Fix for Python3 has_key (now "in")
- Fix for Python 3 xrange (now range)

* - Updated Dockerfile requirements

* - Use of Python3 RDKit base image

* #30 switched service descriptors to yaml

Author: alanbchristie

Dockerfile-rdkit

@@ -1,4 +1,4 @@
-FROM informaticsmatters/rdkit-python-debian:Release_2018_09_1
+FROM informaticsmatters/rdkit-python3-debian:Release_2019_03_1
 LABEL maintainer="Tim Dudgeon<[email protected]>"
 
 USER root
@@ -10,4 +10,5 @@ RUN apt-get -y update && apt-get -y install zip unzip procps
 COPY src/python /opt/python
 RUN pip install -e /opt/python
 # And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit
-RUN pip install molvs standardiser matplotlib im-pipelines-utils==2.2.* im-pipelines-utils-rdkit==1.4.*
+RUN pip install molvs standardiser matplotlib \
+        im-pipelines-utils>=2.4.5 im-pipelines-utils-rdkit>=1.5.7

post-service-descriptors.sh

@@ -10,17 +10,18 @@ POST=${1:-http://coreservices:8080/coreservices/rest/v1/services}
 BASE_D='docker://github.com/InformaticsMatters/pipelines'
 BASE_N='nextflow://github.com/InformaticsMatters/pipelines'
 CT_DJ="application/x-squonk-service-descriptor-docker+json"
+CT_DY="application/x-squonk-service-descriptor-docker+yaml"
 CT_MM="multipart/mixed"
 
 
 for d in 'src/python/pipelines/dmpk' 'src/python/pipelines/docking' 'src/python/pipelines/rdkit'
 do
-    for file in $d/*.dsd.json
+    for file in $d/*.dsd.yml
     do
 	    echo $file
 	    curl -X POST \
          -T $file\
-         -H "Content-Type: $CT_DJ"\
+         -H "Content-Type: $CT_DY"\
          -H "Base-URL: $BASE_D"\
          $POST
          echo ""

requirements.txt

@@ -0,0 +1,7 @@
+im-pipelines-utils==2.4.*
+im-pipelines-utils-rdkit==1.5.*
+matplotlib==2.2.*
+scipy==1.1.*
+numpy==1.14.*
+scikit-learn==0.19.*
+pandas==0.23.*

src/python/pipelines/dmpk/pk_tmax_cmax_sim.dsd.json

@@ -0,0 +1,94 @@
+---
+"@class": org.squonk.core.DockerServiceDescriptor
+serviceConfig:
+  id: pipelines.dmpk.sygnature.tmax_cmax_sim.1
+  name: TmaxCmaxSimulation
+  description: Simulation of Tmax and Cmax
+  tags:
+  - sygnature
+  - dmpk
+  - pk
+  - cmax
+  - tmax
+  - simulation
+  - prediction
+  - docker
+  resourceUrl:
+  icon: icons/program.png
+  outputDescriptors:
+  - primaryType: org.squonk.types.PngImageFile
+    mediaType: image/png
+    name: output
+  optionDescriptors:
+  - modes:
+    - User
+    editable: true
+    visible: true
+    description: Half life(elim)(hr)
+    label: Half life(elim)(hr)
+    key: arg.halfLife
+    minValues: 1
+    maxValues: 1
+    typeDescriptor:
+      type: java.lang.Float
+      "@class": org.squonk.options.SimpleTypeDescriptor
+    "@class": org.squonk.options.OptionDescriptor
+  - modes:
+    - User
+    editable: true
+    visible: true
+    description: Half life(abs)(hr)
+    label: Half life(abs)(hr)
+    key: arg.absorption
+    minValues: 1
+    maxValues: 1
+    typeDescriptor:
+      type: java.lang.Float
+      "@class": org.squonk.options.SimpleTypeDescriptor
+    "@class": org.squonk.options.OptionDescriptor
+  - modes:
+    - User
+    editable: true
+    visible: true
+    description: Dose(mg)
+    label: Dose(mg)
+    key: arg.dose
+    minValues: 1
+    maxValues: 1
+    typeDescriptor:
+      type: java.lang.Float
+      "@class": org.squonk.options.SimpleTypeDescriptor
+    "@class": org.squonk.options.OptionDescriptor
+  - modes:
+    - User
+    editable: true
+    visible: true
+    description: AUC(mg/L.hr)
+    label: AUC(mg/L.hr)
+    key: arg.auc
+    minValues: 1
+    maxValues: 1
+    typeDescriptor:
+      type: java.lang.Float
+      "@class": org.squonk.options.SimpleTypeDescriptor
+    "@class": org.squonk.options.OptionDescriptor
+  - modes:
+    - User
+    editable: true
+    visible: true
+    description: Simulation Time Length(hr)
+    label: Simulation Time Length(hr)
+    key: arg.time
+    minValues: 1
+    maxValues: 1
+    typeDescriptor:
+      type: java.lang.Float
+      "@class": org.squonk.options.SimpleTypeDescriptor
+    "@class": org.squonk.options.OptionDescriptor
+  executorClassName: org.squonk.execution.steps.impl.ThinDatasetDockerExecutorStep
+outputRoutes:
+- route: FILE
+imageName: informaticsmatters/rdkit_pipelines
+command: >-
+  python -m pipelines.dmpk.pk_tmax_cmax_sim -o ${POUT}output --half-life $halfLife
+  --absorption $absorption --dose $dose --auc $auc --time $time

src/python/pipelines/dmpk/pk_tmax_cmax_sim.dsd.yml

@@ -0,0 +1,50 @@
+---
+"@class": org.squonk.core.DockerServiceDescriptor
+serviceConfig:
+  id: pipelines.xchem.obabel.prepare.pdb.v1
+  name: OBabelPreparePDB
+  description: Prepare PDB file using Open Babel
+  tags:
+  - rdkit
+  - xchem
+  - docker
+  - openbabel
+  - obabel
+  - prepare
+  - pdb
+  - convert
+  - protein
+  resourceUrl:
+  icon: icons/transform_molecule.png
+  inputDescriptors:
+  - primaryType: org.squonk.types.PDBFile
+    mediaType: chemical/x-pdb
+    name: pdb
+  outputDescriptors:
+  - primaryType: org.squonk.types.Mol2File
+    mediaType: chemical/x-mol2
+    name: mol2
+  optionDescriptors:
+  - modes:
+    - User
+    editable: true
+    "@class": org.squonk.options.OptionDescriptor
+    typeDescriptor:
+      type: java.lang.Float
+      "@class": org.squonk.options.SimpleTypeDescriptor
+    key: arg.protonate
+    label: Protonate at pH
+    description: Optionally protonate side chains at this pH
+    visible: true
+    minValues: 0
+    maxValues: 1
+  executorClassName: org.squonk.execution.steps.impl.ThinDatasetDockerExecutorStep
+inputRoutes:
+- route: FILE
+outputRoutes:
+- route: FILE
+imageName: informaticsmatters/pipelines-obabel:latest
+command: >-
+  python -m pipelines.docking.obabel_prepare_pdb -i ${PIN}pdb.pdb.gz -o ${POUT}mol2 -mol2
+  ${binding.variables.containsKey('protonate') ? '-prot ' + protonate : ''}
+  --meta