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feat: pretty print HTML #270

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feat: pretty print HTML #270

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aabec42
feat: pretty print HTML
a-frantz Dec 16, 2024
dffba37
Update CHANGELOG.md
a-frantz Dec 16, 2024
18c4c12
Update wdl-doc/CHANGELOG.md
a-frantz Dec 16, 2024
1f47498
revise: add newline after Debug print of html
a-frantz Dec 16, 2024
a27e0b2
chore: clippy
a-frantz Dec 17, 2024
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4 changes: 4 additions & 0 deletions wdl-doc/CHANGELOG.md
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Expand Up @@ -10,3 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added

* `wdl-doc` crate for documenting WDL codebases ([#258](https://github.com/stjude-rust-labs/wdl/pull/248)).

### Changed

* Pretty print HTML ([#270](https://github.com/stjude-rust-labs/wdl/pull/270)).
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4 changes: 2 additions & 2 deletions wdl-doc/src/lib.rs
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Expand Up @@ -93,8 +93,8 @@ impl Display for Document {
let mut preamble = String::new();
pulldown_cmark::html::push_html(&mut preamble, parser);

write!(f, "{}", document_name)?;
write!(f, "{}", version)?;
write!(f, "{:?}", document_name)?;
write!(f, "{:?}", version)?;
write!(f, "{}", preamble)
}
}
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6 changes: 3 additions & 3 deletions wdl-doc/src/parameter.rs
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Expand Up @@ -60,8 +60,8 @@ impl Display for Parameter {
.build()
};

write!(f, "{}", parameter_name)?;
write!(f, "{}", parameter_type)?;
write!(f, "{}", parameter_expr)
write!(f, "{:?}", parameter_name)?;
write!(f, "{:?}", parameter_type)?;
write!(f, "{:?}", parameter_expr)
}
}
4 changes: 2 additions & 2 deletions wdl-doc/src/struct.rs
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Expand Up @@ -49,7 +49,7 @@ impl Display for Struct {
}
let members = members.build();

write!(f, "{}", struct_name)?;
write!(f, "{}", members)
write!(f, "{:?}", struct_name)?;
write!(f, "{:?}", members)
}
}
4 changes: 2 additions & 2 deletions wdl-doc/src/task.rs
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Expand Up @@ -103,7 +103,7 @@ impl Display for Task {
.build(),
);

write!(f, "{}", task_name)?;
write!(f, "{}", content.build())
write!(f, "{:?}", task_name)?;
write!(f, "{:?}", content.build())
}
}
5 changes: 3 additions & 2 deletions wdl-doc/src/workflow.rs
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@@ -1,5 +1,6 @@
//! Create HTML documentation for WDL tasks.

use std::fmt::Debug;
use std::fmt::Display;

use html::content;
Expand Down Expand Up @@ -103,7 +104,7 @@ impl Display for Workflow {
.build(),
);

write!(f, "{}", task_name)?;
write!(f, "{}", content.build())
write!(f, "{:?}", task_name)?;
write!(f, "{:?}", content.build())
}
}
17 changes: 16 additions & 1 deletion wdl-doc/tests/output_docs/data_structures/flag_filter/FlagFilter-struct.html
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@@ -1 +1,16 @@
<h1>FlagFilter</h1><ul><li>include_if_all: String</li><li>exclude_if_any: String</li><li>include_if_any: String</li><li>exclude_if_all: String</li></ul>
<h1>
FlagFilter
</h1><ul>
Copy link
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Seems like this needs some newlines.

<li>
include_if_all: String
</li>
<li>
exclude_if_any: String
</li>
<li>
include_if_any: String
</li>
<li>
exclude_if_all: String
</li>
</ul>
6 changes: 5 additions & 1 deletion wdl-doc/tests/output_docs/data_structures/flag_filter/index.html
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@@ -1,4 +1,8 @@
<h1>flag_filter</h1><p>WDL Version: 1.1</p><h1>FlagFilter</h1>
<h1>
flag_filter
</h1><p>
WDL Version: 1.1
</p><h1>FlagFilter</h1>
<p>A struct to represent the filtering flags used in various <code>samtools</code> commands.
The order of precedence is <code>include_if_all</code>, <code>exclude_if_any</code>, <code>include_if_any</code>,
and <code>exclude_if_all</code>.
Expand Down
39 changes: 37 additions & 2 deletions wdl-doc/tests/output_docs/data_structures/flag_filter/validate_flag_filter-workflow.html
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@@ -1,6 +1,41 @@
<h1>validate_flag_filter</h1><ul><li>Meta:meta {
<h1>
validate_flag_filter
</h1><ul>
<li>
Meta:
meta {
description: "Validates a FlagFilter struct."
outputs: {
check: "Dummy output to enable caching."
}
}</li><li>Inputs:<ul><li><h2>flags</h2><p>Type: FlagFilter</p><p>Expr: None</p></li></ul></li><li>Outputs:<ul><li><h2>check</h2><p>Type: String</p><p>Expr: "passed"</p></li></ul></li></ul>
}
</li>
<li>
Inputs:
<ul>
<li>
<h2>
flags
</h2><p>
Type: FlagFilter
</p><p>
Expr: None
</p>
</li>
</ul>
</li>
<li>
Outputs:
<ul>
<li>
<h2>
check
</h2><p>
Type: String
</p><p>
Expr: "passed"
</p>
</li>
</ul>
</li>
</ul>
39 changes: 37 additions & 2 deletions ...output_docs/data_structures/flag_filter/validate_string_is_12bit_oct_dec_or_hex-task.html
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@@ -1,7 +1,42 @@
<h1>validate_string_is_12bit_oct_dec_or_hex</h1><ul><li>Meta:meta {
<h1>
validate_string_is_12bit_oct_dec_or_hex
</h1><ul>
<li>
Meta:
meta {
description: "Validates that a string is a octal, decimal, or hexadecimal number and less than 2^12."
help: "Hexadecimal numbers must be prefixed with '0x' and only contain the characters [0-9A-F] to be valid (i.e. [a-f] is not allowed). Octal number must start with '0' and only contain the characters [0-7] to be valid. And decimal numbers must start with a digit between 1-9 and only contain the characters [0-9] to be valid."
outputs: {
check: "Dummy output to enable caching."
}
}</li><li>Inputs:<ul><li><h2>number</h2><p>Type: String</p><p>Expr: None</p></li></ul></li><li>Outputs:<ul><li><h2>check</h2><p>Type: String</p><p>Expr: "passed"</p></li></ul></li></ul>
}
</li>
<li>
Inputs:
<ul>
<li>
<h2>
number
</h2><p>
Type: String
</p><p>
Expr: None
</p>
</li>
</ul>
</li>
<li>
Outputs:
<ul>
<li>
<h2>
check
</h2><p>
Type: String
</p><p>
Expr: "passed"
</p>
</li>
</ul>
</li>
</ul>
47 changes: 46 additions & 1 deletion wdl-doc/tests/output_docs/data_structures/read_group/ReadGroup-struct.html
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@@ -1 +1,46 @@
<h1>ReadGroup</h1><ul><li>ID: String</li><li>BC: String?</li><li>CN: String?</li><li>DS: String?</li><li>DT: String?</li><li>FO: String?</li><li>KS: String?</li><li>LB: String?</li><li>PG: String?</li><li>PI: Int?</li><li>PL: String?</li><li>PM: String?</li><li>PU: String?</li><li>SM: String?</li></ul>
<h1>
ReadGroup
</h1><ul>
<li>
ID: String
</li>
<li>
BC: String?
</li>
<li>
CN: String?
</li>
<li>
DS: String?
</li>
<li>
DT: String?
</li>
<li>
FO: String?
</li>
<li>
KS: String?
</li>
<li>
LB: String?
</li>
<li>
PG: String?
</li>
<li>
PI: Int?
</li>
<li>
PL: String?
</li>
<li>
PM: String?
</li>
<li>
PU: String?
</li>
<li>
SM: String?
</li>
</ul>
48 changes: 46 additions & 2 deletions wdl-doc/tests/output_docs/data_structures/read_group/get_read_groups-task.html
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@@ -1,6 +1,50 @@
<h1>get_read_groups</h1><ul><li>Meta:meta {
<h1>
get_read_groups
</h1><ul>
<li>
Meta:
meta {
description: "Gets read group information from a BAM file and writes it out as JSON which is converted to a WDL struct."
outputs: {
read_groups: "An array of ReadGroup structs containing read group information."
}
}</li><li>Inputs:<ul><li><h2>bam</h2><p>Type: File</p><p>Expr: None</p></li><li><h2>modify_disk_size_gb</h2><p>Type: Int</p><p>Expr: 0</p></li></ul></li><li>Outputs:<ul><li><h2>read_groups</h2><p>Type: Array[ReadGroup]</p><p>Expr: read_json("read_groups.json")</p></li></ul></li></ul>
}
</li>
<li>
Inputs:
<ul>
<li>
<h2>
bam
</h2><p>
Type: File
</p><p>
Expr: None
</p>
</li>
<li>
<h2>
modify_disk_size_gb
</h2><p>
Type: Int
</p><p>
Expr: 0
</p>
</li>
</ul>
</li>
<li>
Outputs:
<ul>
<li>
<h2>
read_groups
</h2><p>
Type: Array[ReadGroup]
</p><p>
Expr: read_json("read_groups.json")
</p>
</li>
</ul>
</li>
</ul>
6 changes: 5 additions & 1 deletion wdl-doc/tests/output_docs/data_structures/read_group/index.html
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@@ -1,4 +1,8 @@
<h1>read_group</h1><p>WDL Version: 1.1</p><p>Read groups are defined in the SAM spec</p>
<h1>
read_group
</h1><p>
WDL Version: 1.1
</p><p>Read groups are defined in the SAM spec</p>
<ul>
<li>ID: Read group identifier. Each Read Group must have a unique ID.
The value of ID is used in the RG tags of alignment records.</li>
Expand Down
39 changes: 37 additions & 2 deletions wdl-doc/tests/output_docs/data_structures/read_group/read_group_to_string-task.html
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@@ -1,6 +1,41 @@
<h1>read_group_to_string</h1><ul><li>Meta:meta {
<h1>
read_group_to_string
</h1><ul>
<li>
Meta:
meta {
description: "Stringifies a ReadGroup struct"
outputs: {
stringified_read_group: "Input ReadGroup as a string"
}
}</li><li>Inputs:<ul><li><h2>read_group</h2><p>Type: ReadGroup</p><p>Expr: None</p></li></ul></li><li>Outputs:<ul><li><h2>stringified_read_group</h2><p>Type: String</p><p>Expr: read_string("out.txt")</p></li></ul></li></ul>
}
</li>
<li>
Inputs:
<ul>
<li>
<h2>
read_group
</h2><p>
Type: ReadGroup
</p><p>
Expr: None
</p>
</li>
</ul>
</li>
<li>
Outputs:
<ul>
<li>
<h2>
stringified_read_group
</h2><p>
Type: String
</p><p>
Expr: read_string("out.txt")
</p>
</li>
</ul>
</li>
</ul>
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