fsgl wrote on Friday, August 23, 2013:
God does look out for fools, little children and geezers.
Took out the Cat 5 cable and turned off the wireless adapter on the laptop.
Crossed the fingers and re-did the upgrade (step 6).
Messages:
"Processing 4_1_1-to-4_1_2_upgrade.sql …
Skipping section #IfNotTable report_results
Skipping section #IfMissingColumn version v_acl
Skipping section #IfMissingColumn documents_legal_detail dld_moved
Skipping section #IfMissingColumn documents_legal_detail dld_patient_comments
Skipping section #IfMissingColumn documents_legal_master dlm_upload_type
Skipping section #IfMissingColumn list_options codes
Skipping section #IfNotRow2Dx2 list_options list_id smoking_status option_id 15 title Heavy tobacco smoker
Skipping section #IfNotRow2Dx2 list_options list_id smoking_status option_id 16 title Light tobacco smoker
Skipping section #IfMissingColumn code_types ct_term
Skipping section #IfNotRow code_types ct_key SNOMED-CT
Skipping section #IfNotColumnType codes code varchar(25)
Skipping section #IfNotColumnType billing code varchar(20)
Skipping section #IfNotColumnType ar_activity code varchar(20)
Skipping section #IfNotTable procedure_questions
Skipping section #IfMissingColumn procedure_type activity
Skipping section #IfMissingColumn procedure_type notes
Skipping section #IfNotTable procedure_answers
Skipping section #IfNotTable procedure_providers
Skipping section #IfNotTable procedure_order_code
Skipping section #IfMissingColumn procedure_order lab_id
ALTER TABLE procedure_report ADD COLUMN procedure_order_seq int(11) NOT NULL DEFAULT 1 COMMENT ‘references procedure_order_code.procedure_order_seq’
ALTER TABLE procedure_order ADD COLUMN diagnoses text NOT NULL DEFAULT ‘’ COMMENT ‘diagnoses and maybe other coding (e.g. ICD9:111.11)’
Skipping section #IfMissingColumn procedure_providers remote_host
Skipping section #IfMissingColumn procedure_order_code procedure_source
ALTER TABLE procedure_result ADD COLUMN result_data_type char(1) NOT NULL DEFAULT ‘S’ COMMENT ‘N=Numeric, S=String, F=Formatted, E=External, L=Long text as first line of comments’, ADD COLUMN result_code varchar(31) NOT NULL DEFAULT ‘’ COMMENT ‘LOINC code, might match a procedure_type.procedure_code’, ADD COLUMN result_text varchar(255) NOT NULL DEFAULT ‘’ COMMENT ‘Description of result_code’
UPDATE procedure_result AS ps, procedure_type AS pt SET ps.result_code = pt.procedure_code, ps.result_text = pt.description WHERE pt.procedure_type_id = ps.procedure_type_id
ALTER TABLE procedure_result DROP COLUMN procedure_type_id
Skipping section #IfMissingColumn procedure_questions tips
Skipping section #IfMissingColumn procedure_order_code procedure_name
ALTER TABLE procedure_report ADD COLUMN report_notes text NOT NULL DEFAULT ‘’ COMMENT ‘Notes from the lab’
DROP TABLE IF EXISTS temp_table_one
CREATE TABLE temp_table_one ( id int(11) NOT NULL DEFAULT ‘0’, seq int(11) NOT NULL DEFAULT ‘0’) ENGINE=MyISAM
INSERT INTO temp_table_one (id, seq) VALUES ( IF( ((SELECT MAX(ct_id) FROM code_types)>=100), ((SELECT MAX(ct_id) FROM code_types) + 1), 100 ) , IF( ((SELECT MAX(ct_seq) FROM code_types)>=100), ((SELECT MAX(ct_seq) FROM code_types) + 1), 100 ) )
INSERT INTO code_types (ct_key, ct_id, ct_seq, ct_mod, ct_just, ct_fee, ct_rel, ct_nofs, ct_diag, ct_active, ct_label, ct_external, ct_claim, ct_proc, ct_term ) VALUES (‘SNOMED-PR’ , (SELECT MAX(id) FROM temp_table_one), (SELECT MAX(seq) FROM temp_table_one), 0, ‘SNOMED’, 1, 0, 0, 0, 0, ‘SNOMED Procedure’, 9, 1, 1, 0)
DROP TABLE temp_table_one
Skipping section #IfNotTable background_services
Skipping section #IfNotRow background_services name phimail
INSERT INTO users (username,password,lname,authorized,active) VALUES (‘phimail-service’,‘NoLogin’,‘phiMail Gateway’,0,0)
INSERT INTO users (username,password,lname,authorized,active) VALUES (‘portal-user’,‘NoLogin’,‘Patient Portal User’,0,0)
Skipping section #IfNotTable direct_message_log
Skipping section #IfMissingColumn procedure_order_code diagnoses
ALTER TABLE procedure_order DROP COLUMN diagnoses
ALTER TABLE lists ADD COLUMN modifydate timestamp NOT NULL default CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP
ALTER TABLE code_types ADD COLUMN ct_problem tinyint(1) NOT NULL DEFAULT ‘0’ COMMENT ‘1 if this code type is used as a medical problem’
UPDATE code_types SET ct_problem = 1 WHERE ct_key=‘ICD9’
UPDATE code_types SET ct_problem = 1 WHERE ct_key=‘DSMIV’
UPDATE code_types SET ct_problem = 1 WHERE ct_key=‘ICD10’
UPDATE code_types SET ct_problem = 1 WHERE ct_key=‘SNOMED’
ALTER TABLE procedure_order ADD COLUMN date_transmitted datetime DEFAULT NULL COMMENT ‘time of order transmission, null if unsent’
UPDATE procedure_order SET date_transmitted = date_ordered WHERE date_transmitted IS NULL AND date_ordered IS NOT NULL
INSERT INTO list_options (list_id,option_id,title) VALUES (‘lists’,‘issue_types’,‘Issue Types’)
Skipping section #IfNotMigrateClickOptions
Skipping section #IfNotTable issue_types
Skipping section #IfMissingColumn issue_types active
ALTER TABLE immunizations MODIFY COLUMN administered_date datetime DEFAULT NULL
ALTER TABLE immunizations ADD COLUMN amount_administered int(11) DEFAULT NULL
ALTER TABLE immunizations ADD COLUMN amount_administered_unit varchar(50) DEFAULT NULL
ALTER TABLE immunizations ADD COLUMN expiration_date date DEFAULT NULL
ALTER TABLE immunizations ADD COLUMN route varchar(100) DEFAULT NULL
ALTER TABLE immunizations ADD COLUMN administration_site varchar(100) DEFAULT NULL
ALTER TABLE immunizations ADD COLUMN added_erroneously tinyint(1) NOT NULL DEFAULT ‘0’
ALTER TABLE documents ADD COLUMN path_depth TINYINT DEFAULT ‘1’ COMMENT ‘Depth of path to use in url to find document. Not applicable for CouchDB.’
Skipping section #IfNotTable users_secure
ALTER TABLE patient_access_onsite ADD COLUMN portal_salt VARCHAR(100) NULL
ALTER TABLE procedure_order ADD COLUMN clinical_hx varchar(255) DEFAULT ‘’ COMMENT ‘clinical history text that may be relevant to the order’
Skipping section #IfMissingColumn procedure_order_code do_not_send
Skipping section #IfNotTable misc_address_book
ALTER TABLE documents ADD COLUMN imported TINYINT DEFAULT 0 NULL COMMENT ‘Parsing status for CCR/CCD/CCDA importing’
Updating global configuration defaults…
Updating Access Controls…
UPGRADING ACCESS CONTROLS TO VERSION 1:
Checking to ensure all the proper ACL(access control list) are present:
‘Administrators’ group ‘write’ ACL is present.
‘Physicians’ group ‘write’ ACL is present.
‘Clinicians’ group ‘write’ ACL is present.
‘Clinicians’ group ‘addonly’ ACL is present.
‘Front Office’ group ‘write’ ACL is present.
‘Accounting’ group ‘write’ ACL is present.
Adding new object sections
The ‘Sensitivities’ object section already exist.
The ‘Lists’ object section already exist.
The ‘Placeholder’ object section already exist.
The ‘Nation Notes’ object section already exist.
The ‘Patient Portal’ object section already exist.
Adding new objects
The ‘Normal’ object in the ‘Sensitivities’ section already exist.
The ‘High’ object in the ‘Sensitivities’ section already exist.
The ‘Pharmacy Dispensary’ object in the ‘Administration’ section already exist.
The ‘ACL Administration’ object in the ‘Administration’ section already exist.
The ‘Price Discounting’ object in the ‘Accounting’ section already exist.
The ‘Default List (write,addonly optional)’ object in the ‘Lists’ section already exist.
The ‘State List (write,addonly optional)’ object in the ‘Lists’ section already exist.
The ‘Country List (write,addonly optional)’ object in the ‘Lists’ section already exist.
The ‘Language List (write,addonly optional)’ object in the ‘Lists’ section already exist.
The ‘Ethnicity-Race List (write,addonly optional)’ object in the ‘Lists’ section already exist.
The ‘Placeholder (Maintains empty ACLs)’ object in the ‘Placeholder’ section already exist.
The ‘Sign Lab Results (write,addonly optional)’ object in the ‘Patients’ section already exist.
The ‘Nation Notes Configure’ object in the ‘Nation Notes’ section already exist.
The ‘Patient Portal’ object in the ‘Patient Portal’ section already exist.
Upgrading objects
The ‘High’ object in the ‘Sensitivities’ section has already been updated.
Adding ACLs(Access Control Lists) and groups
‘Physicians’ group ‘addonly’ ACL already exist.
‘Front Office’ group ‘addonly’ ACL already exist.
‘Accounting’ group ‘addonly’ ACL already exist.
‘Emergency Login’ group ‘write’ ACL already exist.
Updating the ACLs(Access Control Lists)
The ‘Superuser’ object of the ‘Administration’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘High’ object of the ‘Sensitivities’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Normal’ object of the ‘Sensitivities’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘High’ object of the ‘Sensitivities’ section is already found in the ‘Physicians’ group ‘write’ ACL.
The ‘Normal’ object of the ‘Sensitivities’ section is already found in the ‘Physicians’ group ‘write’ ACL.
The ‘Normal’ object of the ‘Sensitivities’ section is already found in the ‘Clinicians’ group ‘addonly’ ACL.
The ‘Pharmacy Dispensary’ object of the ‘Administration’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Pharmacy Dispensary’ object of the ‘Administration’ section is already found in the ‘Physicians’ group ‘write’ ACL.
The ‘Pharmacy Dispensary’ object of the ‘Administration’ section is already found in the ‘Clinicians’ group ‘write’ ACL.
The ‘ACL Administration’ object of the ‘Administration’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Price Discounting’ object of the ‘Accounting’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Price Discounting’ object of the ‘Accounting’ section is already found in the ‘Accounting’ group ‘write’ ACL.
The ‘Price Discounting’ object of the ‘Accounting’ section is already found in the ‘Physicians’ group ‘write’ ACL.
The ‘Default List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘State List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Country List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Language List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Ethnicity-Race List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Price Discounting’ object of the ‘Accounting’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Billing (write optional)’ object of the ‘Accounting’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘EOB Data Entry’ object of the ‘Accounting’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Financial Reporting - my encounters’ object of the ‘Accounting’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Financial Reporting - anything’ object of the ‘Accounting’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Calendar Settings’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Database Reporting’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Forms Administration’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Practice Settings’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Superbill Codes Administration’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Users/Groups/Logs Administration’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Batch Communication Tool’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Language Interface Tool’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Superuser’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Pharmacy Dispensary’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘ACL Administration’ object of the ‘Administration’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Authorize - any encounters’ object of the ‘Encounters’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Coding - any encounters (write,wsome optional)’ object of the ‘Encounters’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Notes - any encounters (write,addonly optional)’ object of the ‘Encounters’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Fix encounter dates - any encounters’ object of the ‘Encounters’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Default List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘State List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Country List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Language List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Ethnicity-Race List (write,addonly optional)’ object of the ‘Lists’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Appointments (write,wsome optional)’ object of the ‘Patients’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Demographics (write,addonly optional)’ object of the ‘Patients’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Medical/History (write,addonly optional)’ object of the ‘Patients’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Transactions (write optional)’ object of the ‘Patients’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Documents (write,addonly optional)’ object of the ‘Patients’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Patient Notes (write,addonly optional)’ object of the ‘Patients’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘High’ object of the ‘Sensitivities’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Normal’ object of the ‘Sensitivities’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Sign Lab Results (write,addonly optional)’ object of the ‘Patients’ section is already found in the ‘Physicians’ group ‘write’ ACL.
The ‘Nation Notes Configure’ object of the ‘Nation Notes’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Nation Notes Configure’ object of the ‘Nation Notes’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
The ‘Patient Portal’ object of the ‘Patient Portal’ section is already found in the ‘Administrators’ group ‘write’ ACL.
The ‘Patient Portal’ object of the ‘Patient Portal’ section is already found in the ‘Emergency Login’ group ‘write’ ACL.
UPGRADING ACCESS CONTROLS TO VERSION 2:
Checking to ensure all the proper ACL(access control list) are present:
Adding new object sections
Adding new objects
Upgrading objects
Adding ACLs(Access Control Lists) and groups
The ‘Physicians’ group already exist.
The ‘Physicians’ group ‘wsome’ ACL has been successfully added.
The ‘Clinicians’ group already exist.
The ‘Clinicians’ group ‘wsome’ ACL has been successfully added.
The ‘Front Office’ group already exist.
The ‘Front Office’ group ‘wsome’ ACL has been successfully added.
The ‘Accounting’ group already exist.
The ‘Accounting’ group ‘wsome’ ACL has been successfully added.
The ‘Physicians’ group already exist.
The ‘Physicians’ group ‘view’ ACL has been successfully added.
The ‘Clinicians’ group already exist.
The ‘Clinicians’ group ‘view’ ACL has been successfully added.
The ‘Front Office’ group already exist.
The ‘Front Office’ group ‘view’ ACL has been successfully added.
The ‘Accounting’ group already exist.
The ‘Accounting’ group ‘view’ ACL has been successfully added.
Updating the ACLs(Access Control Lists)
DONE upgrading access controls
Updating version indicators…
Database and Access Control upgrade finished."
Editing problem resolved.
Old problem downloading emr_backup.tar discussed in this thread got fixed as well with the re-install of Apache (just died and went to heaven!).
Thank you, gentlemen, for your kind assistance. Could not have done it without you.