https://github.com/samply/directory-sync
https://github.com/samply/directory-sync
fhir fhir-client
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/samply/directory-sync
- Owner: samply
- License: apache-2.0
- Created: 2019-12-03T08:56:19.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2024-08-14T13:08:15.000Z (9 months ago)
- Last Synced: 2025-02-13T13:14:19.755Z (3 months ago)
- Topics: fhir, fhir-client
- Language: Java
- Size: 350 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://travis-ci.com/samply/directory-sync)
# Directory Sync
The Directory-sync library is designed to synchronize between a FHIR store associated with a biobank and a Directory, such as the (BBMRI Directory)[https://directory.bbmri-eric.eu]. This is a two-way process, information is extracted from the FHIR store and sent to the Directory, and information is pulled from the Directory and inserted into the FHIR store. For this to work, the data in the FHIR store should conform to the (BBMRI Profile)[https://simplifier.net/bbmri.de].
This is meant to make the lives of biobank administrators a little easier, since they must currently perform this synchronization by hand.
The library can update the Directory with the following information, on a per-collection basis:
- number of donors/patients
- number of samples
- sex
- diagnosis
- age range
- sample types
- storage temperatures
It is also possible to send data in the star model format. This aggregates the data into hypercubes.
Data relating to biobank contact details can be retrieved from the Directory and stored in the FHIR store.
The Sync class is the main entrypoint into this library. See the Javadoc in Sync.java for more details.
The library was written to be used from within the (Connector)[https://github.com/samply/share-client]. However, it could be used from within any component that needs Directory-sync functionality.
Based on the mapping from https://samply.github.io/bbmri-fhir-ig/mappings.html.
## Usage
```xml
de.samply
directory-sync
0.1.0
```
# Directory fields and support status
#### Biobank
| BBMRI-ERIC-Field | Source of Truth | Status |
|--|--|--|
|id | Both! |*Used as primary means of biobank identification, should not change* |
|name | Directory | active |
|acronym | Directory | TODO |
|description | Directory | TODO |
|bioresource_reference | Directory | TODO |
|url | Directory | TODO |
|juridical_person | Directory | TODO |
|country | Directory | TODO |
|it_support_available | Directory | TODO |
|it_staff_size | Directory | TODO |
|is_available | Directory | TODO |
|his_available | Directory | TODO |
|partner_charter_signed | Directory | TODO |
|head_title_before_name | Directory | TODO |
|head_firstname | Directory | TODO |
|head_lastname | Directory | TODO |
|head_title_after_name | Directory | TODO |
|head_role | Directory | TODO |
|contact | *see section contact* |
|latitude | Directory | TODO |
|longitude | Directory | TODO |
|network | *see section network* |
|collaboration_commercial | Directory | TODO |
|collaboration_non_for_profit | Directory | TODO |
|capabilities | Directory | TODO |
|quality | Directory | TODO |
#### Contact Information
Unsolved problem: How do we identify corresponding contacts in the directory and FHIR? Contacts have no identifier in FHIR.
| BBMRI-ERIC-Field | Source of Truth | Status |
|--|--|--|
| title_before_name | Directory | TODO |
|first_name | Directory | TODO |
|last_name | Directory | TODO |
|title_after_name | Directory | TODO |
| phone | Directory | TODO |
|email | Directory | TODO |
|address | Directory | TODO |
|zip | Directory | TODO |
|city | Directory | TODO |
|country | Directory | TODO |
#### Collection
| BBMRI-ERIC-Field | Source of Truth | Status |
|--|--|--|
|id | Both! |*Used as primary means of biobank identification, should not change* |
|country | Directory | TODO |
|biobank | -- | *Not expected to change* |
|name | Directory | TODO |
|acronym | Directory | TODO |
|description | Directory | TODO |
|bioresource_reference | Directory | TODO |
|parent_collection | -- | *No FHIR Mapping yet, so no sync* |
|network | *see section network* |
|type | Directory | TODO |
|data_categories | Directory | TODO |
|quality | | Directory | TODO |
|order_of_magnitude | FHIR | TODO |
|order_of_magnitude_donors | FHIR | TODO |
|size | FHIR | active |
|number_of_donors | FHIR | TODO |
|timestamp | FHIR (??) | TODO |
|id_card | Directory | TODO |
|head_title_before_name | Directory | TODO |
|head_firstname | Directory | TODO |
|head_lastname | Directory | TODO |
|head_title_after_name | Directory | TODO |
|head_role | Directory | TODO |
|contact | *see section contact* |
|latitude | Directory | TODO |
|longitude | Directory | TODO |
|sex | FHIR | TODO |
|diagnosis_available | FHIR | TODO |
|age Low| FHIR | TODO |
|age High| FHIR | TODO |
|age Unit| FHIR | *Fixed to years* |
|body_part_examined| -- | *No FHIR Mapping yet, so no sync* |
|imaging_modality| -- | *No FHIR Mapping yet, so no sync* |
|image_dataset_type| -- | *No FHIR Mapping yet, so no sync* |
|materials| FHIR | TODO |
|storage_temperature | FHIR | TODO |
|sample_access_fee | Directory | TODO |
|sample_access_joint_project | Directory | TODO |
|sample_access_description | Directory | TODO |
|sample_access_uri | Directory | TODO |
|data_access_fee | Directory | TODO |
|data_access_joint_project | Directory | TODO |
|data_access_description | Directory | TODO |
|data_access_uri | Directory | TODO |
|image_access_fee | Directory | TODO |
|image_access_joint_project | Directory | TODO |
|image_access_description | Directory | TODO |
|image_access_uri | Directory | TODO |
|collaboration_commercial | Directory | TODO |
|collaboration_non_for_profit | Directory | TODO |
|sample_processing_sop | Directory | TODO |
|sample_transport_sop | Directory | TODO |
|sample_storage_sop | Directory | TODO |
|data_processing_sop | Directory | TODO |
|data_transport_sop | Directory | TODO |
|data_storage_sop | Directory | TODO |
## Docu
| Anfrage | Subject | Stratifier | Scoring |
|---------|---------|------------|---------|
| order_of_magnitude | Specimen | Collection | cohort |
| order_of_magnitude_donors | Patient | Collection | cohort |
| size | Specimen | Collection | cohort |
| number_of_donors | Patient | Collection | cohort |
| age Low| Patient | Collection | continuous-variable |
| age High| Patient | Collection | continuous-variable |
| age Unit| hardcoded years | -- | -- |
| materials| Specimen | Collection, Type | cohort |
| storage_temperature | Specimen | Collection, storageTemp | cohort |
| sex| Patient | Collection, gender | cohort |
| diagnosis_available| Collection, Condition |
## License
Copyright 2020 The Samply Development Community
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.