Improve a query from Explain results - mysql

Question

I have a complex query that is dynamically assembled based upon search criteria. However, in its simplest form, it is still very slow. The main table it runs against has ~10M records. I ran an explain against a 'base' query and the first row of the explain looks bad (at least to a novice dba like me). I have read a couple tutorials about EXPLAIN, but I still am unsure how to fix the query. So, the first row of the results seems to indicate the problem, but I don't know what to do with it. I couldn't make a composite key that long even if I wanted to and some of the field names in that possible_keys column are not even in the patients table. Any help will be greatly appreciated.
id,select_type,table,type,possible_keys,key,key_len,ref,rows,Extra
1,SIMPLE,patients,range,"PRIMARY,location,appt_date,status,radiologist,contract,lastname,paperwork,images_archived,hash,created,document_attached,all_images_archived,last_image_archived,modality,study_uid,company,second_access,firstname,report_delivered,ssn,order_entry_status,dob,tech,doctor,mobile_facility,accession,location_appt_date,location_created,location_lastname,ref,person_seq",location_appt_date,55,NULL,573534,"Using index condition; Using where; Using temporary; Using filesort"
1,SIMPLE,receivable_transactions,ref,patient_seq,patient_seq,4,ris-dev.patients.seq,1,NULL
1,SIMPLE,patients_dispatch,ref,patient_seq,patient_seq,4,ris-dev.patients.seq,1,NULL
1,SIMPLE,mobile_facility,ref,"unique_index,name,location",unique_index,115,"ris-dev.patients.mobile_facility,const",1,"Using where"
1,SIMPLE,mobile_facility_service_areas,eq_ref,PRIMARY,PRIMARY,4,ris-dev.mobile_facility.service_area,1,NULL
Edit: same EXPLAIN, but reformatted to be easier to read:
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE patients range PRIMARY location_appt_date 55 NULL 573534 Using index condition; Using where; Using temporary; Using filesort
location
appt_date
status
radiologist
contract
lastname
paperwork
images_archived
hash
created
document_attached
all_images_archived
last_image_archived
modality
study_uid
company
second_access
firstname
report_delivered
ssn
order_entry_status
dob
tech
doctor
mobile_facility
accession
location_appt_date
location_created
location_lastname
ref
person_seq
1 SIMPLE receivable_transactions ref patient_seq patient_seq 4 ris-dev.patients.seq 1 NULL
1 SIMPLE patients_dispatch ref patient_seq patient_seq 4 ris-dev.patients.seq 1 NULL
1 SIMPLE mobile_facility ref unique_index unique_index 115 ris-dev.patients.mobile_facility,const 1 Using where
name
location
1 SIMPLE mobile_facility_service_areas eq_ref PRIMARY PRIMARY 4 ris-dev.mobile_facility.service_area 1 NULL
The explain is setup against the following query and table structures.
SELECT patients.fax_in_queue, patients.modality, patients.stat, patients.created, patients.seq, patients.lastname,
patients.firstname, patients.appt_date, patients.status, patients.contract, patients.location, patients.unique_hash,
patients.images_archived, patients.report_delivered, patients.doctor, patients.mobile_facility, patients.history,
patients.dob, patients.all_images_archived, patients.order_entry_status, patients.tech, patients.radiologist,
patients.last_image_archived, patients.state, patients.ss_comments, patients.completed, patients.report_status,
patients.have_paperwork, patients.facility_room_number, patients.facility_station_name, patients.facility_bed,
patients.findings_level, patients.document_attached, patients.study_start, patients.company, patients.accession,
patients.number_images, patients.client_number_images, patients.sex, patients.threshhold , GROUP_CONCAT(CONCAT(CONCAT(receivable_transactions.modifier, " "),
receivable_transactions.description) SEPARATOR ", ") AS rt_desc , patients_dispatch.seq AS doc_seq, patients_dispatch.requisition_last_sent,
patients_dispatch.requisition_signed_by_file_seq, patients_dispatch.requisition_signed, patients_dispatch.order_reason, patients_dispatch.order_comments,
patients_dispatch.order_taken, patients_dispatch.order_tech_last_notified, patients_dispatch.order_tech_in_transit, patients_dispatch.order_tech_in,
patients_dispatch.order_tech_out, patients_dispatch.order_tech_ack, patients_dispatch.addr1 AS d_addr1, patients_dispatch.addr2 AS d_addr2,
patients_dispatch.city AS d_city, patients_dispatch.state AS d_state, patients_dispatch.zip AS d_zip, CONCAT(patients.status, order_tech_out,
order_tech_in, order_tech_in_transit) as pseudo_status , mobile_facility.requisition_fax, mobile_facility.station_list, mobile_facility.address1 as mf_addr1,
mobile_facility.address2 as mf_addr2, mobile_facility.city as mf_city, mobile_facility.state as mf_state, mobile_facility.zip as mf_zip,
mobile_facility.phone as mf_phone, mobile_facility.phone2 as mf_phone2, mobile_facility_service_areas.name as mf_service_area
FROM patients LEFT JOIN receivable_transactions ON patients.seq = receivable_transactions.patient_seq
LEFT JOIN patients_dispatch ON patients.seq = patients_dispatch.patient_seq
LEFT JOIN mobile_facility ON patients.location = mobile_facility.location AND patients.mobile_facility = mobile_facility.name
LEFT JOIN mobile_facility_service_areas ON mobile_facility.service_area = mobile_facility_service_areas.seq
WHERE patients.location = "XYZCompany" AND ((patients.appt_date >= '2020-03-19' AND patients.appt_date <= '2020-03-19 23:59:59')
OR (patients.appt_date <= '2020-03-19' AND patients.status < 'X'))
GROUP BY patients.seq DESC
ORDER BY patients.status, patients.order_entry_status, pseudo_status, patients.order_entry_status,patients.lastname);
CREATE TABLE `patients` (
`seq` int(11) NOT NULL AUTO_INCREMENT,
`person_seq` int(11) NOT NULL,
`firstname` varchar(20) NOT NULL DEFAULT '',
`lastname` varchar(30) NOT NULL DEFAULT '',
`middlename` varchar(20) NOT NULL DEFAULT '',
`ref` varchar(50) NOT NULL DEFAULT '',
`location` varchar(50) NOT NULL DEFAULT '',
`doctor` varchar(50) NOT NULL,
`radiologist` varchar(20) NOT NULL DEFAULT '',
`contract` varchar(50) NOT NULL,
`history` mediumtext NOT NULL,
`dob` varchar(15) NOT NULL DEFAULT '0000-00-00',
`appt_date` date NOT NULL DEFAULT '0000-00-00',
`status` tinyint(4) NOT NULL DEFAULT '0',
`tech` varchar(50) NOT NULL DEFAULT '',
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
`ss_comments` mediumtext NOT NULL,
`mobile_facility` varchar(60) NOT NULL DEFAULT '',
`facility_room_number` varchar(50) NOT NULL,
`facility_bed` varchar(20) NOT NULL,
`facility_station_name` varchar(50) NOT NULL,
`stat` tinyint(4) NOT NULL DEFAULT '0',
`have_paperwork` tinyint(4) NOT NULL DEFAULT '0',
`completed` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
`sex` char(1) NOT NULL DEFAULT '',
`unique_hash` varchar(100) NOT NULL DEFAULT '',
`number_images` int(11) NOT NULL DEFAULT '0',
`client_number_images` int(11) NOT NULL,
`images_archived` tinyint(4) NOT NULL DEFAULT '0',
`completed_fax` varchar(10) NOT NULL DEFAULT '0' COMMENT 'This is the number the completed report is faxed to.',
`report_delivered` tinyint(4) NOT NULL DEFAULT '0',
`report_delivered_time` datetime NOT NULL,
`document_attached` tinyint(4) NOT NULL DEFAULT '0',
`modality` varchar(3) NOT NULL,
`last_image_archived` datetime NOT NULL,
`all_images_archived` tinyint(4) NOT NULL DEFAULT '0',
`fax_in_queue` varchar(12) NOT NULL,
`accession` varchar(100) NOT NULL,
`study_uid` varchar(100) NOT NULL,
`order_entry_status` tinyint(4) NOT NULL,
`compare_to` varchar(15) NOT NULL,
`state` varchar(3) NOT NULL,
`company` int(11) NOT NULL,
`second_access` varchar(50) NOT NULL,
`threshhold` datetime NOT NULL,
`report_status` tinyint(4) NOT NULL,
`second_id` varchar(50) NOT NULL,
`rad_alerted` tinyint(4) NOT NULL,
`assigned` datetime NOT NULL,
`findings_level` tinyint(4) NOT NULL,
`report_viewed` tinyint(4) NOT NULL,
`study_received` datetime NOT NULL,
`study_start` datetime NOT NULL,
`study_end` datetime NOT NULL,
`completed_email` varchar(50) NOT NULL,
`completed_send` varchar(255) NOT NULL,
`ssn` varchar(12) NOT NULL,
`exorder_number` varchar(30) NOT NULL,
`exvisit_number` varchar(30) NOT NULL,
`row_updated` timestamp NOT NULL ON UPDATE CURRENT_TIMESTAMP,
PRIMARY KEY (`seq`),
KEY `location` (`location`),
KEY `appt_date` (`appt_date`),
KEY `status` (`status`),
KEY `radiologist` (`radiologist`),
KEY `contract` (`contract`),
KEY `lastname` (`lastname`),
KEY `paperwork` (`have_paperwork`),
KEY `images_archived` (`images_archived`),
KEY `hash` (`unique_hash`),
KEY `created` (`created`),
KEY `document_attached` (`document_attached`),
KEY `all_images_archived` (`all_images_archived`),
KEY `last_image_archived` (`last_image_archived`),
KEY `modality` (`modality`),
KEY `study_uid` (`study_uid`),
KEY `company` (`company`),
KEY `second_access` (`second_access`),
KEY `firstname` (`firstname`),
KEY `report_delivered` (`report_delivered`),
KEY `ssn` (`ssn`),
KEY `order_entry_status` (`order_entry_status`),
KEY `dob` (`dob`),
KEY `tech` (`tech`),
KEY `doctor` (`doctor`),
KEY `mobile_facility` (`mobile_facility`),
KEY `accession` (`accession`),
KEY `location_appt_date` (`location`,`appt_date`),
KEY `location_created` (`location`,`created`),
KEY `location_lastname` (`location`,`lastname`),
KEY `ref` (`ref`),
KEY `person_seq` (`person_seq`)
) ENGINE=InnoDB AUTO_INCREMENT=10242952 DEFAULT CHARSET=latin1;
CREATE TABLE `receivable_transactions` (
`seq` int(11) NOT NULL AUTO_INCREMENT,
`patient_seq` int(11) NOT NULL DEFAULT '0',
`cptcode` varchar(15) NOT NULL DEFAULT '',
`modifier` char(2) NOT NULL DEFAULT '',
`description` varchar(100) NOT NULL DEFAULT '',
`amount` decimal(6,2) NOT NULL DEFAULT '0.00',
`type` char(2) NOT NULL DEFAULT '',
`transaction` varchar(10) NOT NULL DEFAULT '',
`radiologist` varchar(20) NOT NULL DEFAULT '',
`status` tinyint(4) NOT NULL DEFAULT '0',
`completed` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
`report_meta_seq` int(11) NOT NULL DEFAULT '0',
`report_header` varchar(255) NOT NULL,
`report_body` blob NOT NULL,
`report_impression` mediumtext NOT NULL,
`report_hide` tinyint(4) NOT NULL,
`radiologist_group` varchar(50) NOT NULL,
`addendum` int(4) NOT NULL DEFAULT '0',
`addendum_type` varchar(20) NOT NULL,
`peer_review` int(4) NOT NULL DEFAULT '0',
`qa_reason` varchar(255) NOT NULL DEFAULT '',
`qa_agree` decimal(2,1) NOT NULL DEFAULT '0.0',
`findings` tinyint(4) NOT NULL,
`comments` mediumtext NOT NULL,
`company` int(11) NOT NULL,
`row_updated` timestamp NOT NULL ON UPDATE CURRENT_TIMESTAMP,
PRIMARY KEY (`seq`),
KEY `patient_seq` (`patient_seq`),
KEY `cptcode` (`cptcode`),
KEY `transaction` (`transaction`),
KEY `type` (`type`),
KEY `created` (`created`),
KEY `radiologist` (`radiologist`),
KEY `status` (`status`),
KEY `report_meta_seq` (`report_meta_seq`),
KEY `Billing Check Dropdown` (`status`,`completed`),
KEY `qa_agree` (`qa_agree`),
KEY `peer_review` (`peer_review`),
KEY `addendum` (`addendum`),
KEY `company` (`company`),
KEY `completed` (`completed`)
) ENGINE=InnoDB AUTO_INCREMENT=9380351 DEFAULT CHARSET=latin1;
CREATE TABLE `patients_dispatch` (
`seq` int(11) NOT NULL AUTO_INCREMENT,
`patient_seq` int(11) NOT NULL,
`order_taken` datetime NOT NULL,
`order_taken_by` varchar(50) NOT NULL,
`order_person_calling` varchar(50) NOT NULL,
`order_supervising_physician` varchar(50) NOT NULL,
`order_trip_count` tinyint(4) NOT NULL,
`order_trip_count_max` tinyint(4) NOT NULL,
`order_trip_visit` tinyint(4) NOT NULL,
`order_tech_in` datetime NOT NULL,
`order_tech_out` datetime NOT NULL,
`order_ssn` varchar(12) NOT NULL,
`order_service_request_time` datetime NOT NULL,
`order_reason` varchar(255) NOT NULL,
`order_tech_ack` datetime NOT NULL,
`order_tech_assigned` datetime NOT NULL,
`order_tech_last_notified` datetime NOT NULL,
`requisition_last_sent` datetime NOT NULL,
`requisition_signed` datetime NOT NULL,
`requisition_signed_by` varchar(50) NOT NULL,
`requisition_signed_by_text` varchar(75) NOT NULL,
`requisition_signed_by_file_seq` int(11) NOT NULL,
`order_comments` mediumtext NOT NULL,
`order_tech_in_transit` datetime NOT NULL,
`fasting` tinyint(1) NOT NULL,
`collection_time` time DEFAULT NULL,
`addr1` varchar(100) NOT NULL,
`addr2` varchar(100) NOT NULL,
`city` varchar(30) NOT NULL,
`state` varchar(3) NOT NULL,
`zip` varchar(12) NOT NULL,
`phone` varchar(15) NOT NULL,
`mileage_start` int(11) NOT NULL,
`mileage_end` int(11) NOT NULL,
PRIMARY KEY (`seq`),
KEY `patient_seq` (`patient_seq`)
) ENGINE=InnoDB AUTO_INCREMENT=2261091 DEFAULT CHARSET=latin1;
CREATE TABLE `mobile_facility` (
`seq` int(11) NOT NULL AUTO_INCREMENT,
`name` varchar(60) NOT NULL,
`location` varchar(50) DEFAULT NULL,
`address1` varchar(50) NOT NULL,
`address2` varchar(50) NOT NULL,
`city` varchar(50) NOT NULL,
`state` varchar(2) NOT NULL,
`zip` varchar(10) NOT NULL,
`phone` varchar(15) NOT NULL,
`phone2` varchar(15) NOT NULL,
`fax` varchar(110) NOT NULL,
`rads_can_read` text NOT NULL,
`rads_cant_read` text NOT NULL,
`only_techs` text NOT NULL,
`never_modalities` varchar(255) NOT NULL COMMENT 'A serialized list of modalities a facility may not use.',
`station_list` mediumtext NOT NULL,
`email` varchar(255) NOT NULL,
`misc1` varchar(255) NOT NULL,
`latitude` float NOT NULL DEFAULT '0',
`longitude` float NOT NULL DEFAULT '0',
`affiliation` int(11) NOT NULL COMMENT 'mobile_facility_affiliations seq',
`branch` int(11) NOT NULL COMMENT 'mobile_facility_branches seq',
`service_area` int(11) NOT NULL COMMENT 'mobile_facility_service_areas seq',
`other_id` varchar(50) NOT NULL COMMENT 'Usually used for HL7',
`facility_type` varchar(2) DEFAULT NULL,
`no_stat` tinyint(1) NOT NULL DEFAULT '0' COMMENT 'Should the facility allow stat priority on patients?',
`facility_notes` varchar(512) DEFAULT NULL,
`requisition_fax` varchar(110) NOT NULL,
`report_template` text NOT NULL,
`all_orders_stat` tinyint(1) NOT NULL,
`sms_notification` varchar(15) NOT NULL,
`tat` varchar(10) NOT NULL,
`npi` varchar(15) NOT NULL,
`NMXR` tinyint(4) NOT NULL DEFAULT '0',
`billing_type` varchar(10) NOT NULL,
`salesman` varchar(75) NOT NULL,
`created_at` datetime NOT NULL,
`updated_at` datetime NOT NULL,
`default_bill_to` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq`),
UNIQUE KEY `unique_index` (`name`,`location`),
KEY `name` (`name`),
KEY `location` (`location`)
) ENGINE=InnoDB AUTO_INCREMENT=155104 DEFAULT CHARSET=latin1;
CREATE TABLE `mobile_facility_service_areas` (
`seq` int(11) NOT NULL AUTO_INCREMENT,
`name` varchar(50) NOT NULL,
`location` varchar(50) NOT NULL,
PRIMARY KEY (`seq`)
) ENGINE=InnoDB AUTO_INCREMENT=841 DEFAULT CHARSET=latin1;

Answer 1

It's only using the index on location, but that only narrows down the search to about a half a million rows. You'd like it to use an index to further narrow down by the appt_date.
However, the use of OR in your WHERE clause is causing a problem. It can't decide how to use the index.
Here's what I suggest:
Drop the index on location because it's redundant with the other indexes that have location as their first column.
Replace the index on location_appt_date with an index on location_appt_date_status.
ALTER TABLE patients
DROP KEY location,
DROP KEY location_appt_date,
ADD KEY location_appt_date_status (location, appt_date, status);
Refactor the query to use UNION instead of OR:
SELECT ... (all the columns you have) ...
FROM (
SELECT * FROM patients USE INDEX (location_appt_date_status)
WHERE location = 'XYZCompany' AND appt_date >= '2020-03-19' AND appt_date < '2020-03-20'
UNION
SELECT * FROM patients USE INDEX (location_appt_date_status)
WHERE location = 'XYZCompany' AND appt_date <= '2020-03-19' AND status < 'X'
) AS p
LEFT JOIN receivable_transactions FORCE INDEX (patient_seq)
ON p.seq = receivable_transactions.patient_seq
LEFT JOIN patients_dispatch FORCE INDEX (patient_seq)
ON p.seq = patients_dispatch.patient_seq
INNER JOIN mobile_facility FORCE INDEX (unique_index)
ON p.location = mobile_facility.location AND p.mobile_facility = mobile_facility.name
INNER JOIN mobile_facility_service_areas FORCE INDEX (PRIMARY)
ON mobile_facility.service_area = mobile_facility_service_areas.seq
GROUP BY p.seq
ORDER BY p.status, p.order_entry_status, pseudo_status, p.order_entry_status, p.lastname
You might not need all the USE INDEX() / FORCE INDEX() optimizer hints I used. I did those because I was testing with empty tables, and that can confuse the optimizer.

Answer 2

Let me focus on the part that affects optimization the most:
FROM patients AS p
LEFT JOIN receivable_transactions AS rt ON p.seq = rt.patient_seq
LEFT JOIN patients_dispatch AS pd ON p.seq = pd.patient_seq
LEFT JOIN mobile_facility AS mf ON p.location = mf.location
AND p.mobile_facility AS mf = mf.name
LEFT JOIN mobile_facility_service_areas AS sa ON mf.service_area = sa.seq
WHERE p.location = "XYZCompany"
AND ((p.appt_date >= '2020-03-19'
AND p.appt_date <= '2020-03-19 23:59:59')
OR (p.appt_date <= '2020-03-19'
AND p.status < 'X')
)
GROUP BY p.seq DESC
ORDER BY p.status, p.order_entry_status, pseudo_status, p.order_entry_status,
p.lastname);
The biggest issue is the OR. It often prevents most optimizations. The usual fix is to turn it into a UNION:
( SELECT ...
FROM .. JOIN ..
WHERE p.location = "XYZCompany"
AND p.appt_date >= '2020-03-19'
AND p.appt_date < '2020-03-19' + INTERVAL 1 DAY
...
)
UNION ALL
( SELECT ...
FROM .. JOIN ..
WHERE p.location = "XYZCompany"
AND p.appt_date <= '2020-03-19'
AND p.status < 'X'
...
)
Each select can benefit from this composite index on patients:
(location, appt_date, status)
The < 'X' is problematic because two ranges (appt_date and status) cannot both be used effectively. What are the possible values of status? If there is only one value before 'X', say 'M', then this would be much better: p.status = 'M' together with another index: (location, status, appt_date)
SELECT lots of stuff, then GROUP BY p.seq -- This is probably create strange results. (Search for ONLY_FULL_GROUP_BY for more discussion). It may be better to first get the patients.seq values (since that is all you are filtering on), then join to the other tables. This would eliminate the GROUP BY, or at least force you to deal with which row to fetch from each of the other tables.
range location_appt_date 55 573534 Using index condition; Using where; Using temporary; Using filesort -- says
55 = 2+50 (for varchar(50)) + 3 (for date) -- neither is NULL.
Based on the 55, I wonder if it is so well optimized that the OR->UNION is not needed.
"Using index condition" is internally called ICP (Index Condition Pushdown) if you want further understanding.
"Using filesort" may be an understatement -- There are probably two sorts, one for GROUP BY, one for ORDER BY. EXPLAIN FORMAT=JSON SELECT ... would make it clear. (And hence my hint that the GROUP BY should be avoided.
You have some redundant indexes (not relevant to much other than disk space): INDEX(a,b), INDEX(a) --> toss INDEX(a).
patients has an awful number of indexes.
The other tables seem to have adequate indexes for your query.