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First pass at HTML search results #97

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0b5c0a5
First pass at HTML search
beckyjackson Sep 3, 2021
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Change to RuntimeError
beckyjackson Sep 3, 2021
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beckyjackson Sep 3, 2021
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Clarify --limit none
beckyjackson Sep 3, 2021
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Merge branch 'master' into html-table
beckyjackson Jan 2, 2022
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Merge branch 'master' into html-table
beckyjackson May 24, 2022
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27 changes: 23 additions & 4 deletions README.md
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Expand Up @@ -181,7 +181,7 @@ This is a TSV or CSV with the following headers:

The config file can be useful for handling multiple imports with different options in a `Makefile`. If your imports all use the same `--intermediates` option and the same predicates, there is no need to specify a config file.

### `gizmos.search`
### `gizmos.search` - JSON

The `search` module returns a list of JSON objects for use with the tree browser search bar.

Expand All @@ -190,15 +190,20 @@ Usage in the command line:
python3 -m gizmos.search [path-to-database] [search-text] > [output-json]
```

Usage in Python (with defaults for optional parameters):
Usage in Python (with defaults for optional parameters - only the first two parameters are required):
```python
json = gizmos.search( # returns: JSON string
database_connection, # Connection: database connection object
search_text, # string: text to search
label="rdfs:label", # string: term ID for label
short_label=None, # string: term ID for short label
synonyms=None, # list: term IDs for synonyms
limit=30 # int: max results to return
limit=30, # int: max results to return
fmt="json", # str: output format (json or html)
href="?id={curie}", # str: href format for HTML output (see below)
db=None, # str: db name for HTML output (see below)
include_search=False, # boolean: if True, include search bar in HTML (see below)
standalone=True # boolean: if False, do not include HTML headers (see below)
)
```

Expand All @@ -220,7 +225,21 @@ When both short label and synonym(s) are provided and the matching term has both

Search is run over all three properties, so even if a term's label does not match the text, it may still be returned if the synonym matches.

Finally, the search only returns the first 30 results by default. If you wish to return less or more, you can specify this with `--limit <int>`/`-l <int>`.
Finally, the search only returns the first 30 results by default. If you wish to return less or more, you can specify this with `--limit <int>`/`-l <int>`. If you wish to include *all* search results, you can include `-l none`.

### `gizmos.search` - HTML

You can also return the search results as an HTML page. The module includes a few additional options to do this, but minimally, you need to include `-f`/`--format`:

```
python3 -m gizmos.search [path-to-database] [search-text] -f html > [output-html]
```

The additional options for use with the HTML output are:
* `-H`/`--href`: the query string format to use in links to search results, see [Tree Links](#tree-links)
* `d`/`--db-name`: the name of the database if you want to include it in your `href`
* `-r`/`--include-search`: flag to include a search bar at the top of the search results page
* `-c`/`--contents-only`: flag to only produce HTML content without the `<html>` and `<body>` tags

### `gizmos.tree`

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