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Add External Storage (File) #197

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merged 28 commits into from
Mar 31, 2020
Merged

Add External Storage (File) #197

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fe3b4d4
Add some basic scaffolding.
guzman-raphael Feb 7, 2020
df71efb
Added file storage plugin implementation.
guzman-raphael Feb 12, 2020
f77e87e
Add File store methods that are compatible with datajoint-python File…
guzman-raphael Feb 12, 2020
23652ba
[WIP] Add external blob insert and fetch.
guzman-raphael Feb 26, 2020
645383c
[WIP] Add external storage infrastructure.
guzman-raphael Mar 3, 2020
bde3edd
Add working prototype of file store.
guzman-raphael Mar 3, 2020
f6734fb
Clean up declare/makeFK.
guzman-raphael Mar 3, 2020
7e00031
Clean up declare/makeFK.2
guzman-raphael Mar 3, 2020
e299938
Clean up.
guzman-raphael Mar 3, 2020
87fb0c4
Clean up2.
guzman-raphael Mar 3, 2020
7cd9e2d
Add discussed config changes to external.
guzman-raphael Mar 4, 2020
393e3e3
Add backward compatible configuration to current dj-python.
guzman-raphael Mar 4, 2020
17cb122
Fix WIN path issues.
guzman-raphael Mar 4, 2020
f69a14c
Add blob caching feature with backward compatibility.
guzman-raphael Mar 5, 2020
5ae3b81
Clean up.
guzman-raphael Mar 5, 2020
0d08250
Update travis nginx use.
guzman-raphael Mar 5, 2020
f6d89ca
Add tests and fix bugs.
guzman-raphael Mar 6, 2020
001f1f4
Clean up linting.
guzman-raphael Mar 6, 2020
b362a11
Update port mapping bug.
guzman-raphael Mar 6, 2020
70543bf
Update tests to work with WIN64.
guzman-raphael Mar 6, 2020
06d401c
Add mac ignore rule.
guzman-raphael Mar 6, 2020
0a76e14
Merge pull request #196 from guzman-raphael/external
guzman-raphael Mar 6, 2020
711d72a
Update cache/location to require creation by user.
guzman-raphael Mar 9, 2020
db4a971
Merge pull request #198 from guzman-raphael/external
guzman-raphael Mar 9, 2020
abd3091
Update based on review.
guzman-raphael Mar 31, 2020
849b1c8
Merge pull request #200 from guzman-raphael/external
guzman-raphael Mar 31, 2020
13baa18
Update mym setup.
guzman-raphael Mar 31, 2020
ac0aae9
Merge pull request #201 from guzman-raphael/external
guzman-raphael Mar 31, 2020
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107 changes: 72 additions & 35 deletions +dj/+internal/Declare.m
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Original file line number Diff line number Diff line change
Expand Up @@ -3,19 +3,23 @@
% table definitions, and to declare the corresponding mysql tables.

properties(Constant)
UUID_DATA_TYPE = 'binary(16)'
CONSTANT_LITERALS = {'CURRENT_TIMESTAMP'}
EXTERNAL_TABLE_ROOT = '~external'
TYPE_PATTERN = struct( ...
'NUMERIC', '^((tiny|small|medium|big)?int|decimal|double|float)', ...
'STRING', '^((var)?char|enum|date|(var)?year|time|timestamp)', ...
'INTERNAL_BLOB', '^(tiny|medium|long)?blob', ...
'INTERNAL_BLOB', '^(tiny|medium|long)?blob$', ...
'EXTERNAL_BLOB', 'blob@(?<store>[a-z]\w*)$', ...
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'UUID', 'uuid$' ...
)
UUID_DATA_TYPE = 'binary(16)'
SPECIAL_TYPES = {'UUID'}
SPECIAL_TYPES = {'UUID', 'EXTERNAL_BLOB'}
EXTERNAL_TYPES = {'EXTERNAL_BLOB'} % data referenced by a UUID in external tables
SERIALIZED_TYPES = {'EXTERNAL_BLOB'} % requires packing data
end

methods(Static)
function sql = declare(table_instance, def)
function [sql, external_stores] = declare(table_instance, def)
% sql = DECLARE(query, definition)
% Parse table declaration and declares the table.
% sql: <string> Generated SQL to create a table.
Expand All @@ -36,12 +40,13 @@
switch true

case {isa(table_instance, 'dj.internal.UserRelation'), isa(table_instance, ...
'dj.Part'), isa(table_instance, 'dj.Jobs')}
'dj.Part'), isa(table_instance, 'dj.Jobs'), ...
isa(table_instance, 'dj.internal.ExternalTable')}
% New-style declaration using special classes for each tier
tableInfo = struct;
if isa(table_instance, 'dj.Part')
tableInfo.tier = 'part';
else
elseif ~isa(table_instance, 'dj.internal.ExternalTable')
specialClass = find(cellfun(@(c) isa(table_instance, c), ...
dj.Schema.tierClasses));
assert(length(specialClass)==1, ...
Expand Down Expand Up @@ -70,11 +75,14 @@
dj.internal.fromCamelCase(table_instance.className(length( ...
table_instance.master.className)+1:end))));
%#ok<MCNPN>
else
elseif ~isa(table_instance, 'dj.internal.ExternalTable')
tableName = sprintf('%s%s%s', ...
table_instance.schema.prefix, dj.Schema.tierPrefixes{ ...
strcmp(tableInfo.tier, dj.Schema.allowedTiers)}, ...
dj.internal.fromCamelCase(tableInfo.className));
else
tableName = [dj.internal.Declare.EXTERNAL_TABLE_ROOT '_' ...
table_instance.store];
end

otherwise
Expand Down Expand Up @@ -105,12 +113,13 @@
stableInfo.className));
end

sql = sprintf('CREATE TABLE `%s`.`%s` (\n', table_instance.schema.dbname, ...
tableName);

% fields and foreign keys
inKey = true;
primaryFields = {};
foreignKeySql = {};
indexSql = {};
attributeSql = {};
external_stores = {};
fields = {};
for iLine = 1:length(def)
line = def{iLine};
Expand All @@ -119,19 +128,20 @@ case strncmp(line,'---',3)
inKey = false;
% foreign key
case regexp(line, '^(\s*\([^)]+\)\s*)?->.+$')
[sql, newFields] = dj.internal.Declare.makeFK( ...
sql, line, fields, inKey, ...
[fk_attr_sql, fk_sql, newFields] = dj.internal.Declare.makeFK( ...
line, fields, inKey, ...
dj.internal.shorthash(sprintf('`%s`.`%s`', ...
table_instance.schema.dbname, tableName)));
sql = sprintf('%s,\n', sql);
attributeSql = [attributeSql, fk_attr_sql]; %#ok<AGROW>
foreignKeySql = [foreignKeySql, fk_sql]; %#ok<AGROW>
fields = [fields, newFields]; %#ok<AGROW>
if inKey
primaryFields = [primaryFields, newFields]; %#ok<AGROW>
end

% index
case regexpi(line, '^(unique\s+)?index[^:]*$')
sql = sprintf('%s%s,\n', sql, line); % add checks
indexSql = [indexSql, line]; %#ok<AGROW>

% attribute
case regexp(line, ['^[a-z][a-z\d_]*\s*' ... % name
Expand All @@ -144,26 +154,37 @@ case regexp(line, ['^[a-z][a-z\d_]*\s*' ... % name
primaryFields{end+1} = fieldInfo.name; %#ok<AGROW>
end
fields{end+1} = fieldInfo.name; %#ok<AGROW>
sql = sprintf('%s%s', sql, ...
dj.internal.Declare.compileAttribute(fieldInfo));

[attr_sql, store, foreignKeySql] = ...
dj.internal.Declare.compileAttribute(fieldInfo, foreignKeySql);
attributeSql = [attributeSql, attr_sql]; %#ok<AGROW>
if ~isempty(store)
external_stores{end+1} = store; %#ok<AGROW>
end
otherwise
error('Invalid table declaration line "%s"', line)
end
end

% add primary key declaration
% create declaration
create_sql = sprintf('CREATE TABLE `%s`.`%s` (\n', table_instance.schema.dbname,...
tableName);
% add attribute, primary key, foreign key, and index declaration
assert(~isempty(primaryFields), 'table must have a primary key')
sql = sprintf('%sPRIMARY KEY (%s),\n' ,sql, backquotedList(primaryFields));

table_sql = {attributeSql', {['PRIMARY KEY (`' strjoin(primaryFields, '`,`') ...
'`)']}, foreignKeySql', indexSql'};
table_sql = sprintf([strjoin(cat(1, table_sql{:}), ',\n') '\n']);
% finish the declaration
sql = sprintf('%s\n) ENGINE = InnoDB, COMMENT "%s"', sql(1:end-2), ...
tableInfo.comment);
engine_sql = sprintf(') ENGINE = InnoDB, COMMENT "%s"', tableInfo.comment);

sql = sprintf('%s%s%s', create_sql, table_sql, engine_sql);


% execute declaration
fprintf \n<SQL>\n
fprintf(sql)
fprintf \n</SQL>\n\n
if strcmpi(dj.config('loglevel'), 'DEBUG')
fprintf \n<SQL>\n
fprintf(sql)
fprintf \n</SQL>\n\n
end
end

function fieldInfo = parseAttrDef(line)
Expand All @@ -178,7 +199,7 @@ case regexp(line, ['^[a-z][a-z\d_]*\s*' ... % name
'^(?<name>[a-z][a-z\d_]*)\s*' % field name
['=\s*(?<default>".*"|''.*''|\w+|[-+]?[0-9]*\.?[0-9]+([eE][-+]?' ...
'[0-9]+)?)\s*'] % default value
[':\s*(?<type>\w[\w\s]+(\(.*\))?(\s*[aA][uU][tT][oO]_[iI][nN]' ...
[':\s*(?<type>\w[@\w\s]+(\(.*\))?(\s*[aA][uU][tT][oO]_[iI][nN]' ...
'[cC][rR][eE][mM][eE][nN][tT])?)\s*'] % datatype
'#(?<comment>.*)' % comment
'$' % end of line
Expand Down Expand Up @@ -208,7 +229,7 @@ case regexp(line, ['^[a-z][a-z\d_]*\s*' ... % name
fieldInfo.isnullable = strcmpi(fieldInfo.default,'null');
end

function [sql, newattrs] = makeFK(sql, line, existingFields, inKey, hash)
function [all_attr_sql, fk_sql, newattrs] = makeFK(line, existingFields, inKey, hash)
% [sql, newattrs] = MAKEFK(sql, line, existingFields, inKey, hash)
% Add foreign key to SQL table definition.
% sql: <string> Modified in-place SQL to include foreign keys.
Expand All @@ -217,6 +238,8 @@ case regexp(line, ['^[a-z][a-z\d_]*\s*' ... % name
% existingFields: <struct> Existing field attributes.
% inKey: <logical> Set as primary key.
% hash: <string> Current hash as base.
fk_sql = '';
all_attr_sql = '';
pat = ['^(?<newattrs>\([\s\w,]*\))?' ...
'\s*->\s*' ...
'(?<cname>\w+\.[A-Z][A-Za-z0-9]*)' ...
Expand Down Expand Up @@ -269,29 +292,38 @@ case regexp(line, ['^[a-z][a-z\d_]*\s*' ... % name
rel.tableHeader.names));
fieldInfo.name = newattrs{i};
fieldInfo.nullabe = ~inKey; % nonprimary references are nullable
sql = sprintf('%s%s', sql, dj.internal.Declare.compileAttribute(fieldInfo));
[attr_sql, ~, ~] = dj.internal.Declare.compileAttribute(fieldInfo, []);
all_attr_sql = sprintf('%s%s,\n', all_attr_sql, attr_sql);
end
all_attr_sql = all_attr_sql(1:end-2);

fkattrs = rel.primaryKey;
fkattrs(ismember(fkattrs, attrs))=newattrs;
hash = dj.internal.shorthash([{hash rel.fullTableName} newattrs]);
sql = sprintf(...
fk_sql = sprintf(...
['%sCONSTRAINT `%s` FOREIGN KEY (%s) REFERENCES %s (%s) ' ...
'ON UPDATE CASCADE ON DELETE RESTRICT'], sql, hash, backquotedList(fkattrs), ...
rel.fullTableName, backquotedList(rel.primaryKey));
'ON UPDATE CASCADE ON DELETE RESTRICT'], fk_sql, hash, ...
backquotedList(fkattrs), rel.fullTableName, backquotedList(rel.primaryKey));
end

function field = substituteSpecialType(field, category)
function [field, foreignKeySql] = substituteSpecialType(field, category, foreignKeySql)
% field = SUBSTITUTESPECIALTYPE(field, category)
% Substitute DataJoint type with sql type.
% field: <struct> Modified in-place field attributes.
% category: <string> DataJoint type match based on TYPE_PATTERN.
if strcmpi(category, 'UUID')
field.type = dj.internal.Declare.UUID_DATA_TYPE;
elseif any(strcmpi(category, dj.internal.Declare.EXTERNAL_TYPES))
field.store = strtrim(field.type((strfind(field.type,'@')+1):end));
field.type = dj.internal.Declare.UUID_DATA_TYPE;
foreignKeySql = [foreignKeySql, sprintf( ...
['FOREIGN KEY (`%s`) REFERENCES `{database}`.`%s_%s` (`hash`) ON ' ...
'UPDATE RESTRICT ON DELETE RESTRICT'], field.name, ...
dj.internal.Declare.EXTERNAL_TABLE_ROOT, field.store)]; %#ok<AGROW>
end
end

function sql = compileAttribute(field)
function [sql, store, foreignKeySql] = compileAttribute(field, foreignKeySql)
% sql = COMPILEATTRIBUTE(field)
% Convert the structure field with header {'name' 'type' 'default' 'comment'}
% to the SQL column declaration.
Expand All @@ -317,11 +349,16 @@ case regexp(line, ['^[a-z][a-z\d_]*\s*' ... % name
'illegal characters in attribute comment "%s"', field.comment)

category = dj.internal.Declare.matchType(field.type);
store = [];
if any(strcmpi(category, dj.internal.Declare.SPECIAL_TYPES))
field.comment = [':' strip(field.type) ':' field.comment];
field = dj.internal.Declare.substituteSpecialType(field, category);
[field, foreignKeySql] = dj.internal.Declare.substituteSpecialType(field, ...
category, foreignKeySql);
if isfield(field, 'store')
store = field.store;
end
end
sql = sprintf('`%s` %s %s COMMENT "%s",\n', ...
sql = sprintf('`%s` %s %s COMMENT "%s"', ...
field.name, strtrim(field.type), default, field.comment);
end

Expand Down
25 changes: 25 additions & 0 deletions +dj/+internal/ExternalMapping.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
% dj.internal.ExternalMapping - The external manager contains all the tables for all external
% stores for a given schema.
% :Example:
% e = dj.internal.ExternalMapping(schema)
% external_table = e.table(store)
classdef ExternalMapping < handle
properties
schema
tables
end
methods
function self = ExternalMapping(schema)
self.schema = schema;
self.tables = struct();
end
function store_table = table(self, store)
keys = fieldnames(self.tables);
if all(~strcmp(store, keys))
self.tables.(store) = dj.internal.ExternalTable(...
self.schema.conn, store, self.schema);
end
store_table = self.tables.(store);
end
end
end
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