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Updates for v0.3.0
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Multiple breaking changes for v0.3.0.
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jgaff committed Jul 7, 2017
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304 changes: 152 additions & 152 deletions mdf_indexers/converters/converter_template.py
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188 changes: 95 additions & 93 deletions mdf_indexers/converters/khazana_polymer_converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
from ..utils.file_utils import find_files
from ..parsers.ase_parser import parse_ase

# VERSION 0.2.0
# VERSION 0.3.0

# This is the converter for polymer data from Khazana.
# Arguments:
Expand All @@ -24,90 +24,90 @@ def convert(input_path, metadata=None, verbose=False):
# Collect the metadata
if not metadata:
dataset_metadata = {
"mdf-title": "Khazana (Polymer)",
"mdf-acl": ["public"],
"mdf-source_name": "khazana_polymer",
"mdf-citation": ["T. D. Huan, A. Mannodi-Kanakkithodi, C. Kim, V. Sharma, G. Pilania, R. Ramprasad\nA polymer dataset for accelerated property prediction and design Sci. Data, 3, 160012 (2016).", "A. Mannodi-Kanakkithodi, G. M. Treich, T. D. Huan, R. Ma, M. Tefferi, Y. Cao, G A. Sotzing, R. Ramprasad\nRational Co-Design of Polymer Dielectrics for Energy Storage Adv. Mater., 28, 6277 (2016).", "T. D. Huan, A. Mannodi-Kanakkithodi, R. Ramprasad\nAccelerated materials property predictions and design using motif-based fingerprints Phys. Rev. B, 92, 014106 (2015).", "A. Mannodi-Kanakkithodi, G. Pilania, T. D. Huan, T. Lookman, R. Ramprasad\nMachine learning strategy for accelerated design of polymer dielectrics Sci. Rep., 6, 20952 (2016)."],
"mdf-data_contact": {
"mdf": {
"title": "Khazana (Polymer)",
"acl": ["public"],
"source_name": "khazana_polymer",
"citation": ["T. D. Huan, A. Mannodi-Kanakkithodi, C. Kim, V. Sharma, G. Pilania, R. Ramprasad\nA polymer dataset for accelerated property prediction and design Sci. Data, 3, 160012 (2016).", "A. Mannodi-Kanakkithodi, G. M. Treich, T. D. Huan, R. Ma, M. Tefferi, Y. Cao, G A. Sotzing, R. Ramprasad\nRational Co-Design of Polymer Dielectrics for Energy Storage Adv. Mater., 28, 6277 (2016).", "T. D. Huan, A. Mannodi-Kanakkithodi, R. Ramprasad\nAccelerated materials property predictions and design using motif-based fingerprints Phys. Rev. B, 92, 014106 (2015).", "A. Mannodi-Kanakkithodi, G. Pilania, T. D. Huan, T. Lookman, R. Ramprasad\nMachine learning strategy for accelerated design of polymer dielectrics Sci. Rep., 6, 20952 (2016)."],
"data_contact": {

"given_name": "Rampi",
"family_name": "Ramprasad",
"given_name": "Rampi",
"family_name": "Ramprasad",

"email": "[email protected]",
"institution": "University of Connecticut",
"email": "[email protected]",
"institution": "University of Connecticut",

},
},

"mdf-author": [{
"author": [{

"given_name": "Rampi",
"family_name": "Ramprasad",
"given_name": "Rampi",
"family_name": "Ramprasad",

"email": "[email protected]",
"institution": "University of Connecticut",
"email": "[email protected]",
"institution": "University of Connecticut",

},
{
},
{

"given_name": "Chiho",
"family_name": "Kim",
"given_name": "Chiho",
"family_name": "Kim",

"institution": "University of Connecticut",
"institution": "University of Connecticut",

},
{
},
{

"given_name": "Huan",
"family_name": "Tran",
"given_name": "Huan",
"family_name": "Tran",

"institution": "University of Connecticut",
"institution": "University of Connecticut",

},
{
},
{

"given_name": "Arun",
"family_name": "Mannodi-Kanakkithodi",
"given_name": "Arun",
"family_name": "Mannodi-Kanakkithodi",

"institution": "University of Connecticut",
"institution": "University of Connecticut",

}],
}],

# "mdf-license": ,
# "mdf-license": ,

"mdf-collection": "Khazana",
"mdf-data_format": "cif",
"mdf-data_type": "Polymers",
"mdf-tags": ["polymer"],
"collection": "Khazana",
"tags": ["polymer"],

"mdf-description": "Polymer Genome is a recommendation engine for the rapid design and discovery of polymer dielectrics, powered by quantum mechanical computations, experimental data and machine learning based models. Polymer Genome is designed to provide efficient pathways for estimating essential properties of existing/hypothetical polymers and recommending polymer candidates that meet certain property requirements.",
# "mdf-year": ,
"description": "Polymer Genome is a recommendation engine for the rapid design and discovery of polymer dielectrics, powered by quantum mechanical computations, experimental data and machine learning based models. Polymer Genome is designed to provide efficient pathways for estimating essential properties of existing/hypothetical polymers and recommending polymer candidates that meet certain property requirements.",
# "mdf-year": ,

"mdf-links": {
"links": {

"mdf-landing_page": "http://khazana.uconn.edu/polymer_genome/index.php",
"landing_page": "http://khazana.uconn.edu/polymer_genome/index.php",

"mdf-publication": ["https://dx.doi.org/10.1038/sdata.2016.12", "https://dx.doi.org/10.1002/adma.201600377", "https://doi.org/10.1103/PhysRevB.92.014106", "https://dx.doi.org/10.1038/srep20952"],
# "mdf-dataset_doi": ,
"publication": ["https://dx.doi.org/10.1038/sdata.2016.12", "https://dx.doi.org/10.1002/adma.201600377", "https://doi.org/10.1103/PhysRevB.92.014106", "https://dx.doi.org/10.1038/srep20952"],
# "mdf-dataset_doi": ,

# "mdf-related_id": ,
# "mdf-related_id": ,

# data links: {
# data links: {

#"globus_endpoint": ,
#"http_host": ,
#"globus_endpoint": ,
#"http_host": ,

#"path": ,
#}
},
#"path": ,
#}
},

# "mdf-mrr": ,
# "mdf-mrr": ,

"mdf-data_contributor": {
"given_name": "Jonathon",
"family_name": "Gaff",
"email": "[email protected]",
"institution": "The University of Chicago",
"github": "jgaff"
"data_contributor": {
"given_name": "Jonathon",
"family_name": "Gaff",
"email": "[email protected]",
"institution": "The University of Chicago",
"github": "jgaff"
}
}
}
elif type(metadata) is str:
Expand All @@ -132,57 +132,59 @@ def convert(input_path, metadata=None, verbose=False):
for dir_data in tqdm(find_files(input_path, "\.cif$"), desc="Processing data files", disable= not verbose):
file_data = parse_ase(file_path=os.path.join(dir_data["path"], dir_data["filename"]), data_format="cif", verbose=False)
record_metadata = {
"mdf-title": "Khazana Polymer - " + file_data["chemical_formula"],
"mdf-acl": ["public"],
"mdf": {
"title": "Khazana Polymer - " + file_data["chemical_formula"],
"acl": ["public"],

# "mdf-tags": ,
# "mdf-description": ,

"mdf-composition": file_data["chemical_formula"],
# "mdf-raw": ,
# "mdf-tags": ,
# "mdf-description": ,
"composition": file_data["chemical_formula"],
# "mdf-raw": ,

"mdf-links": {
"mdf-landing_page": "http://khazana.uconn.edu/module_search/material_detail.php?id=" + dir_data["filename"].replace(".cif", ""),
"links": {
"landing_page": "http://khazana.uconn.edu/module_search/material_detail.php?id=" + dir_data["filename"].replace(".cif", ""),

# "mdf-publication": ,
# "mdf-dataset_doi": ,
# "mdf-publication": ,
# "mdf-dataset_doi": ,

# "mdf-related_id": ,
# "mdf-related_id": ,

# data links: {

#"globus_endpoint": ,
#"http_host": ,
# data links: {
#"globus_endpoint": ,
#"http_host": ,

#"path": ,
#},
},
#"path": ,
#},
},

# "mdf-citation": ,
# "mdf-data_contact": {
# "mdf-citation": ,
# "mdf-data_contact": {

# "given_name": ,
# "family_name": ,
# "given_name": ,
# "family_name": ,

# "email": ,
# "institution":,
# "email": ,
# "institution":,

# IDs
# },
# IDs
# },

# "mdf-author": ,
# "mdf-author": ,

# "mdf-license": ,
# "mdf-collection": ,
# "mdf-data_format": ,
# "mdf-data_type": ,
# "mdf-year": ,
# "mdf-license": ,
# "mdf-collection": ,
# "mdf-data_format": ,
# "mdf-data_type": ,
# "mdf-year": ,

# "mdf-mrr":
# "mdf-mrr":

# "mdf-processing": ,
# "mdf-structure":,
# "mdf-processing": ,
# "mdf-structure":,
}
}

# Pass each individual record to the Validator
result = dataset_validator.write_record(record_metadata)
Expand Down
1 change: 0 additions & 1 deletion mdf_indexers/schemas/0.2.0_dataset.schema
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