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imedina committed Mar 25, 2022
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138 changes: 69 additions & 69 deletions docs/data-models/clinicalanalysis.md
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Expand Up @@ -69,63 +69,33 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
| **attributes**<br>*Map<String,Object>* <br> | <p>You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.</p> |
| **status**<br>*Status* <br> | <p>Object status.</p> |

### ClinicalPriorityAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalPriorityAnnotation.java).
### ClinicalAudit
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAudit.java).

| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **rank**<br>*int* <br> | <p>ClinicalPriorityAnnotation rank.</p> |
| **date**<br>*String* <br> | <p>ClinicalPriorityAnnotation date.</p> |
| **author**<br>*String* <br> | <p>Audit author</p> |
| **action**<br>*Action* <br> | <p>Enum action that can have the values CREATE_CLINICAL_ANALYSIS, CREATE_INTERPRETATION, UPDATE_CLINICAL_ANALYSIS, DELETE_CLINICAL_ANALYSIS, UPDATE_INTERPRETATION, REVERT_INTERPRETATION, CLEAR_INTERPRETATION, MERGE_INTERPRETATION, SWAP_INTERPRETATION and DELETE_INTERPRETATION</p> |
| **message**<br>*String* <br> | <p>Audit message</p> |
| **date**<br>*String* <br> | <p>Date of the audit</p> |

### ClinicalReport
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalReport.java).
### ClinicalAnalysisQualityControl
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisQualityControl.java).

| Field | Description |
| :--- | :--- |
| **title**<br>*String* <br> | <p>Report title.</p> |
| **overview**<br>*String* <br> | <p>Report overview.</p> |
| **discussion**<br>*String* <br> | <p>Report discussion.</p> |
| **logo**<br>*String* <br> | <p>Report logo.</p> |
| **signedBy**<br>*String* <br> | <p>Indicates who has signed the report.</p> |
| **signature**<br>*String* <br> | <p>Report signature.</p> |
| **date**<br>*String* <br> | <p>Report date.</p> |
| **summary**<br>*QualityControlSummary* <br> | <p>ClinicalAnalysisQualityControl summary that can have the values HIGH, MEDIUM, LOW, DISCARD, NEEDS_REVIEW, UNKNOWN.</p> |
| **comments**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/clinicalanalysis#clinicalcomment"><em>ClinicalComment</em></a>>* <br> | <p>List of ClinicalAnalysisQualityControl comments.</p> |
| **comments**<br>*List<<em>String</em>>* <br> | <p>List of ClinicalAnalysisQualityControl files.</p> |

### Disorder
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Disorder.java).
### FlagAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/common/FlagAnnotation.java).

| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Id to identify the object</p> |
| **name**<br>*String* <br> | <p>Object name</p> |
| **id**<br>*String* <br> | <p>Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **source**<br>*String* <br> | <p>Ontology source</p> |
| **url**<br>*String* <br> | <p>Ontology url</p> |
| **attributes**<br>*Map<String,String>* <br> | <p>Dictionary that can be customised by users to store any additional information users may require..</p> |

### Panel
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/panel/Panel.java).

| Field | Description |
| :--- | :--- |
| **uuid**<br>*String* <br> | <p>Unique 32-character identifier assigned automatically by OpenCGA.</p> |
| **release**<br>*int* <br> | <p>An integer describing the current data release.</p> |
| **version**<br>*int* <br> | <p>OpenCGA version of this panel, this is incremented when the panel is updated.</p> |
| **~~author~~**<br>*String* <br><br>_Deprecated_ | <p>Author of the panel.</p> |
| **status**<br>*[Status](https://docs.opencga.opencb.org/data-models/clinicalanalysis#status)* <br> | <p>Panel status can have the values READY or DELETED.</p> |
| **studyUid**<br>*long* <br> | <p>Panel reference to study.</p> |
| **uid**<br>*long* <br> | <p>Panel reference to study.</p> |

### ClinicalComment
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalComment.java).

| Field | Description |
| :--- | :--- |
| **author**<br>*String* <br> | <p>Clinical comment author</p> |
| **message**<br>*String* <br> | <p>Clinical comment message</p> |
| **tags**<br>*List<<em>String</em>>* <br> | <p>List of tags for the clinical comment</p> |
| **date**<br>*String* <br> | <p>Date of the clinical comment</p> |
| **date**<br>*String* <br> | <p>FlagAnnotation date.</p> |

### Interpretation
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/Interpretation.java).
Expand All @@ -138,15 +108,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
| **internal**<br>*[InterpretationInternal](https://docs.opencga.opencb.org/data-models/clinicalanalysis#interpretationinternal)* <br> | <p>Internal field for manage the object.</p> |
| **release**<br>*int* <br> | <p>An integer describing the current data release.</p> |

### ClinicalAnalysisQualityControl
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisQualityControl.java).

| Field | Description |
| :--- | :--- |
| **summary**<br>*QualityControlSummary* <br> | <p>ClinicalAnalysisQualityControl summary that can have the values HIGH, MEDIUM, LOW, DISCARD, NEEDS_REVIEW, UNKNOWN.</p> |
| **comments**<br>*List<<a href="https://docs.opencga.opencb.org/data-models/clinicalanalysis#clinicalcomment"><em>ClinicalComment</em></a>>* <br> | <p>List of ClinicalAnalysisQualityControl comments.</p> |
| **comments**<br>*List<<em>String</em>>* <br> | <p>List of ClinicalAnalysisQualityControl files.</p> |

### ClinicalConsentAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentAnnotation.java).

Expand Down Expand Up @@ -175,34 +136,63 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop
| **assignedBy**<br>*String* <br> | <p>Assigned by field</p> |
| **date**<br>*String* <br> | <p>Date of the clinical analyst</p> |

### FlagAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/common/FlagAnnotation.java).
### Disorder
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Disorder.java).

| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Id to identify the object</p> |
| **name**<br>*String* <br> | <p>Object name</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **source**<br>*String* <br> | <p>Ontology source</p> |
| **url**<br>*String* <br> | <p>Ontology url</p> |
| **attributes**<br>*Map<String,String>* <br> | <p>Dictionary that can be customised by users to store any additional information users may require..</p> |

### Panel
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/panel/Panel.java).

| Field | Description |
| :--- | :--- |
| **uuid**<br>*String* <br> | <p>Unique 32-character identifier assigned automatically by OpenCGA.</p> |
| **release**<br>*int* <br> | <p>An integer describing the current data release.</p> |
| **version**<br>*int* <br> | <p>OpenCGA version of this panel, this is incremented when the panel is updated.</p> |
| **~~author~~**<br>*String* <br><br>_Deprecated_ | <p>Author of the panel.</p> |
| **status**<br>*[Status](https://docs.opencga.opencb.org/data-models/clinicalanalysis#status)* <br> | <p>Panel status can have the values READY or DELETED.</p> |
| **studyUid**<br>*long* <br> | <p>Panel reference to study.</p> |
| **uid**<br>*long* <br> | <p>Panel reference to study.</p> |

### ClinicalPriorityAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalPriorityAnnotation.java).

| Field | Description |
| :--- | :--- |
| **id**<br>*String* <br> | <p>Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.</p> |
| **description**<br>*String* <br> | <p>Users may provide a description for the entry.</p> |
| **date**<br>*String* <br> | <p>FlagAnnotation date.</p> |
| **rank**<br>*int* <br> | <p>ClinicalPriorityAnnotation rank.</p> |
| **date**<br>*String* <br> | <p>ClinicalPriorityAnnotation date.</p> |

### ClinicalAudit
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAudit.java).
### ClinicalComment
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalComment.java).

| Field | Description |
| :--- | :--- |
| **author**<br>*String* <br> | <p>Audit author</p> |
| **action**<br>*Action* <br> | <p>Enum action that can have the values CREATE_CLINICAL_ANALYSIS, CREATE_INTERPRETATION, UPDATE_CLINICAL_ANALYSIS, DELETE_CLINICAL_ANALYSIS, UPDATE_INTERPRETATION, REVERT_INTERPRETATION, CLEAR_INTERPRETATION, MERGE_INTERPRETATION, SWAP_INTERPRETATION and DELETE_INTERPRETATION</p> |
| **message**<br>*String* <br> | <p>Audit message</p> |
| **date**<br>*String* <br> | <p>Date of the audit</p> |
| **author**<br>*String* <br> | <p>Clinical comment author</p> |
| **message**<br>*String* <br> | <p>Clinical comment message</p> |
| **tags**<br>*List<<em>String</em>>* <br> | <p>List of tags for the clinical comment</p> |
| **date**<br>*String* <br> | <p>Date of the clinical comment</p> |

### InterpretationInternal
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationInternal.java).
### ClinicalReport
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalReport.java).

| Field | Description |
| :--- | :--- |
| **status**<br>*[InterpretationStatus](https://docs.opencga.opencb.org/data-models/clinicalanalysis#interpretationstatus)* <br> | <p>State of the interpretation that can have the values READY, DELETED, NOT_REVIEWED, UNDER_REVIEW, REVIEWED and REJECTED.</p> |
| **status**<br>*[Status](https://docs.opencga.opencb.org/data-models/clinicalanalysis#status)* <br> | <p>Status of the internal object.</p> |
| **registrationDate**<br>*String* <br> | <p>Registration date of the internal object.</p> |
| **lastModified**<br>*String* <br> | <p>Date of the last modification of the internal object.</p> |
| **title**<br>*String* <br> | <p>Report title.</p> |
| **overview**<br>*String* <br> | <p>Report overview.</p> |
| **discussion**<br>*String* <br> | <p>Report discussion.</p> |
| **logo**<br>*String* <br> | <p>Report logo.</p> |
| **signedBy**<br>*String* <br> | <p>Indicates who has signed the report.</p> |
| **signature**<br>*String* <br> | <p>Report signature.</p> |
| **date**<br>*String* <br> | <p>Report date.</p> |

### ClinicalConsentParam
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentParam.java).
Expand All @@ -218,6 +208,16 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java).


### InterpretationInternal
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationInternal.java).

| Field | Description |
| :--- | :--- |
| **status**<br>*[InterpretationStatus](https://docs.opencga.opencb.org/data-models/clinicalanalysis#interpretationstatus)* <br> | <p>State of the interpretation that can have the values READY, DELETED, NOT_REVIEWED, UNDER_REVIEW, REVIEWED and REJECTED.</p> |
| **status**<br>*[Status](https://docs.opencga.opencb.org/data-models/clinicalanalysis#status)* <br> | <p>Status of the internal object.</p> |
| **registrationDate**<br>*String* <br> | <p>Registration date of the internal object.</p> |
| **lastModified**<br>*String* <br> | <p>Date of the last modification of the internal object.</p> |

### InterpretationStatus
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationStatus.java).

8 changes: 4 additions & 4 deletions docs/data-models/cohort.md
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Expand Up @@ -37,10 +37,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
| **internal**<br>*[CohortInternal](https://docs.opencga.opencb.org/data-models/cohort#cohortinternal)* <br> | <p>Internal field for manage the object.</p> |
| **attributes**<br>*Map<String,Object>* <br> | <p>You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.</p> |

### Status
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java).


### CohortInternal
You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/models/cohort/CohortInternal.java).

Expand All @@ -49,3 +45,7 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1
| **status**<br>*[Status](https://docs.opencga.opencb.org/data-models/cohort#status)* <br> | <p>Status of the internal object.</p> |
| **registrationDate**<br>*String* <br> | <p>Registration date of the internal object.</p> |
| **lastModified**<br>*String* <br> | <p>Date of the last modification of the internal object.</p> |

### Status
You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java).

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