Skip to content

Latest commit

 

History

History
230 lines (157 loc) · 5.61 KB

README.md

File metadata and controls

230 lines (157 loc) · 5.61 KB
Raw

Collections that load on startup

  • grid_json
  • BFI_andOAI
  • alias_org_name_hospital
  • alias_org_type
  • alias_topic_type
  • alias_uni_org_type
  • KarenExtraRecords

Note: there must be a collection called grid_json, which is the json file downloaded from https://www.grid.ac/downloads

DB

  1. dimension_grid: Contains all the documents downloaded from dimension based on the GRIDs obtained in the grid.ac search engine, filtering by Education, Healthcare and country Denmark.
  2. ddf: contains all the DOIs downloaded from the DDF API.
  3. dimension_ddf: DOI DDF based documents found in dimension.
  4. dimension_all: contains the combination of the dimension_grid and dimension_ddf collections, this collection does not contain the documents that were NOT found in dimension (DOI obtained from DDF API)
  5. organizations: contains the information of the grid_json collection but in an already standardized format to be consumed directly by the opera parser.
  6. parsed: contains all the information of dimension_all parsed to be inserted in Neo4j.
  7. dimension_all_flags: contains all the doi of the dimension_all collection and the related flags dim_ddf and dim_grid
  8. extra_documents: contains all the extra documents that must be entered into the system, it is the homogable of ddf.

Main Process

We download all the information from Dimension (collection: dimension_grid)

time python3.6  getraw.py  -c dimension_grid -bd "2014-01-01" -ed "2019-12-31'" --dbname publications
real    320m51.697s

time python3.6  getraw.py  -c dimension_grid -bd "2014-01-01" -ed "2019-12-31'" --dbname patents
real    2m39.879s

time python3.6  getraw.py  -c dimension_grid -bd "2014-01-01" -ed "2019-12-31'" --dbname grants
real    3m50.482s

time python3.6  getraw.py  -c dimension_grid -bd "2014-01-01" -ed "2019-12-31'" --dbname clinical_trials
real    3m29.265s

time python3.6  getraw.py  -c dimension_grid -bd "2014-01-01" -ed "2019-12-31'" --dbname datasets
real    5m2.404s

We download all DOIs from the DDF API (collection: ddf)

time python3.6  getddf.py -cfg /home/ubuntu/dataverz/projects/opera/config.yml -y "2013,2014,2015,2016,2017,2018,2019"
real    3m39.410s

We download all the documents from dimension based on the DOIs downloaded from DDF (collection: dimension_ddf)

time python3.6  getddf-dimension.py
real    192m32.858s

We combine both collections containing documents downloaded from Dimension (dimension ddf + dimension_grid) (collection: dimension_all)

time python3.6 combine-ddf-grid-dimension.py 
real    5m50.531s

Organization collection creation (based on grid json)

time python3.6 create-collection-organisations.py 
real    0m33.713

We generate the parsed collection related to dimension_all collections and organizations (collection: parsed)

time python3.6 parseraw.py 
real    6m57.671s

We generate collection dimension_all_flags with all the DOIs of all the collections (dimension_grid, dimension_ddf, ddf)

time python3.6 create-collection-all-doi.py 
real    1m9.880s

We update the dimension_all_flags collection with the flags corresponding to dim_ddf and dim_grid

time python3.6 dimension-all-flags.py 
real    2m31.858s

Load

We generate all the Nodes from the parsed collection

time python3.6 create-nodes-neo4j.py 
real    6m52.106s

time python3.6 create-nodes-neo4j.py

We generate all the relationships of the nodes

time python3.6 create-relationships-neo4j.py
real    72m50.981s

time python3.6 create-relationships-neo4j.py

Afterload

Add extra fields from collections delivered by Opera

* BFI_andOAI
* alias_org_name_hospital
* alias_org_type 
* alias_topic_type
* alias_uni_org_type

time python3.6 create-aliases.py 
real	0m6.013s

Insert all DOIs that were not found in Dimension into Neo4j.

time python3.6 insert-only-doi-ddf.py 
real	0m3.019s

Associate all DDF DOIs with their corresponding GRIDs within Neo4j.

time python3.6 relation-doi-grid.py  
real	2m47.016s

Insert the DDF DOI flags into Neo4j.

time python3.6 insert-flag-neo4j.py   
real	0m13.599s

Insert all raw attributes into Neo4j.

time python3.6 append-data-neo4j.py 
real	1m0.569s

New Documents Update Process (KarenExtraRecords) - Manual DOI process.

We sort the information in KarenExtraRecords in a standard collection eliminating the docs that your organization could not find based on the records provided (example: https://app.dimensions.ai/details/publication/pub.1065208274). (collection: extra_documents)

time python3.6 karen-extra-records-parse.py
real	2m8.802s

We download the information from Dimension in dimension_all

time python3.6 karen-extra-records-download-dimension.py  
real	2m12.416s

We parse the new records, they will be inserted into the parsed collection

time python3.6 parseraw.py 
real	3m57.495s

We create the new Nodes

time python3.6 create-nodes-neo4j.py  
real	0m4.853s

We create new relationships

time python3.6 create-relationships-neo4j.py 
real	0m5.382s

We add aliases to new documents

time python3.6 create-aliases.py  
real	0m5.404s

Insert all raw attributes into Neo4j.

time python3.6 append-data-neo4j.py 
real	1m7.722s

Generate the DOCUMENT_ORGANIZATION Relationship between karen's documents and the organizations.

time python3.6 relation-doi-grid-karen.py 
real	0m1.396s

Add the extra_documents field to all the documents that are in karen's collection.

time python3.6 insert-flag-neo4j-karen.py 
real	0m1.384s