14.3.197. crate_anon.crateweb.research.views

crate_anon/crateweb/research/views.py

Copyright (C) 2015, University of Cambridge, Department of Psychiatry. Created by Rudolf Cardinal (rnc1001@cam.ac.uk).

This file is part of CRATE.

CRATE is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

CRATE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with CRATE. If not, see <https://www.gnu.org/licenses/>.

CRATE views on the research database.

class crate_anon.crateweb.research.views.NlpSourceResult(fieldnames: List[str] | None = None, results: Sequence[Sequence[Any]] | None = None, sql: str | None = None, error: str | None = None)[source]

Serves as the return value for get_source_results().

__init__(fieldnames: List[str] | None = None, results: Sequence[Sequence[Any]] | None = None, sql: str | None = None, error: str | None = None) → None[source]
Parameters:

  • fieldnames – fieldnames in source record

  • results – source record result

  • sql – SQL used in getting source text

  • error – error message

crate_anon.crateweb.research.views.all_text_from_pid(request: HttpRequest) → HttpResponse[source]

Picks a database, then redirects to all_text_from_pid_with_db().

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.all_text_from_pid_with_db(request: HttpRequest, dbname: str) → HttpResponse[source]

Clinician view to look up a patient’s RID from their PID and display text from any field.

Parameters:

  • request – the django.http.request.HttpRequest

  • dbname – name of the research database to use

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.archive_attachment(request: HttpRequest) → HttpResponseBase[source]

Serve a binary file from the archive.

The patient_id is not required to find the file – but is used for the audit trail. (It would be possible for the end user to look up a file by name via a faked patient_id. However, this could be established from the audit log.)

Parameters:

request – the Django HttpRequest object

crate_anon.crateweb.research.views.archive_static(request: HttpRequest) → HttpResponseBase[source]

Serve a static file from the archive.

Parameters:

request – the Django HttpRequest object

crate_anon.crateweb.research.views.archive_template(request: HttpRequest) → HttpResponse[source]

Provides the views for the configurable “archive” system.

Parameters:

request – the Django HttpRequest object

Returns:

a Django HttpResponse.

Note:

  • The archive template name is in request.GET; this allows the use of special (e.g. filename) characters.

  • The patient ID is also in request.GET; this allows the optional use of more complex strings, e.g. JSON, to represent multiple ID numbers for use with several databases.

  • Additional arguments are also in request.GET.

  • To create a URL within a Django template, one would use e.g.

    <a href="{% url 'archive' patient_id template_name %}">link text</a>

    (the 'archive' bit being configured in crate_anon.crateweb.config.urls).

  • But to create a URL within a Mako template, there are several ways… for example, in CamCOPS via Pyramid, we use request.route_url(...). We can make this simple by passing patient-specific function to the context; see the Python Mako context.

  • If we use DMP, it will add a request.dmp object; see https://doconix.github.io/django-mako-plus/topics_variables.html. (We won’t use DMP.)

crate_anon.crateweb.research.views.common_find_text(request: HttpRequest, dbinfo: SingleResearchDatabase, form_class: Type[SQLHelperFindAnywhereForm], default_values: Dict[str, Any], permit_pid_search: bool, html_filename: str) → HttpResponse[source]

Finds and displays text anywhere in the database(s), via a UNION query.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.datetime_iso_for_filename() → str[source]

Returns a date/time as a string formatted for filenames.

crate_anon.crateweb.research.views.drugmatch(drug_type: str, colname: str) → str[source]

Returns SQL to check for the presence of any drug of type ‘drug_type’ anywhere in a field.

Parameters:

  • drug_type – drug type to look for

  • colname – name of the column

crate_anon.crateweb.research.views.edit_display(request: HttpRequest, query_id: str) → HttpResponse[source]

Edit the ‘display’ attribute of the selected query by choosing a list of columns to show when the results are displayed.

crate_anon.crateweb.research.views.generic_error(request: HttpRequest, error: str) → HttpResponse[source]

Returns a generic error response.

Parameters:

  • request – the django.http.request.HttpRequest

  • error – the error text

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.get_all_pes(request: HttpRequest) → QuerySet[source]

Return all Patient Explorers for the current user.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.db.models.QuerySet for crate_anon.crateweb.research.models.PatientExplorer objects

Return type:

request

crate_anon.crateweb.research.views.get_all_queries(request: HttpRequest) → QuerySet[source]

Return all database queries for the current user.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.db.models.QuerySet for crate_anon.crateweb.research.models.Query objects

Return type:

request

crate_anon.crateweb.research.views.get_all_sitewide_queries() → QuerySet[source]

Returns all site-wide queries.

Returns:

a django.db.models.QuerySet for crate_anon.crateweb.research.models.SitewideQuery objects

Return type:

request

crate_anon.crateweb.research.views.get_highlight_descriptions(highlight_dict: Dict[int, List[Highlight]]) → List[str][source]

Returns a list of length up to N_CSS_HIGHLIGHT_CLASSES of HTML elements illustrating the highlights.

Parameters:

highlight_dict – a dictionary mapping highlight colour to all the crate_anon.crateweb.research.models.Highlight objects that use it (e.g.: 2 maps to highlight objects for all the separate pieces of text to be highlighted in colour 2)

Returns:

HTML describing the highlights

Return type:

str

crate_anon.crateweb.research.views.get_identical_pes(request: HttpRequest, pmq: PatientMultiQuery) → List[PatientExplorer][source]

Return all Patient Explorers for the current user whose query is identical to the query specified.

Parameters:
Returns:

a list of crate_anon.crateweb.research.models.PatientExplorer objects

crate_anon.crateweb.research.views.get_identical_queries(request: HttpRequest, sql: str, sitewide: bool = False) → List[Query][source]

Returns all queries that are identical to the SQL provided.

This saves us creating a new query when one exists already that’s identical.

We check by hash.

Parameters:

  • request – the django.http.request.HttpRequest

  • sql – SQL text

  • sitewide – check sitewide, rather than user-specific, queries?

Returns:

crate_anon.crateweb.research.models.Query objects

Return type:

list

crate_anon.crateweb.research.views.highlight_activate(request: HttpRequest, highlight_id: str) → HttpResponse[source]

Activate a highlight.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.highlight_deactivate(request: HttpRequest, highlight_id: str) → HttpResponse[source]

Deactivate a highlight.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.highlight_delete(request: HttpRequest, highlight_id: str) → HttpResponse[source]

Delete a highlight.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.highlight_edit_select(request: HttpRequest) → HttpResponse[source]

Edit or activate highlighting (which will apply to any queries that the user runs).

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.launch_archive(request: HttpRequest) → HttpResponse[source]

Takes the submitted patient_id (from request.POST) and launches the archive’s root page for that patient.

Parameters:

request – the Django HttpRequest object

crate_anon.crateweb.research.views.local_structure_help(request: HttpRequest) → HttpResponse[source]

Serves a locally specifed help page.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.no_query_selected(request: HttpRequest) → HttpResponse[source]

View to say “no query selected” when one should have been.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.parse_privileged_sql(request: HttpRequest, sql: str) → List[Any][source]

Parses clinicians’ queries to find rid from pid.

SQL should be, e.g.: ‘SELECT * FROM tablename WHERE ~pid:dbname = pidnumber’ or ‘SELECT * FROM tablename WHERE ~mpid:dbname IN (value1, value2, …)’ where dbname has the secret lookup table the user wants to use.

Parameters:

  • request – the django.http.request.HttpRequest

  • sql – SQL text

Returns:

[bool, str] where the bool is success (0) or failure (1). If success, the str is the new sql and if failure it’s the error message.

crate_anon.crateweb.research.views.pe_activate(request: HttpRequest, pe_id: str) → HttpResponse[source]

Activate one of the user’s Patient Explorers.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_build(request: HttpRequest) → HttpResponse[source]

View to build/edit a Patient Explorer (see crate_anon.crateweb.research.models.PatientExplorer).

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_choose(request: HttpRequest) → HttpResponse[source]

Choose one of the user’s Patient Explorers (see crate_anon.crateweb.research.models.PatientExplorer).

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_data_finder_excel(request: HttpRequest, pe_id: str) → HttpResponse[source]

Serves the data finder view of a crate_anon.crateweb.research.models.PatientExplorer (see pe_data_finder_results()) as an Excel XLSX file.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_data_finder_results(request: HttpRequest, pe_id: str) → HttpResponse[source]

Shows the data finder view of a crate_anon.crateweb.research.models.PatientExplorer. This counts records for each table (by patient), without showing all the data.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_delete(request: HttpRequest, pe_id: str) → HttpResponse[source]

Delete one of the user’s Patient Explorers.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_edit(request: HttpRequest, pe_id: str) → HttpResponse[source]

Edit one of the user’s Patient Explorers.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_excel(request: HttpRequest, pe_id: str) → HttpResponse[source]

Return the results of a crate_anon.crateweb.research.models.PatientExplorer as an Excel XLSX file.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_monster_results(request: HttpRequest, pe_id: str) → HttpResponse[source]

Shows the monster data view of a crate_anon.crateweb.research.models.PatientExplorer. This performs a SELECT(*) for all rows retrieved by the PatientExplorer.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_one_table(request: HttpRequest, pe_id: str, schema: str, table: str, db: str = '') → HttpResponse[source]

Shows the single table view of a crate_anon.crateweb.research.models.PatientExplorer. This shows results from a single table.

Parameters:

  • request – the django.http.request.HttpRequest

  • pe_id – string form of the integer PK of a crate_anon.crateweb.research.models.PatientExplorer

  • schema – name of the table’s schema

  • table – name of the table

  • db – name of the table’s database (above the schema level), if appliable

Returns:

a django.http.response.HttpResponse

Todo

pe_one_table

Might it be better to feed the resulting query back into the main Query system, allowing users to turn columns on/off, etc.?

At present it forces query_id to None and this is detected by query_result.html.

crate_anon.crateweb.research.views.pe_results(request: HttpRequest, pe_id: str) → HttpResponse[source]

Show the results of a Patient Explorer, in paginated tabular form.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_submit(request: HttpRequest, pmq: PatientMultiQuery, run: bool = False) → HttpResponse[source]

Save a crate_anon.crateweb.research.models.PatientMultiQuery as a crate_anon.crateweb.research.models.PatientExplorer for the current user.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_table_browser(request: HttpRequest, pe_id: str) → HttpResponse[source]

Shows the table browser view of a crate_anon.crateweb.research.models.PatientExplorer. This shows a list of all tables in the database, with hyperlinks to a single-table Patient Explorer view for each.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pe_tsv_zip(request: HttpRequest, pe_id: str) → HttpResponse[source]

Return the results of a crate_anon.crateweb.research.models.PatientExplorer as a ZIP file of TSV files.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pid_rid_lookup(request: HttpRequest, with_db_url_name: str, html_filename: str) → HttpResponse[source]

Common functionality for :func`pidlookup`, ridlookup().

Provides a view/form allowing the user to choose a database, if more than one is possible, and then redirect to another view once we have that database choice.

Parameters:

  • request – the django.http.request.HttpRequest

  • with_db_url_name – URL name to redirect to, passed as a parameter to django.urls.reverse()

  • html_filename – Django HTML template filename

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pid_rid_lookup_with_db(request: HttpRequest, dbname: str, form_html_filename: str, formclass: Any, result_html_filename: str) → HttpResponse[source]

Common functionality for pidlookup_with_db(), ridlookup_with_db().

Parameters:

  • request – the django.http.request.HttpRequest

  • dbname – name of the research database to use

  • form_html_filename – Django HTML template filename to ask for PID/RID/etc. details

  • formclass – form class to use for requesting PID/RID/etc.

  • result_html_filename – Django HTML template filename to display results

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pidlookup(request: HttpRequest) → HttpResponse[source]

Look up PID information from RID information.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.pidlookup_with_db(request: HttpRequest, dbname: str) → HttpResponse[source]

Look up PID information from RID information, for a specific database.

Parameters:

  • request – the django.http.request.HttpRequest

  • dbname – name of the research database to use

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_activate(request: HttpRequest, query_id: str) → HttpResponse[source]

Activate the specified query for the current user.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_add_sitewide(request: HttpRequest) → HttpResponse[source]

Superuser view to add or edit sitewide queries and their descriptions.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_build(request: HttpRequest) → HttpResponse[source]

Assisted query builder, based on the data structure read from the research database.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_context(request: HttpRequest) → Dict[str, Any][source]

Query context dictionary used for (nearly?) every request.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a dictionary with core information about the request, like the currently selected query/Patient Explorer ID for the user.

Return type:

dict

Notes:

crate_anon.crateweb.research.views.query_count(request: HttpRequest, query_id: str) → HttpResponse[source]

View COUNT(*) from the specific query.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_count_current(request: HttpRequest) → HttpResponse[source]

View COUNT(*) from the user’s current query.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_delete(request: HttpRequest, query_id: str) → HttpResponse[source]

Delete (or hide if required for audit purposes) the specified query for the current user.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_edit_select(request: HttpRequest) → HttpResponse[source]

View to edit SQL for the current SELECT query (and/or run it).

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_excel(request: HttpRequest, query_id: str) → HttpResponse[source]

Serves an XLSX (Excel) file with the results of the specified query.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_results(request: HttpRequest, query_id: str) → HttpResponse[source]

View the results of chosen query, in conventional tabular format.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_results_recordwise(request: HttpRequest, query_id: str) → HttpResponse[source]

View results of chosen query, in recordwise tabular format.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_submit(request: HttpRequest, sql: str, run: bool = False, filter_display: bool = False) → HttpResponse[source]

Ancillary function to add a query, and redirect to the editing or run page.

Parameters:

  • request – the django.http.request.HttpRequest

  • sql – SQL text

  • run – execute the query and show the results? Otherwise, save the query and return to the editing page

  • filter_display – after saving the query, redirect to the filter page?

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.query_tsv(request: HttpRequest, query_id: str) → HttpResponse[source]

Download TSV of the specified query.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.render_bad_pe(request: HttpRequest, pe: PatientExplorer, exception: Exception) → HttpResponse[source]

A view saying “your Patient Explorer failed”.

Parameters:

  • request – the django.http.request.HttpRequest

  • pe – the crate_anon.crateweb.research.models.PatientExplorer that went wrong

  • exception – the Python exception that resulted, which may have had extra information attached via cardinal_pythonlib.exceptions.add_info_to_exception()

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.render_bad_query(request: HttpRequest, query: Query, exception: Exception) → HttpResponse[source]

A view saying “your query failed”. This is the normal thing to see if the user has entered bad SQL.

Parameters:

  • request – the django.http.request.HttpRequest

  • query – the crate_anon.crateweb.research.models.Query that went wrong

  • exception – the Python exception that resulted, which may have had extra information attached via cardinal_pythonlib.exceptions.add_info_to_exception()

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.render_bad_query_id(request: HttpRequest, query_id: str) → HttpResponse[source]

A view saying “bad query ID”.

Parameters:

  • request – the django.http.request.HttpRequest

  • query_id – the query ID that was bad

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.render_lookup(request: HttpRequest, dbinfo: SingleResearchDatabase, result_html_filename: str, trids: List[int] | None = None, rids: List[str] | None = None, mrids: List[str] | None = None, pids: List[int] | None = None, mpids: List[int] | None = None) → HttpResponse[source]

Shows the output of a PID/RID lookup.

Parameters:

  • request – the django.http.request.HttpRequest

  • dbinfo – a crate_anon.crateweb.research.research_db_info.SingleResearchDatabase detailing the research database to use

  • result_html_filename – Django HTML template filename to display results

  • trids – list of TRIDs to look up from

  • rids – list of RIDs to look up from

  • mrids – list of MRIDs to look up from

  • pids – list of PIDs to look up from

  • mpids – list of MPIDs to look up from

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.render_missing_pe(request: HttpRequest) → HttpResponse[source]

Tell the user that there’s no Patient Explorer selected, when there should have been.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.render_missing_query(request: HttpRequest) → HttpResponse[source]

A view saying “missing query”.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.render_resultcount(request: HttpRequest, query: Query) → HttpResponse[source]

Displays the number of rows that a given query will fetch.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.render_resultset(request: HttpRequest, query: Query, highlights: Iterable[Highlight], collapse_at_len: int | None = None, collapse_at_n_lines: int | None = None, line_length: int | None = None, ditto: bool = True, ditto_html: str = '″') → HttpResponse[source]

Show the results of a user’s query in paginated, tabular format.

Parameters:

  • request – the django.http.request.HttpRequest

  • query – a crate_anon.crateweb.research.models.Query to execute

  • highlights – an iterable of crate_anon.crateweb.research.models.Highlight objects to apply colourful highlighting to the results

  • collapse_at_len – if specified, the string length beyond which the cell will be collapsed

  • collapse_at_n_lines – if specified, the number of lines beyond which the cell will be collapsed

  • line_length – if specified, the line length to word-wrap at

  • ditto – whether to replace cells that are identical to the cell immediately above with ditto marks

  • ditto_html – the HTML string to use as a ditto mark

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.render_resultset_recordwise(request: HttpRequest, query: Query, highlights: Iterable[Highlight], collapse_at_len: int | None = None, collapse_at_n_lines: int | None = None, line_length: int | None = None) → HttpResponse[source]

Show the results of a user’s query in recordwise format.

Parameters:

  • request – the django.http.request.HttpRequest

  • query – a crate_anon.crateweb.research.models.Query to execute

  • highlights – an iterable of crate_anon.crateweb.research.models.Highlight objects to apply colourful highlighting to the results

  • collapse_at_len – if specified, the string length beyond which the cell will be collapsed

  • collapse_at_n_lines – if specified, the number of lines beyond which the cell will be collapsed

  • line_length – if specified, the line length to word-wrap at

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.resultset_html_table(fieldnames: List[str], rows: List[List[Any]], element_counter: HtmlElementCounter, start_index: int = 0, highlight_dict: Dict[int, List[Highlight]] | None = None, collapse_at_len: int | None = None, collapse_at_n_lines: int | None = None, line_length: int | None = None, ditto: bool = True, ditto_html: str = '″', no_ditto_cols: List[int] | None = None, null: str = '<i>NULL</i>') → str[source]

Returns an HTML table representing a set of results from a query. Its columns are the database columns; its rows are the database rows.

Parameters:

  • fieldnames – list of column names

  • rows – list of rows (each row being a list of values in the same order as fieldnames)

  • element_counter – a crate_anon.crateweb.research.html_functions.HtmlElementCounter, which will be modified

  • start_index – the zero-based index of the first row in this table (used for pagination, when the second and subsequent tables don’t start with the first row of the result set)

  • highlight_dict – an optional dictionary mapping highlight colour to all the crate_anon.crateweb.research.models.Highlight objects that use it (e.g.: 2 maps to highlight objects for all the separate pieces of text to be highlighted in colour 2)

  • collapse_at_len – if specified, the string length beyond which the cell will be collapsed

  • collapse_at_n_lines – if specified, the number of lines beyond which the cell will be collapsed

  • line_length – if specified, the line length to word-wrap at

  • ditto – whether to replace cells that are identical to the cell immediately above with ditto marks

  • ditto_html – the HTML string to use as a ditto mark

  • no_ditto_cols – column indexes (zero-based) for which ditto marks should never be used

  • null – the HTML string to use for database NULL (Python None) values

Returns:

HTML

Return type:

str

crate_anon.crateweb.research.views.ridlookup(request: HttpRequest) → HttpResponse[source]

Look up RID information from PID information.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.ridlookup_with_db(request: HttpRequest, dbname: str) → HttpResponse[source]

Look up RID information from PID information, for a specific database.

Parameters:

  • request – the django.http.request.HttpRequest

  • dbname – name of the research database to use

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.save_display(request: HttpRequest, query_id: str) → HttpResponse[source]

Save changes to the ‘display’ attribute of the selected query, and to the value of ‘no_null’.

crate_anon.crateweb.research.views.show_sitewide_queries(request: HttpRequest) → HttpResponse[source]

View to show all site-wide queries.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.single_record_html_table(fieldnames: List[str], record: List[Any], element_counter: HtmlElementCounter, highlight_dict: Dict[int, List[Highlight]] | None = None, collapse_at_len: int | None = None, collapse_at_n_lines: int | None = None, line_length: int | None = None) → str[source]

Returns an HTML table representing a set of results from a query, in recordwise format. It has two columns, effectively “database column” and “value”; its rows are the database columns; it displays a single database result row.

Parameters:

  • fieldnames – list of column names

  • record – a single result row, i.e. a list of values in the same order as fieldnames

  • element_counter – a crate_anon.crateweb.research.html_functions.HtmlElementCounter, which will be modified

  • highlight_dict – an optional dictionary mapping highlight colour to all the crate_anon.crateweb.research.models.Highlight objects that use it (e.g.: 2 maps to highlight objects for all the separate pieces of text to be highlighted in colour 2)

  • collapse_at_len – if specified, the string length beyond which the cell will be collapsed

  • collapse_at_n_lines – if specified, the number of lines beyond which the cell will be collapsed

  • line_length – if specified, the line length to word-wrap at

Returns:

HTML

Return type:

str

crate_anon.crateweb.research.views.sitewide_query_delete(request: HttpRequest, query_id: str) → HttpResponse[source]

Delete a site-wide query.

Parameters:
Returns:

a django.http.response.HttpResponse

Note:

  • When sitewide queries are used, their SQL is added to the user’s personal libraries. All auditing therefore relates to users’ personal query libraries. Sitewide queries cannot be executed “standalone”.

  • As a result, we use a raw crate_anon.crateweb.research.models.SitewideQuery.delete`(), rather than the system used by crate_anon.crateweb.research.models.Query.delete_if_permitted().

crate_anon.crateweb.research.views.sitewide_query_process(request: HttpRequest, query_id: str) → HttpResponse[source]

Takes a sitewide query ID and receives (through POST) replacements for the placeholders. Then adds the code to user’s personal library or adds and runs it.

Parameters:
Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.source_info(request: HttpRequest, srcdb: str, srctable: str, srcfield: str, srcpkfield: str, srcpkval: str | None, srcpkstr: str | None) → HttpResponse[source]

Show source information for a record in a CRATE NLP table.

Parameters:

  • request – the django.http.request.HttpRequest

  • srcdb – source database as given by the nlp record

  • srctable – source table

  • srcfield – source field

  • srcpkfield – the fieldname in the source table which contains the primary key

  • srcpkval – primary key value in source table - may be ‘None’

  • srcpkstr – primary key string in source table - may be ‘None’

Returns:

a django.http.response.HttpResponse

Only one of srcpkval and srcpkstr should be ‘None’, and this will be given as a string because it’s through a URL link.

crate_anon.crateweb.research.views.sqlhelper_drug_type(request: HttpRequest) → HttpResponse[source]

Picks a database, then redirects to sqlhelper_drug_type_with_db().

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.sqlhelper_drug_type_with_db(request: HttpRequest, dbname: str) → HttpResponse[source]

Finds drugs of a given type anywhere in the database(s) via a UNION query.

Parameters:

  • request – the django.http.request.HttpRequest

  • dbname – name of the research database to use

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.sqlhelper_text_anywhere(request: HttpRequest) → HttpResponse[source]

Picks a database, then redirects to sqlhelper_text_anywhere_with_db().

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.sqlhelper_text_anywhere_with_db(request: HttpRequest, dbname: str) → HttpResponse[source]

Finds text anywhere in the database(s) via a UNION query.

Parameters:

  • request – the django.http.request.HttpRequest

  • dbname – name of the research database to use

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.structure_excel(request: HttpRequest) → HttpResponse[source]

Serves the table structure of the research database(s) as an Excel XLSX file.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.structure_table_long(request: HttpRequest) → HttpResponse[source]

Shows the table structure of the research database(s) in long format.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.structure_table_paginated(request: HttpRequest) → HttpResponse[source]

Shows the table structure of the research database(s) in paginated format.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.structure_tree(request: HttpRequest) → HttpResponse[source]

Shows an expand-and-collapse tree view of the table structure of the research database(s).

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.structure_tsv(request: HttpRequest) → HttpResponse[source]

Serves the table structure of the research database(s) as TSV.

Parameters:

request – the django.http.request.HttpRequest

Returns:

a django.http.response.HttpResponse

crate_anon.crateweb.research.views.textfinder_sql(patient_id_fieldname: str, min_length: int, use_fulltext_index: bool, include_content: bool, include_datetime: bool, fragment: str = '', drug_type: str = '', patient_id_value: int | str | None = None, extra_fieldname: str | None = None, extra_value: int | str | None = None) → str[source]

Returns SQL to find the text in fragment across all tables that contain the field indicated by patient_id_fieldname, where the length of the text field is at least min_length.

Parameters:

  • patient_id_fieldname – field (column) name across all tables that contains the patient ID; any tables that don’t contain this column will be ignored

  • fragment – fragment of text to find (e.g. “paracetamol”)

  • drug_type – type of drug to find any example of

  • min_length – text fields must be at least this large to bother searching; use this option to exclude e.g. VARCHAR(1) columns from the search

  • use_fulltext_index – use database full-text indexing?

  • include_content – include the text fields in the output?

  • include_datetime – include the date/time of each record, if known (see crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo.get_default_date_column()

  • patient_id_value – specify this to restrict to a single patient; the value of the patient ID column (see patient_id_fieldname) to restrict to

  • extra_fieldname –

  • extra_value –

Returns:

SQL query

Return type:

str

Raises:

ValueError –

crate_anon.crateweb.research.views.textmatch(column_name: str, fragment: str, as_fulltext: bool, dialect: str = 'mysql') → str[source]

Returns SQL to check for the presence of text anywhere in a field.

Parameters:

  • column_name – name of the column

  • fragment – piece of text to look for

  • as_fulltext – use a FULLTEXT search if the database dialect supports it

  • dialect – dialect name (mysql, mssql are known)

Returns:

SQL fragment like:

  • column LIKE '%fragment%' (ANSI SQL)

  • MATCH(column) AGAINST ('fragment') (MySQL full-text)

  • CONTAINS(column, 'fragment') (Microsoft SQL Server full-text)

Return type:

str

crate_anon.crateweb.research.views.validate_blank_form(request: HttpRequest) → None[source]

Checks that the request is (a) a POST request, and (b) passes CRSF validation.

Parameters:

request – the django.http.request.HttpRequest

Raises:

django.core.exceptions.ValidationError –