Skip to content

Commit

Permalink
minor refactoring
Browse files Browse the repository at this point in the history
  • Loading branch information
@sbilge
sbilge committed Aug 31, 2023
1 parent 0b9b688 commit d0aad70
Show file tree
Hide file tree
Showing 22 changed files with 490 additions and 421 deletions.
11 changes: 8 additions & 3 deletions .sheet_documentation_template.md.jinja
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,20 +7,25 @@
## Fields

{% for slot in slots %}
**{{ slot.name }}** : {{ slot.description }}<br>
### ***{{ slot.name }}***<br>
**description** : {{ slot.description }}<br>
**required** : {{ slot.required }}<br>
{% if 'Enum' in slot.data_type.range %}
**data type** : Controlled Vocabulary <br>
{% else %}
**data type** : {{ slot.data_type.range }} <br>
{% endif %}

{% if slot.data_type.enum %}

<details>
<summary> <span style="color:#DAF7A6">Permissible Values</span> </summary>

| Permissible Values | Description |
| --- | --- |
{% for val in slot.data_type.enum.permissible_values%}
| `{{ val.name }}` | `{{ val.description }}` |
{% endfor %} {{ '\n' }}
{% endif %}
</details>

{% endif %}
{% endfor %}
26 changes: 11 additions & 15 deletions docs/metadata/worksheets/Analysis.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,31 +6,27 @@ An Analysis is a data transformation that transforms input data to output data.

## Fields

**title** : The title that describes an entity.<br>
### ***title***<br>
**description** : The title that describes an entity.<br>
**required** : None<br>
**data type** : string <br>


### ***description***<br>
**description** : Describing how an Analysis was carried out. (e.g.: computational tools, settings, etc.).<br>
**required** : False<br>
**data type** : string <br>


**type** : The type of the Analysis. Either Reference Alignment (BAM) or Sequence Variation (VCF)<br>
### ***type***<br>
**description** : The type of the Analysis. Either Reference Alignment (BAM) or Sequence Variation (VCF)<br>
**required** : False<br>
**data type** : string <br>


**reference_genome** : A published genetic sequence that is used as a reference sequence against which other sequences are compared. Reference genome(s) or annotation(s) used for prior analyses (eg: GRCh38.p13).<br>
### ***reference_genome***<br>
**description** : A published genetic sequence that is used as a reference sequence against which other sequences are compared. Reference genome(s) or annotation(s) used for prior analyses (eg: GRCh38.p13).<br>
**required** : True<br>
**data type** : string <br>


**reference_chromosome** : The reference chromosome used for this Analysis.<br>
### ***reference_chromosome***<br>
**description** : The reference chromosome used for this Analysis.<br>
**required** : True<br>
**data type** : string <br>


**alias** : The alias for an entity at the time of submission.<br>
### ***alias***<br>
**description** : The alias for an entity at the time of submission.<br>
**required** : True<br>
**data type** : string <br>
23 changes: 10 additions & 13 deletions docs/metadata/worksheets/AnalysisProcess.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,26 +6,23 @@ None

## Fields

**analysis** : The Analysis the AnalysisProcess was part of<br>
### ***analysis***<br>
**description** : The Analysis the AnalysisProcess was part of<br>
**required** : True<br>
**data type** : Analysis <br>


**study_input_files** : The StudyFile associated used as an input for an entity.<br>
### ***study_input_files***<br>
**description** : The StudyFile associated used as an input for an entity.<br>
**required** : False<br>
**data type** : StudyFile <br>


**sample_input_files** : The SampleFile associated used as an input for an entity.<br>
### ***sample_input_files***<br>
**description** : The SampleFile associated used as an input for an entity.<br>
**required** : False<br>
**data type** : SampleFile <br>


**sequencing_process_input_files** : The SequencingProcessFile associated used as an input for an entity.<br>
### ***sequencing_process_input_files***<br>
**description** : The SequencingProcessFile associated used as an input for an entity.<br>
**required** : False<br>
**data type** : SequencingProcessFile <br>


**alias** : The alias for an entity at the time of submission.<br>
### ***alias***<br>
**description** : The alias for an entity at the time of submission.<br>
**required** : True<br>
**data type** : string <br>
47 changes: 26 additions & 21 deletions docs/metadata/worksheets/AnalysisProcessOutputFile.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,20 +6,22 @@ A AnalysisProcessOutputFile is a File that is associated as an output file with

## Fields

**analysis_process** : The AnalysisProcess associated with an entity.<br>
### ***analysis_process***<br>
**description** : The AnalysisProcess associated with an entity.<br>
**required** : True<br>
**data type** : AnalysisProcess <br>


**name** : The given filename.<br>
### ***name***<br>
**description** : The given filename.<br>
**required** : True<br>
**data type** : string <br>


**format** : The format of the file: BAM, SAM, CRAM, BAI, etc.<br>
### ***format***<br>
**description** : The format of the file: BAM, SAM, CRAM, BAI, etc.<br>
**required** : True<br>
**data type** : Controlled Vocabulary <br>

<details>
<summary> <span style="color:#DAF7A6">Permissible Values</span> </summary>

| Permissible Values | Description |
| --- | --- |
| `AGP` | `None` |
Expand Down Expand Up @@ -50,38 +52,41 @@ A AnalysisProcessOutputFile is a File that is associated as an output file with
| `WIG` | `None` |


</details>

**size** : The size of a file in bytes.<br>
### ***size***<br>
**description** : The size of a file in bytes.<br>
**required** : True<br>
**data type** : integer <br>


**checksum** : A computed value which depends on the contents of a block of data and which is transmitted or stored along with the data in order to detect corruption of the data. The receiving system recomputes the checksum based upon the received data and compares this value with the one sent with the data. If the two values are the same, the receiver has some confidence that the data was received correctly.<br>
### ***checksum***<br>
**description** : A computed value which depends on the contents of a block of data and which is transmitted or stored along with the data in order to detect corruption of the data. The receiving system recomputes the checksum based upon the received data and compares this value with the one sent with the data. If the two values are the same, the receiver has some confidence that the data was received correctly.<br>
**required** : True<br>
**data type** : string <br>


**forward_or_reverse** : Denotes whether a submitted FASTQ file contains forward (R1) or reverse (R2) reads for paired-end sequencing. The number that identifies each read direction in a paired-end nucleotide sequencing reaction.<br>
### ***forward_or_reverse***<br>
**description** : Denotes whether a submitted FASTQ file contains forward (R1) or reverse (R2) reads for paired-end sequencing. The number that identifies each read direction in a paired-end nucleotide sequencing reaction.<br>
**required** : False<br>
**data type** : Controlled Vocabulary <br>

<details>
<summary> <span style="color:#DAF7A6">Permissible Values</span> </summary>

| Permissible Values | Description |
| --- | --- |
| `FORWARD` | `The reads are forward (R1) reads` |
| `REVERSE` | `The reads are reverse (R2) reads` |


</details>

**checksum_type** : The type of algorithm used to generate the checksum of a file.<br>
### ***checksum_type***<br>
**description** : The type of algorithm used to generate the checksum of a file.<br>
**required** : True<br>
**data type** : string <br>


**dataset** : The Dataset associated with an entity.<br>
### ***dataset***<br>
**description** : The Dataset associated with an entity.<br>
**required** : True<br>
**data type** : Dataset <br>


**alias** : The alias for an entity at the time of submission.<br>
### ***alias***<br>
**description** : The alias for an entity at the time of submission.<br>
**required** : True<br>
**data type** : string <br>
50 changes: 27 additions & 23 deletions docs/metadata/worksheets/Biospecimen.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,40 +6,38 @@ A Biospecimen is any natural material taken from a biological entity (usually a

## Fields

**name** : The name for an entity.<br>
### ***name***<br>
**description** : The name for an entity.<br>
**required** : False<br>
**data type** : string <br>


**type** : The type of Biospecimen.<br>
### ***type***<br>
**description** : The type of Biospecimen.<br>
**required** : False<br>
**data type** : string <br>


### ***description***<br>
**description** : Description of an entity.<br>
**required** : False<br>
**data type** : string <br>


**isolation** : Method or device employed for collecting/isolating a biospecimen or a sample.<br>
### ***isolation***<br>
**description** : Method or device employed for collecting/isolating a biospecimen or a sample.<br>
**required** : False<br>
**data type** : string <br>


**storage** : Methods by which a biospecimen or a sample is stored (e.g. frozen in liquid nitrogen).<br>
### ***storage***<br>
**description** : Methods by which a biospecimen or a sample is stored (e.g. frozen in liquid nitrogen).<br>
**required** : False<br>
**data type** : string <br>


**individual** : The Individual entity from which this Biospecimen was derived.<br>
### ***individual***<br>
**description** : The Individual entity from which this Biospecimen was derived.<br>
**required** : True<br>
**data type** : Individual <br>


**age_at_sampling** : Age of an individual.<br>
### ***age_at_sampling***<br>
**description** : Age of an individual.<br>
**required** : True<br>
**data type** : Controlled Vocabulary <br>

<details>
<summary> <span style="color:#DAF7A6">Permissible Values</span> </summary>

| Permissible Values | Description |
| --- | --- |
| `0_TO_5` | `Age between 0 to 5.` |
Expand All @@ -62,24 +60,30 @@ A Biospecimen is any natural material taken from a biological entity (usually a
| `UNKNOWN` | `Age range unknown.` |


</details>

**vital_status_at_sampling** : Vital Status of an Individual at the point of sampling (eg:'Alive', 'Deceased').<br>
### ***vital_status_at_sampling***<br>
**description** : Vital Status of an Individual at the point of sampling (eg:'Alive', 'Deceased').<br>
**required** : False<br>
**data type** : Controlled Vocabulary <br>

<details>
<summary> <span style="color:#DAF7A6">Permissible Values</span> </summary>

| Permissible Values | Description |
| --- | --- |
| `ALIVE` | `Showing characteristics of life; displaying signs of life.` |
| `DECEASED` | `The cessation of life.` |
| `UNKNOWN` | `Vital status is unknown.` |


</details>

**tissue** : None<br>
### ***tissue***<br>
**description** : None<br>
**required** : True<br>
**data type** : string <br>


**alias** : The alias for an entity at the time of submission.<br>
### ***alias***<br>
**description** : The alias for an entity at the time of submission.<br>
**required** : True<br>
**data type** : string <br>
47 changes: 29 additions & 18 deletions docs/metadata/worksheets/Condition.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,37 +6,43 @@ An condition that is linked to comparable samples.

## Fields

**title** : The title that describes an entity.<br>
### ***title***<br>
**description** : The title that describes an entity.<br>
**required** : None<br>
**data type** : string <br>


### ***description***<br>
**description** : Description of an entity.<br>
**required** : True<br>
**data type** : string <br>


**name** : The name for an entity.<br>
### ***name***<br>
**description** : The name for an entity.<br>
**required** : True<br>
**data type** : string <br>


**disease_or_healthy** : Whether a condition corresponds to a disease or a healthy state.<br>
### ***disease_or_healthy***<br>
**description** : Whether a condition corresponds to a disease or a healthy state.<br>
**required** : True<br>
**data type** : Controlled Vocabulary <br>

<details>
<summary> <span style="color:#DAF7A6">Permissible Values</span> </summary>

| Permissible Values | Description |
| --- | --- |
| `DISEASE` | `Disease state.` |
| `HEALTHY` | `Healthy state.` |
| `NOT_APPLICABLE` | `The distinction is not applicaple.` |


</details>

**case_control_status** : Whether a condition corresponds to a treatment or a control.<br>
### ***case_control_status***<br>
**description** : Whether a condition corresponds to a treatment or a control.<br>
**required** : True<br>
**data type** : Controlled Vocabulary <br>

<details>
<summary> <span style="color:#DAF7A6">Permissible Values</span> </summary>

| Permissible Values | Description |
| --- | --- |
| `NEITHER_CASE_OR_CONTROL_STATUS` | `None` |
Expand All @@ -47,29 +53,34 @@ An condition that is linked to comparable samples.
| `UNABLE_TO_ASSESS_CASE_OR_CONTROL_STATUS` | `None` |


</details>

**mutant_or_wildtype** : Whether a condition corresponds to a mutant or a wildtype.<br>
### ***mutant_or_wildtype***<br>
**description** : Whether a condition corresponds to a mutant or a wildtype.<br>
**required** : True<br>
**data type** : Controlled Vocabulary <br>

<details>
<summary> <span style="color:#DAF7A6">Permissible Values</span> </summary>

| Permissible Values | Description |
| --- | --- |
| `MUTANT` | `Mutant state.` |
| `WILDTYPE` | `Wildtype state.` |
| `NOT_APPLICABLE` | `The distinction is not applicaple.` |


</details>

**study** : The study associated with an entity.<br>
### ***study***<br>
**description** : The study associated with an entity.<br>
**required** : True<br>
**data type** : Study <br>


**attributes** : Key/value pairs corresponding to an entity.<br>
### ***attributes***<br>
**description** : Key/value pairs corresponding to an entity.<br>
**required** : False<br>
**data type** : Attribute <br>


**alias** : The alias for an entity at the time of submission.<br>
### ***alias***<br>
**description** : The alias for an entity at the time of submission.<br>
**required** : True<br>
**data type** : string <br>
Loading

0 comments on commit d0aad70

Please sign in to comment.