various typo fixes and clearer language

Author: alistairewj

mimic-iii/buildmimic/duckdb/README.md

@@ -4,11 +4,6 @@ The scripts in this folder create the schema for MIMIC-III and
 loads the data into the appropriate tables for
 [DuckDB](https://duckdb.org/).
 
-The Python script (`import_duckdb.py`) also includes the option to 
-add the [concepts views](../../concepts/README.md) to the database.
-This makes it much easier to use the concepts views as you do not
-have to install and setup PostgreSQL or use BigQuery.
-
 DuckDB, like SQLite, is serverless and
 stores all information in a single file.
 Unlike SQLite, an OLTP database,
@@ -34,8 +29,6 @@ wget -r -N -c -np -nH --cut-dirs=1 --user YOURUSERNAME --ask-password https://ph
 
 Replace `YOURUSERNAME` with your physionet username.
 
-This will make you `mimic_data_dir` be `mimiciii/1.4`.
-
 The rest of these intructions assume the CSV files are in the folder structure as follows:
 
 ```
@@ -45,7 +38,7 @@ mimic_data_dir/
     ...
 ```
 
-The CSV files can be uncompressed (end in `.csv`) or compressed (end in `.csv.gz`).
+By default, the above `wget` downloads the data into `mimiciii/1.4` (as we used `--cut-dirs=1` to remove the base folder). Thus, by default, `mimic_data_dir` is `mimiciii/1.4` (relative to the current folder). The CSV files can be uncompressed (end in `.csv`) or compressed (end in `.csv.gz`).
 
 
 ## Shell script method (`import_duckdb.sh`)
@@ -74,7 +67,7 @@ e.g. `/usr/local/bin`.
 
 ### Create DuckDB database and load data
 
-You can do all of this will one shell script, `import_duckdb.sh`,
+You can do all of this with one shell script, `import_duckdb.sh`,
 located in this repository.
 
 See the help for it below:
@@ -105,66 +98,7 @@ The script will print out progress as it goes.
 Be patient, this can take minutes to hours to load
 depending on your computer's configuration.
 
-## Python script method (`import_duckdb.py`)
-
-This method does not require the DuckDB executable, it only requires the DuckDB Python
-module and the [SQLGlot](https://github.com/tobymao/sqlglot) Python module, both of which can be
-easily installed with `pip`. 
-
-### Install dependencies
-
-Install the dependencies by using the included `requirements.txt` file:
-
-```sh
-python3 -m pip install -r ./requirements.txt
-```
-
-### Create DuckDB database and load data
-
-Create the MIMIC-III database with `import_duckdb.py` like so:
-
-```sh
-python ./import_duckdb.py /path/to/mimic_data_dir ./mimic3.db
-```
-
-...where `/path/to/mimic_data_dir` is the path containing the .csv or .csv.gz
-data files downloaded above.
-
-This command will create the `mimic3.db` file in the current directory. Be aware that
-for the full MIMIC-III v1.4 dataset the resulting file will be about 34GB in size.
-This process will take some time, as with the shell script version.
-
-The default options will create only the tables and load the data, and assume
-that you are running the script from the same directory where this README.md
-is located. See the full options below if the defaults are insufficient.
-
-### Create the concepts views
-
-In most cases you will want to create the concepts views at the same time as
-the database. To do this, add the `--make-concepts` option:
-
-```sh
-python ./import_duckdb.py /path/to/mimic_data_dir ./mimic3.db --make-concepts
-```
-
-If you want to add the concepts to a database already created without this
-option (or created with the shell script version), you can add the
-`--skip-tables` option as well:
-
-```sh
-python ./import_duckdb.py /path/to/mimic_data_dir ./mimic3.db --make-concepts --skip-tables
-```
-
-### Additional options
-
-There are a few additional options for special situations:
-
-| Option | Description
-| - | -
-| `--skip-indexes` | Don't create additional indexes when creating tables and loading data. This may be useful in memory-constrained systems or to save a little time.
-| `--mimic-code-root [path]` | This argument specifies the location of the mimic-code repository files. This is needed to find the concepts SQL files. This is useful if you are running the script from a different directory than the one where this README.md file is located (the default is `../../../`)
-| `--schema-name [name]` | This puts the tables and concepts views into a named schema in the database. This is mainly useful to mirror the behavior of the PostgreSQL version of the database, which places objects in a schema named `mimiciii` by default--if you have existing code designed for the PostgreSQL version, this may make migration easier. Note that--like the PostgreSQL version--the `ccs_dx` view is *not* placed in the specified schema, but in the default schema (which is `main` in DuckDB, not `public` as in PostgreSQL).
 
 # Help
 
-Please see the [issues page](https://github.com/MIT-LCP/mimic-iii/issues) to discuss other issues you may be having.
+Please see the [issues page](https://github.com/MIT-LCP/mimic-code/issues) to discuss other issues you may be having.

mimic-iii/buildmimic/duckdb/duckdb_add_indexes.sql

@@ -551,4 +551,3 @@ CREATE INDEX TRANSFERS_idx03
 
 -- FIXME: Remove this index when the PK can be re-added...
 CREATE UNIQUE INDEX chartevents_rowid_pk ON CHARTEVENTS (ROW_ID);
-

mimic-iii/buildmimic/duckdb/duckdb_add_tables.sql

@@ -487,4 +487,4 @@ CREATE TABLE TRANSFERS
 	OUTTIME TIMESTAMP,
 	LOS DOUBLE PRECISION,
 	CONSTRAINT transfers_rowid_pk PRIMARY KEY (ROW_ID)
-) ;
+) ;

mimic-iv/buildmimic/duckdb/README.md

@@ -45,7 +45,7 @@ e.g. `/usr/local/bin`.
 
 Download the CSV files for [MIMIC-IV](https://physionet.org/content/mimiciv/)
 by any method you wish.
-These instructionds were tested with MIMIC-IV v2.2.
+These instructions were tested with MIMIC-IV v2.2.
 
 The CSV files should be a folder structure as follows:
 

mimic-iv/concepts_duckdb/README.md

@@ -2,7 +2,7 @@
 
 This folder has SQL compatible with [DuckDB](https://duckdb.org/).
 These concepts were generated automatically from the BigQuery SQL dialect using the [sqlglot](https://sqlglot.com/) package.
-If you would like to contribute a correction, it should be for the corresponding file in the concepts folder.
+If you would like to contribute a correction, do not make it here. Instead, make your correction in the [concepts folder](/mimic-iv/concepts/) using the BigQuery SQL syntax.
 
 See the [README](/mimic-iv/README.md) in the parent folder for more information.