You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| | **status**Object status.
| -### 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). +### 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 | | :--- | :--- | -| **title**Report title.
| -| **overview**Report overview.
| -| **discussion**Report discussion.
| -| **logo**Report logo.
| -| **signedBy**Indicates who has signed the report.
| -| **signature**Report signature.
| -| **date**Report date.
| +| **author**Clinical comment author
| +| **message**Clinical comment message
| +| **tags**List of tags for the clinical comment
| +| **date**Date of the clinical comment
| -### 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). +### 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 | | :--- | :--- | -| **studyUid**Study identifier.
| -| **uid**Interpretation identifier.
| -| **panels**Interpretation panel list.
| -| **internal**Internal field for manage the object.
| +| **uuid**Unique 32-character identifier assigned automatically by OpenCGA.
| | **release**An integer describing the current data release.
| +| **version**OpenCGA version of this panel, this is incremented when the panel is updated.
| +| **~~author~~**Author of the panel.
| +| **status**Panel status can have the values READY or DELETED.
| +| **studyUid**Panel reference to study.
| +| **uid**Panel reference to study.
| + +### ClinicalAnalysisInternal +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/ClinicalAnalysisInternal.java). + +| Field | Description | +| :--- | :--- | +| **status**Status of the internal object.
| +| **registrationDate**Registration date of the internal object.
| +| **lastModified**Date of the last modification of the internal object.
| ### 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). @@ -102,41 +110,49 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **description**Users may provide a description for the entry.
| | **date**FlagAnnotation date.
| -### 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). +### 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 | | :--- | :--- | -| **consents**List of ClinicalConsentParam.
| -| **date**Date of the ClinicalConsentAnnotation.
| +| **author**Audit author
| +| **action**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
| +| **message**Audit message
| +| **date**Date of the audit
| -### ClinicalAnalysisInternal -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/ClinicalAnalysisInternal.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**Status of the internal object.
| -| **registrationDate**Registration date of the internal object.
| -| **lastModified**Date of the last modification of the internal object.
| +| **title**Report title.
| +| **overview**Report overview.
| +| **discussion**Report discussion.
| +| **logo**Report logo.
| +| **signedBy**Indicates who has signed the report.
| +| **signature**Report signature.
| +| **date**Report date.
| -### 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). +### ClinicalAnalyst +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java). | Field | Description | | :--- | :--- | -| **summary**ClinicalAnalysisQualityControl summary that can have the values HIGH, MEDIUM, LOW, DISCARD, NEEDS_REVIEW, UNKNOWN.
| -| **comments**List of ClinicalAnalysisQualityControl comments.
| -| **comments**List of ClinicalAnalysisQualityControl files.
| +| **id**Id to identify the object
| +| **name**Object name
| +| **email**Email of the analyst
| +| **assignedBy**Assigned by field
| +| **date**Date of the clinical analyst
| -### 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). +### 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 | | :--- | :--- | -| **author**Audit author
| -| **action**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
| -| **message**Audit message
| -| **date**Date of the audit
| +| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| +| **description**Users may provide a description for the entry.
| +| **rank**ClinicalPriorityAnnotation rank.
| +| **date**ClinicalPriorityAnnotation date.
| ### 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). @@ -150,53 +166,43 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop | **url**Ontology url
| | **attributes**Dictionary that can be customised by users to store any additional information users may require..
| -### 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). +### 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 | | :--- | :--- | -| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **description**Users may provide a description for the entry.
| -| **rank**ClinicalPriorityAnnotation rank.
| -| **date**ClinicalPriorityAnnotation date.
| +| **summary**ClinicalAnalysisQualityControl summary that can have the values HIGH, MEDIUM, LOW, DISCARD, NEEDS_REVIEW, UNKNOWN.
| +| **comments**List of ClinicalAnalysisQualityControl comments.
| +| **comments**List of ClinicalAnalysisQualityControl files.
| -### 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). +### 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). | Field | Description | | :--- | :--- | -| **author**Clinical comment author
| -| **message**Clinical comment message
| -| **tags**List of tags for the clinical comment
| -| **date**Date of the clinical comment
| +| **consents**List of ClinicalConsentParam.
| +| **date**Date of the ClinicalConsentAnnotation.
| -### 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). +### 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). | Field | Description | | :--- | :--- | -| **uuid**Unique 32-character identifier assigned automatically by OpenCGA.
| +| **studyUid**Study identifier.
| +| **uid**Interpretation identifier.
| +| **panels**Interpretation panel list.
| +| **internal**Internal field for manage the object.
| | **release**An integer describing the current data release.
| -| **version**OpenCGA version of this panel, this is incremented when the panel is updated.
| -| **~~author~~**Author of the panel.
| -| **status**Panel status can have the values READY or DELETED.
| -| **studyUid**Panel reference to study.
| -| **uid**Panel reference to study.
| -### ClinicalAnalyst -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java). +### 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). | Field | Description | | :--- | :--- | -| **id**Id to identify the object
| -| **name**Object name
| -| **email**Email of the analyst
| -| **assignedBy**Assigned by field
| -| **date**Date of the clinical analyst
| - -### 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). - +| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| +| **name**Name of the .
| +| **description**Users may provide a description for the entry.
| +| **value**Value of the param that can have the values YES, NO and UNKNOWN.
| ### 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). @@ -208,15 +214,9 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **registrationDate**Registration date of the internal object.
| | **lastModified**Date of the last modification of the internal object.
| -### 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). +### 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). -| Field | Description | -| :--- | :--- | -| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **name**Name of the .
| -| **description**Users may provide a description for the entry.
| -| **value**Value of the param that can have the values YES, NO and UNKNOWN.
| ### 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). diff --git a/docs/data-models/cohort.md b/docs/data-models/cohort.md index 020b345bc1e..c1f1f554ac8 100644 --- a/docs/data-models/cohort.md +++ b/docs/data-models/cohort.md @@ -37,10 +37,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **internal**Internal field for manage the object.
| | **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| -### 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). @@ -49,3 +45,7 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **status**Status of the internal object.
| | **registrationDate**Registration date of the internal object.
| | **lastModified**Date of the last modification of the internal object.
| + +### 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). + diff --git a/docs/data-models/family.md b/docs/data-models/family.md index 69ca95f6e7a..a49510610fd 100644 --- a/docs/data-models/family.md +++ b/docs/data-models/family.md @@ -47,9 +47,19 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **release**An integer describing the current data release.
| | **version**Autoincremental version assigned to the registered entry. By default, updates does not create new versions. To enable versioning, users must set the `incVersion` flag from the /update web service when updating the document.
| -### 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). +### Phenotype +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Phenotype.java). +| Field | Description | +| :--- | :--- | +| **id**Id to identify the object
| +| **ageOfOnset**Indicates the age of on set of the phenotype
| +| **status**Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN
| +| **name**Object name
| +| **description**Users may provide a description for the entry.
| +| **source**Ontology source
| +| **url**Ontology url
| +| **attributes**Dictionary that can be customised by users to store any additional information users may require..
| ### FamilyInternal 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/family/FamilyInternal.java). @@ -60,40 +70,40 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **registrationDate**Registration date of the internal object.
| | **lastModified**Date of the last modification of the internal object.
| -### 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). +### FamilyQualityControl +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/family/FamilyQualityControl.java). | Field | Description | | :--- | :--- | -| **id**Id to identify the object
| -| **name**Object name
| -| **description**Users may provide a description for the entry.
| -| **source**Ontology source
| -| **url**Ontology url
| -| **attributes**Dictionary that can be customised by users to store any additional information users may require..
| +| **relatedness**Reports of family relationship.
| +| **files**File IDs related to the quality control.
| +| **comments**Comments related to the quality control.
| -### Phenotype -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Phenotype.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**Id to identify the object
| -| **ageOfOnset**Indicates the age of on set of the phenotype
| -| **status**Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN
| | **name**Object name
| | **description**Users may provide a description for the entry.
| | **source**Ontology source
| | **url**Ontology url
| | **attributes**Dictionary that can be customised by users to store any additional information users may require..
| -### FamilyQualityControl -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/family/FamilyQualityControl.java). +### 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). + + +### 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 | | :--- | :--- | -| **relatedness**Reports of family relationship.
| -| **files**File IDs related to the quality control.
| -| **comments**Comments related to the quality control.
| +| **author**Clinical comment author
| +| **message**Clinical comment message
| +| **tags**List of tags for the clinical comment
| +| **date**Date of the clinical comment
| ### RelatednessReport You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/RelatednessReport.java). @@ -104,13 +114,3 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop | **maf**Minor allele frequency to filter variants, e.g.: 1kg_phase3:CEU>0.35, cohort:ALL>0.05
| | **scores**Relatedness scores for pair of samples
| | **files**List of files of Relatedness Report
| - -### 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**Clinical comment author
| -| **message**Clinical comment message
| -| **tags**List of tags for the clinical comment
| -| **date**Date of the clinical comment
| diff --git a/docs/data-models/file.md b/docs/data-models/file.md index 9989da6c79e..210dbbc086f 100644 --- a/docs/data-models/file.md +++ b/docs/data-models/file.md @@ -65,16 +65,36 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **internal**Internal field for manage the object.
| | **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| +### 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). + + ### FileExperiment 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/file/FileExperiment.java). -### URI -You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URI.java). +### Software +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Software.java). + +| Field | Description | +| :--- | :--- | +| **name**Software name
| +| **version**Software version
| +| **repository**Software repository
| +| **commit**Software commit
| +| **website**Software website
| +| **params**Software params
| +### FileQualityControl +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/file/FileQualityControl.java). -### 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). + +### FileRelatedFile +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/file/FileRelatedFile.java). + + +### URI +You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URI.java). ### FileInternal @@ -91,28 +111,8 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **registrationDate**Registration date of the internal object.
| | **lastModified**Date of the last modification of the internal object.
| -### FileQualityControl -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/file/FileQualityControl.java). - - -### FileRelatedFile -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/file/FileRelatedFile.java). - - -### Software -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Software.java). - -| Field | Description | -| :--- | :--- | -| **name**Software name
| -| **version**Software version
| -| **repository**Software repository
| -| **commit**Software commit
| -| **website**Software website
| -| **params**Software params
| - -### FileInternalVariant -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/file/FileInternalVariant.java). +### FileInternalAlignment +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/file/FileInternalAlignment.java). ### MissingSamples @@ -123,10 +123,10 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **existing**List of existing samples.
| | **nonExisting**List of non existing samples.
| -### FileStatus -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/file/FileStatus.java). +### FileInternalVariant +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/file/FileInternalVariant.java). -### FileInternalAlignment -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/file/FileInternalAlignment.java). +### FileStatus +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/file/FileStatus.java). diff --git a/docs/data-models/individual.md b/docs/data-models/individual.md index de0bdf82be1..651dc986e3b 100644 --- a/docs/data-models/individual.md +++ b/docs/data-models/individual.md @@ -63,19 +63,8 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **release**An integer describing the current data release.
| | **version**Autoincremental version assigned to the registered entry. By default, updates does not create new versions. To enable versioning, users must set the `incVersion` flag from the /update web service when updating the document.
| -### IndividualQualityControl -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/individual/IndividualQualityControl.java). - -| Field | Description | -| :--- | :--- | -| **inferredSexReports**List of inferred sex reports, it depends on the method (currently by coverage ratio).
| -| **sampleRelatednessReport**Reports of samples relatedness.
| -| **mendelianErrorReports**Mendelian errors.
| -| **files**File IDs related to the quality control.
| -| **author**Comments related to the quality control.
| - -### OntologyTermAnnotation -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/core/OntologyTermAnnotation.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 | | :--- | :--- | @@ -86,29 +75,42 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop | **url**Ontology url
| | **attributes**Dictionary that can be customised by users to store any additional information users may require..
| -### Location -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/individual/Location.java). +### IndividualInternal +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/individual/IndividualInternal.java). | Field | Description | | :--- | :--- | -| **address**Location address.
| -| **postalCode**Location postal code.
| -| **city**Location city.
| -| **state**Location state.
| -| **country**Location country.
| +| **status**Status of the internal object.
| +| **registrationDate**Registration date of the internal object.
| +| **lastModified**Date of the last modification of the internal object.
| -### 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). +### Phenotype +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Phenotype.java). | Field | Description | | :--- | :--- | | **id**Id to identify the object
| +| **ageOfOnset**Indicates the age of on set of the phenotype
| +| **status**Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN
| | **name**Object name
| | **description**Users may provide a description for the entry.
| | **source**Ontology source
| | **url**Ontology url
| | **attributes**Dictionary that can be customised by users to store any additional information users may require..
| +### IndividualPopulation +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/individual/IndividualPopulation.java). + +| Field | Description | +| :--- | :--- | +| **name**Name of the individual population.
| +| **subpopulation**Subpopulation of the individual population.
| +| **description**Description of the individual population.
| + +### 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). + + ### SexOntologyTermAnnotation You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/core/SexOntologyTermAnnotation.java). @@ -121,51 +123,43 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop | **url**Ontology url
| | **attributes**Dictionary that can be customised by users to store any additional information users may require..
| -### IndividualPopulation -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/individual/IndividualPopulation.java). +### Location +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/individual/Location.java). | Field | Description | | :--- | :--- | -| **name**Name of the individual population.
| -| **subpopulation**Subpopulation of the individual population.
| -| **description**Description of the individual population.
| +| **address**Location address.
| +| **postalCode**Location postal code.
| +| **city**Location city.
| +| **state**Location state.
| +| **country**Location country.
| -### Phenotype -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Phenotype.java). +### OntologyTermAnnotation +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/core/OntologyTermAnnotation.java). | Field | Description | | :--- | :--- | | **id**Id to identify the object
| -| **ageOfOnset**Indicates the age of on set of the phenotype
| -| **status**Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN
| | **name**Object name
| | **description**Users may provide a description for the entry.
| | **source**Ontology source
| | **url**Ontology url
| | **attributes**Dictionary that can be customised by users to store any additional information users may require..
| -### 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). - - -### IndividualInternal -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/individual/IndividualInternal.java). +### IndividualQualityControl +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/individual/IndividualQualityControl.java). | Field | Description | | :--- | :--- | -| **status**Status of the internal object.
| -| **registrationDate**Registration date of the internal object.
| -| **lastModified**Date of the last modification of the internal object.
| +| **inferredSexReports**List of inferred sex reports, it depends on the method (currently by coverage ratio).
| +| **sampleRelatednessReport**Reports of samples relatedness.
| +| **mendelianErrorReports**Mendelian errors.
| +| **files**File IDs related to the quality control.
| +| **author**Comments related to the quality control.
| -### 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). +### InferredSexReport +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/InferredSexReport.java). -| Field | Description | -| :--- | :--- | -| **author**Clinical comment author
| -| **message**Clinical comment message
| -| **tags**List of tags for the clinical comment
| -| **date**Date of the clinical comment
| ### MendelianErrorReport You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/MendelianErrorReport.java). @@ -175,6 +169,12 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SampleRelatednessReport.java). -### InferredSexReport -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/InferredSexReport.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**Clinical comment author
| +| **message**Clinical comment message
| +| **tags**List of tags for the clinical comment
| +| **date**Date of the clinical comment
| diff --git a/docs/data-models/job.md b/docs/data-models/job.md index c08dc5ad6dc..b4e700044d3 100644 --- a/docs/data-models/job.md +++ b/docs/data-models/job.md @@ -59,28 +59,24 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **study**Job study.
| | **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| -### JobStudyParam -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/job/JobStudyParam.java). +### ToolInfo +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/job/ToolInfo.java). | Field | Description | | :--- | :--- | | **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **others**List of strings.
| +| **description**Users may provide a description for the entry.
| +| **scope**Tool info scope can have the values GLOBAL, PROJECT and STUDY.
| +| **type**Tool info type can have the values OPERATION and ANALYSIS.
| +| **resource**Tool info resource can have the values AUDIT, USER, PROJECT, STUDY, FILE, SAMPLE, JOB, INDIVIDUAL, COHORT, DISEASE_PANEL, FAMILY, CLINICAL_ANALYSIS, INTERPRETATION, VARIANT, ALIGNMENT, CLINICAL, EXPRESSION, RGA and FUNCTIONAL.
| -### ExecutionResult -You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/tools/result/ExecutionResult.java). +### JobStudyParam +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/job/JobStudyParam.java). | Field | Description | | :--- | :--- | | **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **executor**Object describes execution information.
| -| **start**Date the execution started.
| -| **end**Date the execution was completed.
| -| **status**Executor status can have the values PENDING, RUNNING, DONE and ERROR.
| -| **externalFiles**List of uris to the external files.
| -| **steps**List of ToolStep.
| -| **events**List of Event.
| -| **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| +| **others**List of strings.
| ### JobInternal 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/job/JobInternal.java). @@ -94,27 +90,38 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **registrationDate**Registration date of the internal object.
| | **lastModified**Date of the last modification of the internal object.
| -### ToolInfo -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/job/ToolInfo.java). +### ExecutionResult +You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/tools/result/ExecutionResult.java). | Field | Description | | :--- | :--- | | **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **description**Users may provide a description for the entry.
| -| **scope**Tool info scope can have the values GLOBAL, PROJECT and STUDY.
| -| **type**Tool info type can have the values OPERATION and ANALYSIS.
| -| **resource**Tool info resource can have the values AUDIT, USER, PROJECT, STUDY, FILE, SAMPLE, JOB, INDIVIDUAL, COHORT, DISEASE_PANEL, FAMILY, CLINICAL_ANALYSIS, INTERPRETATION, VARIANT, ALIGNMENT, CLINICAL, EXPRESSION, RGA and FUNCTIONAL.
| +| **executor**Object describes execution information.
| +| **start**Date the execution started.
| +| **end**Date the execution was completed.
| +| **status**Executor status can have the values PENDING, RUNNING, DONE and ERROR.
| +| **externalFiles**List of uris to the external files.
| +| **steps**List of ToolStep.
| +| **events**List of Event.
| +| **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| -### Date -You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/util/Date.java). +### ExecutorInfo +You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/tools/result/ExecutorInfo.java). +| Field | Description | +| :--- | :--- | +| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| +| **clazz**ExecutorInfo class.
| +| **params**ExecutorInfo params.
| +| **source**Executor info source can have the values FILE, PARQUET_FILE, MONGODB, HBASE, STORAGE.
| +| **framework**Executor info framework can have the values LOCAL, MAP_REDUCE, SPARK.
| -### Status -You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/tools/result/Status.java). +### ExecutionStatus +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/Enums/ExecutionStatus.java). -### URI -You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URI.java). +### 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). ### JobInternalWebhook @@ -136,20 +143,13 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **status**Executor status can have the values PENDING, RUNNING, DONE and ERROR.
| | **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| -### ExecutionStatus -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/Enums/ExecutionStatus.java). +### URI +You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URI.java). -### ExecutorInfo -You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/org/opencb/opencga/core/tools/result/ExecutorInfo.java). +### Date +You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/util/Date.java). -| Field | Description | -| :--- | :--- | -| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **clazz**ExecutorInfo class.
| -| **params**ExecutorInfo params.
| -| **source**Executor info source can have the values FILE, PARQUET_FILE, MONGODB, HBASE, STORAGE.
| -| **framework**Executor info framework can have the values LOCAL, MAP_REDUCE, SPARK.
| ### URL You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URL.java). diff --git a/docs/data-models/project.md b/docs/data-models/project.md index 4d291e0ad2d..b27571132ee 100644 --- a/docs/data-models/project.md +++ b/docs/data-models/project.md @@ -37,6 +37,10 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **release**An integer describing the current data release.
| | **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| +### ProjectOrganism +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/project/ProjectOrganism.java). + + ### ProjectInternal 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/project/ProjectInternal.java). @@ -48,10 +52,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **registrationDate**Registration date of the internal object.
| | **lastModified**Date of the last modification of the internal object.
| -### ProjectOrganism -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/project/ProjectOrganism.java). - - ### 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). diff --git a/docs/data-models/sample.md b/docs/data-models/sample.md index 9a3bbcf7a5f..a93b3a0631b 100644 --- a/docs/data-models/sample.md +++ b/docs/data-models/sample.md @@ -51,17 +51,23 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **version**Autoincremental version assigned to the registered entry. By default, updates does not create new versions. To enable versioning, users must set the `incVersion` flag from the /update web service when updating the document.
| | **internal**Sample internal information.
| -### SampleCollection -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/sample/SampleCollection.java). +### 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). + + +### Phenotype +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Phenotype.java). | Field | Description | | :--- | :--- | -| **from**OntologyTermAnnotation list.
| -| **type**Type of the sample collection.
| -| **quantity**Quantity collected for the sample.
| -| **method**Describes which method was used to collect the sample.
| -| **date**Date when the sample was collected.
| -| **attributes**Attributes of the sample collection.
| +| **id**Id to identify the object
| +| **ageOfOnset**Indicates the age of on set of the phenotype
| +| **status**Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN
| +| **name**Object name
| +| **description**Users may provide a description for the entry.
| +| **source**Ontology source
| +| **url**Ontology url
| +| **attributes**Dictionary that can be customised by users to store any additional information users may require..
| ### SampleInternal 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/sample/SampleInternal.java). @@ -73,6 +79,17 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **registrationDate**Registration date of the internal object.
| | **lastModified**Date of the last modification of the internal object.
| +### ExternalSource +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/ExternalSource.java). + +| Field | Description | +| :--- | :--- | +| **id**Source ID...
| +| **name**Source name...
| +| **description**Source description...
| +| **source**Source ...
| +| **url**Source ID
| + ### SampleQualityControl 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/sample/SampleQualityControl.java). @@ -82,16 +99,17 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **comments**Comments for the quality control of the sample.
| | **variant**Describes variant quality control.
| -### ExternalSource -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/ExternalSource.java). +### SampleCollection +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/sample/SampleCollection.java). | Field | Description | | :--- | :--- | -| **id**Source ID...
| -| **name**Source name...
| -| **description**Source description...
| -| **source**Source ...
| -| **url**Source ID
| +| **from**OntologyTermAnnotation list.
| +| **type**Type of the sample collection.
| +| **quantity**Quantity collected for the sample.
| +| **method**Describes which method was used to collect the sample.
| +| **date**Date when the sample was collected.
| +| **attributes**Attributes of the sample collection.
| ### SampleProcessing 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/sample/SampleProcessing.java). @@ -106,23 +124,13 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **date**Date when the sample was processed in the lab.
| | **attributes**Attributes of the processing.
| -### 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). - - -### Phenotype -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Phenotype.java). +### RgaIndex +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/RgaIndex.java). | Field | Description | | :--- | :--- | -| **id**Id to identify the object
| -| **ageOfOnset**Indicates the age of on set of the phenotype
| -| **status**Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN
| -| **name**Object name
| -| **description**Users may provide a description for the entry.
| -| **source**Ontology source
| -| **url**Ontology url
| -| **attributes**Dictionary that can be customised by users to store any additional information users may require..
| +| **status**Status of the Rga index NOT_INDEXED, INDEXED, INVALID_PERMISSIONS, INVALID_METADATA, INVALID.
| +| **date**Date of Rga index.
| ### OntologyTermAnnotation You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/core/OntologyTermAnnotation.java). @@ -156,13 +164,18 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **genomePlot**Genome plot for the quality control of the sample.
| | **files**File for the quality control metrics of the sample.
| -### RgaIndex -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/RgaIndex.java). +### Signature +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature.java). | Field | Description | | :--- | :--- | -| **status**Status of the Rga index NOT_INDEXED, INDEXED, INVALID_PERMISSIONS, INVALID_METADATA, INVALID.
| -| **date**Date of Rga index.
| +| **id**Id to identify the object
| +| **description**Users may provide a description for the entry.
| +| **query**Map for query
| +| **type**Signature type SNV, INDEL...
| +| **counts**List of GenomeContextCount
| +| **files**List of files of signature
| +| **fitting**Signature fitting
| ### SampleQcVariantStats You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SampleQcVariantStats.java). @@ -175,19 +188,6 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop | **stats**Stats result set
| | **sampleId**Stats result set
| -### Signature -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature.java). - -| Field | Description | -| :--- | :--- | -| **id**Id to identify the object
| -| **description**Users may provide a description for the entry.
| -| **query**Map for query
| -| **type**Signature type SNV, INDEL...
| -| **counts**List of GenomeContextCount
| -| **files**List of files of signature
| -| **fitting**Signature fitting
| - ### GenomePlot You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/GenomePlot.java). @@ -198,15 +198,17 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop | **config**Config of the genomePlot
| | **file**File of the genomePlot
| -### GenomePlotConfig -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/GenomePlotConfig.java). +### SignatureFitting +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java). | Field | Description | | :--- | :--- | -| **title**Title of the genome plot configuration
| -| **density**Density of the genome plot configuration
| -| **generalQuery**Map for the general query of the genome plot configuration
| -| **tracks**List of GenomePlotTrack
| +| **method**Method used to fit the signature
| +| **signatureSource**Source of the fitting signature
| +| **signatureVersion**Signature version of the fitting signature
| +| **scores**Scores of the fitting signature
| +| **coeff**Coefficient of the fitting signature
| +| **file**Files of the fitting signature
| ### GenomeContextCount You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature/GenomeContextCount.java). @@ -216,17 +218,15 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop | **context**Genome context to count
| | **total**Counted integer
| -### SignatureFitting -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java). +### GenomePlotConfig +You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/GenomePlotConfig.java). | Field | Description | | :--- | :--- | -| **method**Method used to fit the signature
| -| **signatureSource**Source of the fitting signature
| -| **signatureVersion**Signature version of the fitting signature
| -| **scores**Scores of the fitting signature
| -| **coeff**Coefficient of the fitting signature
| -| **file**Files of the fitting signature
| +| **title**Title of the genome plot configuration
| +| **density**Density of the genome plot configuration
| +| **generalQuery**Map for the general query of the genome plot configuration
| +| **tracks**List of GenomePlotTrack
| ### GenomePlotTrack You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/GenomePlotTrack.java). diff --git a/docs/data-models/study.md b/docs/data-models/study.md index 25983981a9a..aa541806238 100644 --- a/docs/data-models/study.md +++ b/docs/data-models/study.md @@ -71,39 +71,21 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **additionalInfo**Dictionary that can be customised by users to store any additional information users may require.
| | **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| -### 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). - - -### StudyInternal -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/StudyInternal.java). +### StudyNotification +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/StudyNotification.java). | Field | Description | | :--- | :--- | -| **status**Object status.
| -| **index**Study index.
| -| **configuration**Study configuration.
| -| **status**Status of the internal object.
| -| **registrationDate**Registration date of the internal object.
| -| **lastModified**Date of the last modification of the internal object.
| +| **webhook**Url of the study notification.
| -### PermissionRule -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/PermissionRule.java). +### URI +You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URI.java). -| Field | Description | -| :--- | :--- | -| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **query**PermissionRule query.
| -| **members**List of members of the permission rule.
| -| **permissions**List of permissions of the permission rule.
| -### StudyType -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/StudyType.java). +### Enum Entity +_Enumeration class._ +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/Enums/Entity.java). -| Field | Description | -| :--- | :--- | -| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **description**Users may provide a description for the entry.
| ### 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). @@ -118,10 +100,28 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **studyUid**Panel reference to study.
| | **uid**Panel reference to study.
| -### Enum Entity -_Enumeration class._ -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/Enums/Entity.java). +### StudyInternal +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/StudyInternal.java). + +| Field | Description | +| :--- | :--- | +| **status**Object status.
| +| **index**Study index.
| +| **configuration**Study configuration.
| +| **status**Status of the internal object.
| +| **registrationDate**Registration date of the internal object.
| +| **lastModified**Date of the last modification of the internal object.
| + +### ExternalSource +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/ExternalSource.java). +| Field | Description | +| :--- | :--- | +| **id**Source ID...
| +| **name**Source name...
| +| **description**Source description...
| +| **source**Source ...
| +| **url**Source ID
| ### VariableSet 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/VariableSet.java). @@ -138,36 +138,36 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **type**Type of the additional info.
| | **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| -### ExternalSource -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/ExternalSource.java). +### StudyType +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/StudyType.java). | Field | Description | | :--- | :--- | -| **id**Source ID...
| -| **name**Source name...
| -| **description**Source description...
| -| **source**Source ...
| -| **url**Source ID
| +| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| +| **description**Users may provide a description for the entry.
| -### StudyNotification -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/StudyNotification.java). +### 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). -| Field | Description | -| :--- | :--- | -| **webhook**Url of the study notification.
| ### Group 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/Group.java). -### URI -You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URI.java). - - -### URL -You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URL.java). +### PermissionRule +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/PermissionRule.java). +| Field | Description | +| :--- | :--- | +| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| +| **query**PermissionRule query.
| +| **members**List of members of the permission rule.
| +| **permissions**List of permissions of the permission rule.
| ### StudyIndex 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/StudyIndex.java). + +### URL +You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1806/opencga-core/src/main/java/java/net/URL.java). + diff --git a/docs/data-models/user.md b/docs/data-models/user.md index baa64174192..93b6dbb1293 100644 --- a/docs/data-models/user.md +++ b/docs/data-models/user.md @@ -37,18 +37,8 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **filters**A List with related filters.
| | **attributes**You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| -### Account -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/user/Account.java). - -| Field | Description | -| :--- | :--- | -| **type**User account type can have the values GUEST, FULL and ADMINISTRATOR.
| -| **creationDate**Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was first registered.
| -| **expirationDate**Date the account expires.
| -| **authentication**How the account is authenticated
| - -### UserInternal -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/user/UserInternal.java). +### UserQuota +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/user/UserQuota.java). ### UserFilter @@ -62,8 +52,18 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/issue-1 | **query**User filter query
| | **query**User filter query options
| -### UserQuota -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/user/UserQuota.java). +### Account +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/user/Account.java). + +| Field | Description | +| :--- | :--- | +| **type**User account type can have the values GUEST, FULL and ADMINISTRATOR.
| +| **creationDate**Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was first registered.
| +| **expirationDate**Date the account expires.
| +| **authentication**How the account is authenticated
| + +### UserInternal +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/user/UserInternal.java). ### AuthenticationOrigin diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 26c167b64af..3601e477884 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -37,7 +37,7 @@ * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. * Command line version: 2.2.0-SNAPSHOT -* Command line commit: 30999663dad10beecad1dec77aed13ce463a9c5e +* Command line commit: 702f60984784cc9075007a64edfda00abac966fb */ public abstract class OpenCgaCompleter implements Completer { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index 7b917bb4cfc..dce18b92a6f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -31,7 +31,7 @@ * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. * Command line version: 2.2.0-SNAPSHOT -* Command line commit: 30999663dad10beecad1dec77aed13ce463a9c5e +* Command line commit: 702f60984784cc9075007a64edfda00abac966fb */ public class OpencgaCliOptionsParser extends ParentCliOptionsParser { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java index 8dddff6b3f5..7c7aade464a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java @@ -39,6 +39,7 @@ public class OpencgaMain { public static Level logLevel = Level.OFF; public static void main(String[] args) { + if (args.length == 0) { CliOptionsParser parser = new OpencgaCliOptionsParser(); parser.printUsage(); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/parent/ParentUsersCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/parent/ParentUsersCommandExecutor.java index 2eebc19d3b6..f022dd7ed26 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/parent/ParentUsersCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/parent/ParentUsersCommandExecutor.java @@ -68,7 +68,9 @@ protected RestResponse