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Commit 34f8018

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Christopher Henry
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Updating to support new redox template, plus improved gapfilling
1 parent 061b8d2 commit 34f8018

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‎.dockerignore

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‎.github/workflows/kb_sdk_test.yaml

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‎.github/workflows/template-cleanup.yml

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‎.github/workflows/unit_tests.yaml

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‎.gitignore

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‎.pydevproject

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‎.travis.yml

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‎Dockerfile

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@@ -35,10 +35,10 @@ RUN pip install chemw==0.3.2
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RUN pip install deepdiff
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RUN pip install h5py
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RUN echo '31' >/dev/null && pip install --use-deprecated=legacy-resolver git+https://github.com/cshenry/ModelSEEDpy.git
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RUN echo '10' >/dev/null && pip install git+https://github.com/cshenry/cobrakbase.git@525409070d11fc1efd8fe5daf9069fd519d563c2
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RUN echo '32' >/dev/null && pip install --use-deprecated=legacy-resolver git+https://github.com/cshenry/ModelSEEDpy.git
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RUN echo '11' >/dev/null && pip install git+https://github.com/cshenry/cobrakbase.git@f0b3aa300fb153fc83b2fd5e83be231fc6992fae
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RUN echo '29' >/dev/null && mkdir deps && cd deps && \
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RUN echo '30' >/dev/null && mkdir deps && cd deps && \
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git clone --branch main https://github.com/cshenry/KBBaseModules.git
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RUN mkdir test
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‎LICENSE

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‎Makefile

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‎ModelSEEDReconstruction.spec

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‎README.md

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‎RELEASE_NOTES.md

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‎data/README.md

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‎data/ReportTemplate.html

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‎data/SSO_dictionary.json

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‎dependencies.json

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‎deploy.cfg

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‎kbase.yml

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‎lib/ModelSEEDReconstruction/ModelSEEDReconstructionImpl.py

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‎lib/ModelSEEDReconstruction/ModelSEEDReconstructionImpl.py.bak-2022-07-12-05-31-58

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‎lib/ModelSEEDReconstruction/ModelSEEDReconstructionImpl.py.bak-2022-07-12-05-32-21

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‎lib/ModelSEEDReconstruction/ModelSEEDReconstructionServer.py

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‎lib/ModelSEEDReconstruction/__init__.py

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‎lib/ModelSEEDReconstruction/modelseedrecon.py

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@@ -88,13 +88,22 @@ def build_metabolic_models(self,params):
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params["genome_refs"] = self.process_genome_list(params["genome_refs"],params["workspace"])
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#Processing media
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params["gapfilling_media_objs"] = self.process_media_list(params["gapfilling_media_list"],default_media,params["workspace"])
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#Preloading core and preselected template
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#Preloading core and preselected template - note the default GS template is None because this signals for the classifier to be used to select the template
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self.gs_template = None
93+
if params["gs_template_ref"] != None and not isinstance(params["gs_template_ref"],str):
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#Allows user to directly set the GS template object by passing the object in gs_template_ref
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self.gs_template = params["gs_template_ref"]
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if params["gs_template_ref"]:
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#Allows user to set the workspace ID of the GS template to be used
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self.gs_template = self.get_template(params["gs_template_ref"],None)
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if params["core_template_ref"]:
99+
if params["core_template_ref"] != None and not isinstance(params["core_template_ref"],str):
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#Allows user to directly set the core template object by passing the object in core_template_ref
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self.core_template = params["core_template_ref"]
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elif params["core_template_ref"]:
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#Allows user to set the workspace ID of the core template to be used
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self.core_template = self.get_template(params["core_template_ref"],None)
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else:
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#Setting the default core template
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self.core_template = self.get_template(self.templates["core"],None)
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#Initializing classifier
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genome_classifier = self.get_classifier()
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#if params["output_core_models"]:
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#TODO: Remove noncore reactions and change biomass and change model ID and then resave
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#Filling in model output
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result_table = result_table.append(current_output, ignore_index = True)
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result_table = pd.concat([result_table, pd.DataFrame([current_output])], ignore_index=True)
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mdllist.append(mdlutl)
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output = {}
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self.build_dataframe_report(result_table,mdllist)

‎lib/README.md

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‎lib/installed_clients/DataFileUtilClient.py

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‎lib/installed_clients/KBaseReportClient.py

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‎lib/installed_clients/RAST_SDKClient.py

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‎lib/installed_clients/WorkspaceClient.py

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‎lib/installed_clients/__init__.py

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‎lib/installed_clients/authclient.py

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‎lib/installed_clients/baseclient.py

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‎lib/installed_clients/cb_annotation_ontology_apiClient.py

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